Table of Contents Author Guidelines Submit a Manuscript
Biochemistry Research International
Volume 2016 (2016), Article ID 7264080, 13 pages
http://dx.doi.org/10.1155/2016/7264080
Research Article

In Silico Screening, Alanine Mutation, and DFT Approaches for Identification of NS2B/NS3 Protease Inhibitors

1Medicinal Chemistry Group, Institute of Chemistry of Sao Carlos, University of Sao Paulo, Sao Carlos, Brazil
2Department of Applied Chemistry, National Chiao Tung University, Hsinchu, Taiwan
3King Institute of Preventive Medicine, Guindy, Chennai, India

Received 26 September 2015; Revised 13 December 2015; Accepted 15 December 2015

Academic Editor: Roberta Chiaraluce

Copyright © 2016 R. Balajee 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. S. Idrees and U. A. Ashfaq, “A brief review on dengue molecular virology, diagnosis, treatment and prevalence in Pakistan,” Genetic Vaccines and Therapy, vol. 10, article 6, 2012. View at Publisher · View at Google Scholar · View at Scopus
  2. S. C. Weaver and N. Vasilakis, “Molecular evolution of dengue viruses: contributions of phylogenetics to understanding the history and epidemiology of the preeminent arboviral disease,” Infection, Genetics and Evolution, vol. 9, no. 4, pp. 523–540, 2009. View at Publisher · View at Google Scholar · View at Scopus
  3. http://www.who.int/mediacentre/factsheets/fs117/en/.
  4. S.-W. Wan, C.-F. Lin, S. Wang et al., “Current progress in dengue vaccines,” Journal of Biomedical Science, vol. 20, no. 1, article 37, 2013. View at Publisher · View at Google Scholar · View at Scopus
  5. S. Clum, K. E. Ebner, and R. Padmanabhan, “Cotranslational membrane insertion of the serine proteinase precursor NS2B-NS3(Pro) of dengue virus type 2 is required for efficient in vitro processing and is mediated through the hydrophobic regions of NS2B,” The Journal of Biological Chemistry, vol. 272, no. 49, pp. 30715–30723, 1997. View at Publisher · View at Google Scholar · View at Scopus
  6. E. G. Westaway, J. M. Mackenzie, M. T. Kenney, M. K. Jones, and A. A. Khromykh, “Ultrastructure of Kunjin virus-infected cells: colocalization of NS1 and NS3 with double-stranded RNA, and of NS2B with NS3, in virus-induced membrane structures,” Journal of Virology, vol. 71, no. 9, pp. 6650–6661, 1997. View at Google Scholar · View at Scopus
  7. H. Li, S. Clum, S. You, K. E. Ebner, and R. Padmanabhan, “The serine protease and RNA-stimulated nucleoside triphosphatase and RNA helicase functional domains of dengue virus type 2 NS3 converge within a region of 20 amino acids,” Journal of Virology, vol. 73, no. 4, pp. 3108–3116, 1999. View at Google Scholar · View at Scopus
  8. L.-R. Jan, C.-S. Yang, D. W. Trent, B. Falgout, and C.-J. Lai, “Processing of Japanese encephalitis virus non-structural proteins: NS2B-NS3 complex and heterologous proteases,” Journal of General Virology, vol. 76, no. 3, pp. 573–580, 1995. View at Publisher · View at Google Scholar · View at Scopus
  9. R. Khumthong, C. Angsuthanasombat, S. Panyim, and G. Katzenmeier, “In vitro determination of dengue virus type 2 NS2B-NS3 protease activity with fluorescent peptide substrates,” Journal of Biochemistry and Molecular Biology, vol. 35, no. 2, pp. 206–212, 2002. View at Publisher · View at Google Scholar · View at Scopus
  10. T. T. H. Nguyen, S. Lee, H.-K. Wang et al., “In vitro evaluation of novel inhibitors against the NS2B-NS3 protease of dengue fever virus type 4,” Molecules, vol. 18, no. 12, pp. 15600–15612, 2013. View at Publisher · View at Google Scholar · View at Scopus
  11. R. I. Brinkworth, D. P. Fairlie, D. Leung, and P. R. Young, “Homology model of the dengue 2 virus NS3 protease: putative interactions with both substrate and NS2B cofactor,” Journal of General Virology, vol. 80, no. 5, pp. 1167–1177, 1999. View at Publisher · View at Google Scholar · View at Scopus
  12. A. E. Matusan, M. J. Pryor, A. D. Davidson, and P. J. Wright, “Mutagenesis of the Dengue virus type 2 NS3 protein within and outside helicase motifs: effects on enzyme activity and virus replication,” Journal of Virology, vol. 75, no. 20, pp. 9633–9643, 2001. View at Publisher · View at Google Scholar · View at Scopus
  13. T. J. Chambers, A. Nestorowicz, S. M. Amberg, and C. M. Rice, “Mutagenesis of the yellow fever virus NS2B protein: effects on proteolytic processing, NS2B-NS3 complex formation, and viral replication,” Journal of Virology, vol. 67, no. 11, pp. 6797–6807, 1993. View at Google Scholar · View at Scopus
