Xiong, Yanchao; Cheng, Fei; Zhang, Junyi; Su, Haixia; Hu, Hangchen; Zou, Yi; Li, Minjun; Xu, Yechun

BIOORGANIC CHEMISTRY

2022, 128, 0045-2068

Xiong, Yanchao; Cheng, Fei; Zhang, Junyi; Su, Haixia; Hu, Hangchen; Zou, Yi; Li, Minjun; Xu, Yechun

Zika virus (ZIKV) has been a serious public health problem, and there is no vaccine or drug approved for the prevention or treatment of ZIKV yet. The ZIKV NS2B/NS3 protease plays an important role in processing the virus precursor polyprotein and is thus a promising target for antiviral drugs development. In order to discover novel inhibitors of this protease, we carried out a fragment-based hit screening and characterized protein -inhibitor interactions using the X-ray crystallography together with isothermal titration calorimetry. We re-ported two high-resolution crystal structures of the protease (bZiPro(C143S)) in complex with an active fragment as well as a tetrapeptide, revealing that there is domain swapping in the protein structures and two ligands only occupy the substrate-binding pocket of one copy in a symmetric unit. Based on the detailed binding modes of two ligands revealed by crystal structures, we designed a novel inhibitor which inhibits the NS2B/NS3 protease with a higher potency than the fragment and possesses a higher ligand-binding efficiency and a comparable IC50 compared to the tetrapeptide. These results thus provide a structural basis and valuable hint for development of more potent inhibitors of the ZIKV NS2B/NS3 protease.