Fig 1.
Strategy for structure-based virtual screening.
Table 1.
Quality verifications of initial models of IF-CsSBAT according to different programs.
Table 2.
Comparison on refined structural evaluation.
Fig 2.
Conformation changes of CsSBAT accompanied with transport of Na+ and taurocholate (TCH).
Both OF-CsSBAT (A) and IF-CsSBAT (B) are colored in tan. OF-YfASBT (A) is colored in pink and IF-NmASBT (B) in blue. ASBTs presenting identical conformation are superposed. Tunnel leading to the TCH-binding site is visualized in yellow eclipse. Residues forming TCH-binding cavity are depicted as green spheres in CsSBAT. Other residues participating in TCH-binding site are provided at each side. Na+ ions are in purple circle (Na1 and Na2). Taurocholate (TCH) is depicted as maroon pentagon.
Fig 3.
Taurocholate re-docking into the substrate-binding pocket of NmASBT.
Superposition of taurocholate in the best-re-docking pose (yellow) and crystal structure (blue) (RMSD = 2.0 Å). Hydrogen bonds between the residues of NmASBT binding pocket and taurocholate in both the crystal (blue; Lys13 and Asn295) and the best-re-docked (yellow; Thr112 and His294) complex structures are shown as yellow dotted lines, and NmASBT interacting residues (green) are depicted as sticks. The known hydrogen bonds are marked in red asterisks.
Table 3.
Binding energy for bile acids to OF-/IF-SBAT of Clonorchis sinensis and OF-/IF-ASBT of Homo sapiens using AutoDock Vina.
Fig 4.
A Venn diagram presents compounds interacting with two SBATs and two ASBTs.
Ellipse represents compounds screened against each of the four ASBTs. Gray area indicates compounds which interact with either OF-CsSBAT or IF-CsSBAT. Black area depicts compounds that interact with both CsSBATs, but not with other ASBTs.
Fig 5.
Docked pose of two compounds with IF-CsSBAT and OF-CsSBAT following the Lipinski’s rule of five.
Binding modes of compounds were obtained from the MTiOpenScreen [52]. In each panel, left box ribbon and stick indicate a compound placed in the active site of OF-CsSBAT (A and C) and IF-CsSBAT (B and D). Right panel generated by LigPlot+ v1.4.3 [59] indicates the schematic interactions of CsSBAT with 124948115 (A and B) and 49734421 (C and D). The compound and residues with hydrophobic interactions are visualized with 2D diagrams. Amino acid residues involved in hydrophobic interactions are presented as red spoked arcs. Residues contributing to hydrogen bonds are depicted in green and atomic distance (Å) is given as green number. Nitrogen, oxygen, carbon, and sulfur atoms are shown in blue, red, black, and yellow, respectively. Black arrow indicates compound movement.
Table 4.
Inhibitory compounds subjected to virtual screening using MTiOpenScreen and selected by applying the Lipinski’s rule of five.
Fig 6.
Docked poses of large compounds with OF-CsSBAT and IF-CsSBAT.
The binding modes of compounds were obtained from the AutoDock Vina v1.1.2 [55]. Left (A, C, E, G, and I) and right (B, D, F, H, and J) panels represent OF-CsSBAT and IF-CsSBAT, respectively. The schematic interactions of CsSBAT with 45375808 (A and B), 9806452 (C and D), 441243 (E and F), 4701 (G and H), and 92727 (I and J) were generated using LigPlot+ v1.4.3 [59]. The compound and residues with hydrophobic interactions are visualized with 2D diagrams. The residues contributing to hydrogen bonds are colored green. Hydrogen bond is indicated as a broken line with length (Å). Amino acid residues involved in the hydrophobic interactions are marked with red spoked arcs. Black arrow indicates compound movement.
Table 5.
Inhibitory compounds with high molecular weight (Mr > 500 Da) selected using AutoDock Vina v1.1.2.
Fig 7.
Stability assessment of two SBATs and two ASBTs docking with compound 9806452.
(A) OF-CsSBAT, (B) IF-CsSBAT, (C) OF-HsASBT, and (D) IF-HsASBT. (Left panel) RMSD values of Cα (RMSDCa in blue), backbone (RMSDBb in red), and all heavy atoms (RMSDAll in green) from each initial structure during 50 ns simulation time. (Right panel) The RMSD pattern of the compound within each complex.
Table 6.
Binding free energy and its components during MD simulation.