  14. H.-Y. Sun and F.-Q. Ji, “A molecular dynamics investigation on the crizotinib resistance mechanism of C1156Y mutation in ALK,” Biochemical and Biophysical Research Communications, vol. 423, no. 2, pp. 319–324, 2012. View at Publisher · View at Google Scholar · View at Scopus
  15. Y. Zhao and D. G. Truhlar, “The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals,” Theoretical Chemistry Accounts, vol. 120, no. 1–3, pp. 215–241, 2008. View at Publisher · View at Google Scholar · View at Scopus
  16. D. F. Veber, S. R. Johnson, H.-Y. Cheng, B. R. Smith, K. W. Ward, and K. D. Kopple, “Molecular properties that influence the oral bioavailability of drug candidates,” Journal of Medicinal Chemistry, vol. 45, no. 12, pp. 2615–2623, 2002. View at Publisher · View at Google Scholar · View at Scopus
  17. M. J. Frisch, G. W. Trucks, H. B. Schlegel et al., Gaussian 09, Revision A.1, Gaussian, Wallingford, Conn, USA, 2009.
  18. https://pubchem.ncbi.nlm.nih.gov/.
  19. http://www.drugbank.ca.
  20. Chemical Diversity, http://www.chemdiv.com/.
  21. T. Hou, J. Wang, Y. Li, and W. Wang, “Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations,” Journal of Chemical Information and Modeling, vol. 51, no. 1, pp. 69–82, 2011. View at Publisher · View at Google Scholar
  22. M. Umamaheswari, A. Madeswaran, and K. Asokkumar, “Virtual screening analysis and in-vitro xanthine oxidase inhibitory activity of some commercially available flavonoids,” Iranian Journal of Pharmaceutical Research, vol. 12, no. 3, pp. 317–323, 2013. View at Google Scholar · View at Scopus
  23. I.-J. Chen and N. Foloppe, “Drug-like bioactive structures and conformational coverage with the ligprep/confgen suite: comparison to programs MOE and catalyst,” Journal of Chemical Information and Modeling, vol. 50, no. 5, pp. 822–839, 2010. View at Publisher · View at Google Scholar · View at Scopus
  24. Protein Databank, http://www.rcsb.org/pdb/home/home.do.
  25. IMPACT, Schrodinger Suite.
  26. R. A. Friesner, J. L. Banks, R. B. Murphy et al., “Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy,” Journal of Medicinal Chemistry, vol. 47, no. 7, pp. 1739–1749, 2004. View at Publisher · View at Google Scholar · View at Scopus
  27. R. P. C. Valle and B. Falgout, “Mutagenesis of the NS3 protease of dengue virus type 2,” Journal of Virology, vol. 72, no. 1, pp. 624–632, 1998. View at Google Scholar · View at Scopus
  28. T. A. Halgren, R. B. Murphy, R. A. Friesner et al., “Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening,” Journal of Medicinal Chemistry, vol. 47, no. 7, pp. 1750–1759, 2004. View at Publisher · View at Google Scholar · View at Scopus
  29. R. A. Friesner, R. B. Murphy, M. P. Repasky et al., “Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes,” Journal of Medicinal Chemistry, vol. 49, no. 21, pp. 6177–6196, 2006. View at Publisher · View at Google Scholar · View at Scopus
  30. N. Moitessier, E. Therrien, and S. Hanessian, “A method for induced-fit docking, scoring, and ranking of flexible ligands. Application to peptidic and pseudopeptidic β-secretase (BACE 1) inhibitors,” Journal of Medicinal Chemistry, vol. 49, no. 20, pp. 5885–5894, 2006. View at Publisher · View at Google Scholar · View at Scopus
  31. D. Das, Y. Koh, Y. Tojo, A. K. Ghosh, and H. Mitsuya, “Prediction of potency of protease inhibitors using free energy simulations with polarizable quantum mechanics-based ligand charges and a hybrid water model,” Journal of Chemical Information and Modeling, vol. 49, no. 12, pp. 2851–2862, 2009. View at Publisher · View at Google Scholar · View at Scopus
  32. Y. Koh, D. Das, S. Leschenko et al., “GRL-02031, a novel nonpeptidic protease inhibitor (PI) containing a stereochemically defined fused cyclopentanyltetrahydrofuran potent against multi-pi-resistant human immunodeficiency virus type 1 in vitro,” Antimicrobial Agents and Chemotherapy, vol. 53, no. 3, pp. 997–1006, 2009. View at Publisher · View at Google Scholar
  33. 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 Publisher · View at Google Scholar · View at Scopus
  34. 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 Publisher · View at Google Scholar · View at Scopus
