Discovery studio 2018r2

Discovery Studio 2018R2 software (Accelrys, San Diego, CA, USA) was applied to perform the virtual screening. The crystal structure of ZIKV NS5 RdRp with a resolution of 1.90 Å was downloaded from the Protein Data Bank (PDB ID: 5U04). RdRp protein was prepared to remove the heteroatoms and water, add hydrogen, protonate, ionize and minimize energy. 935 compounds from an anti-infection compound library and a natural product library were all prepared and different conformations of the compounds were optimized. ATP, the natural substrate of RdRp, was used as a control. The docking pocket of RdRp was defined according to the key amino acids of D535, D665 and D666 reported previously [41 (link)]. The virtual screening of NS5 RdRp inhibitors was carried out by docking all the prepared ligands at the defined docking pocket using the LibDock program. Based on the LibDock score, all the docking poses were ranked. Compounds with the top five LibDock scores were selected for further study.

Dithiothreitol, imidazol, Tris-HCl and other common assay reagents were purchased from Sigma (St. Louis, MO, USA). The ZIKV cDNA was synthesized by Invitrogen (Waltham, MA, USA). The ZIKV RNA sequence for methyltransferase reaction was synthesized de novo by Genscript (Nanjing, Jiangsu, CHN). The RNA capping kit was purchased from New England Biolabs (Ipswich, MA, USA). MTase-Glo Methyltransferase Assay kit was purchased from Promega (Madison, WI, USA). HisTrap FF crude and CM5 sensor chip were purchased from GE (Uppsala, Sweden). 384-well white plates were obtained from Corning (Corning, NY, USA). Discovery Studio 2018 R2 software was provided by Accelrys (San Diego, CA, USA). The screening library was a natural product library provided by MedChem Express (Monmouth Junction, NJ, USA).