Surflex dock

To investigate the probable binding conformation of Paeonol to the active site of AMPK, molecular docking studies were performed using the Surflex-Dock program (Jain, 1996 (link)) in SYBYL7.1 (Tripos, Inc., St. Louis, MO, United States). The crystal structures of human AMPK [PDB ID: 4CFE (Xiao et al., 2013 (link)), resolution = 3.02 Å] used for docking were obtained from the RSCB Protein Data Bank¹. Water molecules and other heteroatoms were removed from the protein and hydrogen atoms were added subsequently. The 3D structure of Paeonol was prepared in MOL2 format and docked into the protein after energy was minimized. The default parameters of the Surflex-Dock program were used. Finally, the conformation with the highest-scored conformation was selected for studying the interactions between AMPK and Paeonol.

Structures of NDGA, 4-OHE₂, or DNC as ligands bound to the human COMT active site were constructed using the SYBYL-X2.1.1 molecular modeling software (Tripos Inc., St. Louis, MO, USA) and energy was minimized by the Powell method using the Gasteiger−Marsili charge and the Tripos force field [29 (link)]. The crystal structure of DNC-bound COMT was obtained from the Protein Data Bank (PDB code 3BWM) [21 (link)]. All water molecules from the crystal structures were removed, whereas the missing hydrogen atoms were added to the structures. Docking was performed using Surflex-Dock in SYBYL-X2.1.1 (Tripos Inc.) [30 (link)]. For the protein, the protocol that characterizes the binding site of the enzyme was generated using a ligand/substrate-based approach. All other parameters were set to default. Either NDGA or 4-OHE₂ in 3BWM was subjected to a redocking process and the best docked conformation of the NDGA-bound substrate binding pocket was superimposed on that of the 4-OHE₂-bound substrate binding pocket. Finally, the Surplex-Dock scoring function was the sum of the hydrophobic, polar, repulsive, and entropic terms including crash and solvation over the appropriate atom pairs.

The molecular modeling and virtual screening were performed using the Surflex-Dock module implemented in the SYBYL-X 2.1 program (Tripos Inc., St. Louis, MO, USA). Before the docking procedures, water molecules and other ligands were removed from the crystal structure (PDB: 1GC1 [21 (link)]), and energy minimization was performed. The NCI diversity dataset, which contains 1,974 diversity compound structures, was selected for the virtual screening study and prepared using the preparation protocol of Surflex-for-searching in the ligand structure preparation tool. The protomol (an idealized active site ligand to generate putative poses of molecules [58 (link)]) was generated, selecting the critical amino acids (residues 29, 35, 40–49) in the interaction of CD4 and gp120 [21 (link),59 (link)]. In the docking procedure, the minimization was performed pre-dock and post-dock. A total of 20 poses were generated from each docked ligand. Forty compounds of top-ranking total scores were selected for further bioassays. All compounds were ordered from the Division of Cancer Treatment & Diagnosis (DCTD) of the National Cancer Institute (NCI) (website: https://dtp.cancer.gov/organization/dscb/obtaining/vialed.htm) [60 ].