Identification of novel target sites and an inhibitor of the dengue virus E protein

  • Ragothaman Yennamalli
  • Naidu Subbarao
  • Thorsten Kampmann
  • Ross P. McGeary
  • Paul R. Young
  • Bostjan Kobe


Dengue and related flaviviruses represent a significant global health threat. The envelope glycoprotein E mediates virus attachment to a host cell and the subsequent fusion of viral and host cell membranes. The fusion process is driven by conformational changes in the E protein and is an essential step in the virus life cycle. In this study, we analyzed the pre-fusion and post-fusion structures of the dengue virus E protein to identify potential novel sites that could bind small molecules, which could interfere with the conformational transitions that mediate the fusion process. We used an in silico virtual screening approach combining three different docking algorithms (DOCK, GOLD and FlexX) to identify compounds that are likely to bind to these sites. Seven structurally diverse molecules were selected to test experimentally for inhibition of dengue virus propagation. The best compound showed an IC50 in the micromolar range against dengue virus type 2.


Dengue virus Envelope protein Flavivirus Virtual drug screening 



Bovine serum albumin


Dengue virus


Dulbecco’s modified Eagle’s medium


Fetal calf serum


Japanese encephalitis virus


Methyl thiazole tetrazolium


Protein Data Bank


Phosphate buffered saline


Plaque-forming units


Tick-borne encephalitis virus


West Nile virus



We thank Drs Kolaskar and Kulkarni-Kale, University of Pune, India, for providing the coordinates of the structure of Japanese encephalitis virus E protein, and Charlie Huang for helpful discussions. This work was funded by a grant from the National Health and Medical Research Council (NHMRC, Australia) to PRY and BK. BK is an Australian Research Council (ARC) Federation Fellow and NHMRC Honorary Research Fellow. RY was a recipient of the 2006 Endeavour Australia Cheung Kong Award for Asian Scholars and was supported by a Research Fellowship from the Indian Council of Medical Research.

Supplementary material

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Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  • Ragothaman Yennamalli
    • 1
    • 2
  • Naidu Subbarao
    • 1
  • Thorsten Kampmann
    • 2
  • Ross P. McGeary
    • 2
  • Paul R. Young
    • 2
    • 3
  • Bostjan Kobe
    • 2
    • 3
  1. 1.Centre for Computational Biology and Bioinformatics, School of Information TechnologyJawaharlal Nehru UniversityNew DelhiIndia
  2. 2.School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneAustralia
  3. 3.Institute for Molecular BioscienceUniversity of QueenslandBrisbaneAustralia

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