Research

Theoretical study of the Usutu virus helicase 3D structure, by means of computer-aided homology modelling

Dimitrios Vlachakis

Institute of Biology, National Centre for Scientific Research Demokritos, 15310 Ag. Paraskevi Attikis, Greece

author email corresponding author email

Theoretical Biology and Medical Modelling 2009, 6:9doi:10.1186/1742-4682-6-9

Published:	25 June 2009

Abstract

Background

Usutu virus belongs to the Flaviviridae viral family and constitutes an important pathogen. The viral helicase is an ideal target for inhibitor design, since this enzyme is essential for the survival, proliferation and transmission of the virus.

Results

Towards a drug-design approach, the 3D model of the Usutu virus helicase structure has been designed, using conventional homology modelling techniques and the known 3D-structure of the Murray Valley Encephalitis virus helicase, of the same viral family, as template. The model was then subjected to extended molecular dynamics simulations in a periodic box, filled with explicit water molecules for 10 nanoseconds. The reliability of the model was confirmed by obtaining acceptable scores from a variety of in silico scoring tools, including Procheck and Verify3D.

Conlcusion

The 3D model of the Usutu virus helicase exhibits in silico all known structural characteristics of the Flaviviridae viral family helicase enzymes and could provide the platform for further de novo structure-based design of novel anti-Usutu agents.