3.5. Molecular Docking

The molecular docking experiment was based on the molecular modeling package SYBYL-X 1.3 (Tripos associate Inc., St. Louis, MO, USA). The 3D structure of PARP-1 receptor for the molecular docking study was downloaded from Protein Data Bank (PDB ID: 2RD6) [16]. The selected ligands were compound 5cj and 5cp in this experiment. The molecular docking experiment was implemented in four steps: (1) The water molecules in the protein crystal structure downloaded from PDB were deleted; (2) The energy of receptor and ligand was optimized; (3) The intrinsic ligand in the binding site of the receptor was deleted, and then the selected target compound was docked into the receptor according to Sybyl-X modules; (4) The molecular docking results obtained by the above steps were handled and analyzed.