Molecular Docking

The three-dimensional structure of AhR (Uniprot AC: {"type":"entrez-protein","attrs":{"text":"P35869","term_id":"3041653","term_text":"P35869"}}P35869) (Ma et al., 2019) were obtained by homology modeling using an online protein structure prediction server, SWISS-MODEL⁵. The chain A of 4zp4.1.B (resolution: 2.36 Å, identity: 27.12%). All the work of molecular docking was done on the Yin Fu cloud computing platform⁶. The initial structures of compounds were constructed and assigned hydrogens by the UCSF Chimera software (Eric et al., 2004), and AMBER ff14SB forcefield and AM1-BCC partial charges (Araz et al., 2000, 2002) were assigned for them. The box center was set at (−87.037, 100.739, −27.384) and the dimensions (27.597, 34.48, 32.672). At last, the affinity was evaluated by the grid-based score using DOCK 6.7 (Lang et al., 2009; Sudipto et al., 2010) to conduct semi-flexible docking with 10,000 different orientations generated. And then the Grid-based score was calculated for each pose. Finally, clustering analysis was performed (RMSD threshold was set 2 Å) to obtain the best-scored poses.