Structural bioinformatics of dengue virus and opportunities for inhibitors design

Abstract

Biomolecular structure modeling remains one of the most compound and challenging tasks in molecular biology. One of the techniques used to meet this challenge is homology modeling, which aids in predicting the 3D details of unknown biomolecular structures, relying heavily on resources such as sequence-structure information and prototype-function relationship. Three dimensional models of Dengue Envelope and NS3 proteins were created. Ramachandran plot was used to verify the correctness of the models in terms of geometry and root-mean-square deviation from PDB templates. The present work provides an insight into the determination of the three dimensional structures of the envelope and NS3 proteins of seven dengue viruses isolated in Singapore and correlation of their three dimensional structures with experimentally available antigenic data. The residues essential for the function of these proteins can be known and this may serve as a guide for further investigation on these proteins. The amino acid residues in the dengue viral proteins important for the interaction with inhibitors have also been highlighted. Potential chemical compounds which might serve as Dengue inhibitors were docked with these proteins, and this information may pave the way for the design of new anti-dengue drugs thereby aiding the discovery of vaccines and a therapeutic cure for this infectious disease.