Homology model of the dengue 2 virus NS3 protease: putative interactions with both substrate and NS2B cofactor

The crystal structure coordinates of the hepatitis C virus NS3 protease (HC Vpro) were used to develop an homology model of the dengue 2 virus NS3 prot ease (DEN2pro). The amino acid sequence of DEN2pro accommodates the same al pha-helices, beta-sheets and protein-binding domains as its HCVpro counterp art, but the model predicts a number of significant differences for DEN2pro and its interactions with substrates and cofactor. Whereas HCVpro contains a Zn2+-binding site, there is no equivalent metal-binding motif in DEN2pro . It is possible that the structural role played by the zinc ion may be pro vided by a salt bridge between Glu(93) and Lys(145). The two-component vira l protease comprises NS3 and a virus-encoded cofactor, NS4A for HCV and NS2 B for DEN2. Previous studies have identified a central 40 amino acid cofact or domain of the dengue virus NS2B that is required for protease activity. Modelling of the putative interactions between DEN2pro and its cofactor sug gests that a 12 amino acid hydrophobic region within this sequence ((70)GSS PILSITISE(81)) may associate directly with NS3. Modelling also suggests tha t the substrate binds in an extended conformation to the solvent-exposed su rface of the protease, with a P1-binding site that is significantly differe nt from its HCV counterpart. The model described in this study not only rev eals unique features of the flavivirus protease but also provides a structu ral basis for both cofactor and substrate binding that should prove useful in the early design and development of inhibitors.