Rational Discovery of Dengue Type 2 Non-Competitive Inhibitors

Various works have been carried out in developing therapeutics against dengue. However, to date, no effective vaccine or anti‐dengue agent has yet been discovered. The development of protease inhibitors is considered as a promising option, but most previous works have involved competitive inhibition. In this study, we focused on rational discovery of potential anti‐dengue agents based on non‐competitive inhibition of DEN‐2 NS2B/NS3 protease. A homology model of the DEN‐2 NS2B/NS3 protease (using West Nile Virus NS2B/NS3 protease complex, 2FP7, as the template) was used as the target, and pinostrobin, a flavanone, was used as the standard ligand. Virtual screening was performed involving a total of 13 341 small compounds, with the backbone structures of chalcone, flavanone, and flavone, available in the ZINC database. Ranking of the resulting compounds yielded compounds with higher binding affinities compared with the standard ligand. Inhibition assay of the selected top‐ranking compounds against DEN‐2 NS2B/NS3 proteolytic activity resulted in significantly better inhibition compared with the standard and correlated well with in silico results. In conclusion, via this rational discovery technique, better inhibitors were identified. This method can be used in further work to discover lead compounds for anti‐dengue agents. Compound 1 was found to be the best non‐competitive inhibitor of DEN‐2 NS2B/NS3. For non‐competitive inhibition studies on DEN‐2 NS2B/NS3 protease, we propose that an appropriate model should exhibit a conformation of the allosteric binding site that resembles the homology model DH‐1. Lys74, Glu88, Gly124 and Asn167 play important roles in the interactions with the non‐competitive inhibitors and are worthy of further study.