Molecular Docking

The docking studies of liquiritin and BPSA with AKR1C1, AKR1C2, AKR1C3, and AKR1C4 were performed using the AutoDock Vina program (Version 1.1.2) (Trott and Olson, 2010). Protein Data Bank (PDB) entries 1MRQ (Couture et al., 2003), 1IHI (Jin et al., 2001), 3R43 (Flanagan et al., 2012), and 2FVL (Waxman et al., 1988) were selected as the AKR1C1, AKR1C2, AKR1C3, and AKR1C4, respectively. Auto Dock Tools (Sanner et al., 2007) were applied for preparation of receptors and ligands. For preparing receptors, the solvent molecules and original ligands from the crystals were removed, with retaining one molecule of the respective enzyme and the NADP+ cofactor. And the binding pocket was defined to cover around the original ligand within 15 Å radius sphere. For preparing ligands, the 3D-structure of ligands were generated by ChemBio3D and optimized under a Minimization field using the MM2 forcefield initially, and then processed by Auto Dock Tools via adding hydrogens, and assigning Gasteiger charges. The docking experiments were carried out taking into account the flexibility of ligands only. Each run produced nine docking poses which were ranked according to scoring energy. Those conformations with the lowest energy were selected and visualized by PyMOL.