  35. P. Erbel, N. Schiering, A. D'Arcy et al., “Structural basis for the activation of flaviviral NS3 proteases from dengue and West Nile virus,” Nature Structural and Molecular Biology, vol. 13, no. 4, pp. 372–373, 2006. View at Publisher · View at Google Scholar · View at Scopus
  36. R. Yusof, S. Clum, M. Wetzel, H. M. K. Murthy, and R. Padmanabhan, “Purified NS2B/NS3 serine protease of dengue virus type 2 exhibits cofactor NS2B dependence for cleavage of substrates with dibasic amino acids in vitro,” The Journal of Biological Chemistry, vol. 275, no. 14, pp. 9963–9969, 2000. View at Publisher · View at Google Scholar · View at Scopus
  37. H. M. K Murthy, K. Judge, L. DeLucas, and R. Padmanabhan, “Crystal structure of dengue virus NS3 protease in complex with a bowman-birk inhibitor: implications for flaviviral polyprotein processing and drug design,” Journal of Molecular Biology, vol. 301, no. 4, pp. 759–767, 2000. View at Publisher · View at Google Scholar · View at Scopus
  38. L. Y. Kee, T. S. Kiat, H. A. Wahab, R. Yusof, and N. A. Rahman, “Nonsubstrate based inhibitors of dengue virus serine protease: a molecular docking approach to study binding interactions between protease and inhibitors,” Asia-Pacific Journal of Molecular Biology and Biotechnology, vol. 15, no. 2, pp. 53–59, 2007. View at Google Scholar · View at Scopus
  39. S. Sanjay and G. R. Desiraju, “N-H...O, O-H...O, and C-H...O hydrogen bonds in protein-ligand complexes: strong and weak interactions in molecular recognition,” PROTEINS: Structure, Functions and Bioinformatics, vol. 54, no. 2, pp. 247–259, 2004. View at Google Scholar
  40. F. Neni, F. C. Chin, M. Z. Sharifuddin, and A. R. Noorsaadah, “Nonsubstrate based inhibitors of dengue virus serine protease: a molecular docking approach to study binding interactions between protease and inhibitors,” Asia Pacific Journal of Molecular Biology and Biotechnology, vol. 15, pp. 53–59, 2007. View at Google Scholar
  41. W. Salaemae, M. Junaid, C. Angsuthanasombat, and G. Katzenmeier, “Structure-guided mutagenesis of active site residues in the dengue virus two-component protease NS2B-NS3,” Journal of Biomedical Science, vol. 17, no. 1, pp. 68–75, 2010. View at Publisher · View at Google Scholar · View at Scopus
  42. G. Robin, K. Chappell, M. J. Stoermer et al., “Structure of West Nile Virus NS3 protease: Ligand stabilization of the catalytic conformation,” Journal of Molecular Biology, vol. 385, no. 5, pp. 1568–1577, 2009. View at Publisher · View at Google Scholar · View at Scopus
  43. S. A. Shiryaev, A. E. Aleshin, B. I. Ratnikov, J. W. Smith, R. C. Liddington, and A. Y. Strongin, “Expression and purification of a two-component flaviviral proteinase resistant to autocleavage at the NS2B-NS3 junction region,” Protein Expression and Purification, vol. 52, no. 2, pp. 334–339, 2007. View at Publisher · View at Google Scholar · View at Scopus
  44. N. H. Mueller, C. Yon, V. K. Ganesh, and R. Padmanabhan, “Characterization of the West Nile virus protease substrate specificity and inhibitors,” International Journal of Biochemistry and Cell Biology, vol. 39, no. 3, pp. 606–614, 2007. View at Publisher · View at Google Scholar · View at Scopus
  45. P. Niyomrattanakit, P. Winoyanuwattikun, S. Chanprapaph, C. Angsuthanasombat, S. Panyim, and G. Katzenmeier, “Identification of residues in the dengue virus type 2 NS2B cofactor that are critical for NS3 protease activation,” Journal of Virology, vol. 78, no. 24, pp. 13708–13716, 2004. View at Publisher · View at Google Scholar · View at Scopus
  46. Y. C. Mi, K.-O. Lee, W. K. Jong et al., “Discovery of a novel Her-1/Her-2 dual tyrosine kinase inhibitor for the treatment of Her-1 selective inhibitor-resistant non-small cell lung cancer,” Journal of Medicinal Chemistry, vol. 52, no. 21, pp. 6880–6888, 2009. View at Publisher · View at Google Scholar · View at Scopus
  47. S. Niwata, H. Fukami, M. Sumida et al., “Substituted 3-(phenylsulfonyl)-1-phenylimidazolidine-2,4-dione derivatives as novel nonpeptide inhibitors of human heart chymase,” Journal of Medicinal Chemistry, vol. 40, no. 14, pp. 2156–2163, 1997. View at Publisher · View at Google Scholar · View at Scopus
  48. Qikprop, Schrodinger, USA.
  49. C. A. Lipinski, F. Lombardo, B. W. Dominy, and P. J. Feeney, “Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings,” Advanced Drug Delivery Reviews, vol. 23, no. 1–3, pp. 3–25, 1997. View at Publisher · View at Google Scholar · View at Scopus