Ab initio modeling and ligand docking of quercetin and the MC-LR transporter protein Oatp1b2/OATP1B3

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Trans-membrane proteins (TMPs) play a crucial role in the translocation of organic and inorganic molecules. Unlike other proteins, TMPs are difficult to model structurally because of their location within the amphipathic plasma membrane. In this study, we focused on examining the transport of the cyanotoxin microcystin-LR (MC-LR) through organic ion transporting polypeptides (OATPs) and whether the bioactive phytoconstituent quercetin can function as a barrier to the transportation of MC-LR. To test this hypothesis, we first modeled the transporters OATP1B3 and Oatp1b2 localized in the human and mouse liver, respectively, by ab initio modeling with the Iterative Threading ASSEmbly Refinement server and refined the generated model using the refinement tool of the ModLoop server. Using different tools and servers, the structural quality of the transmembrane helices was validated and found to be an accurate structure of a TMP. Docking analysis was performed with the ligands MC-LR and quercetin with both OATPs using the PatchDock and FireDock online servers. The results, in the form of the global energy of both docked structures, were based on predictions made earlier. The Oatp1b2 global energy for quercetin was −36.4 ​kcal/mol, compared with the corresponding value at the MC-LR location which was only −5.59 ​kcal/mol. Similarly, in the case of OATP1B3 with quercetin, the global energy was found to be −39.0 ​kcal/mol, whereas with MC-LR it was −15.6 ​kcal/mol. These results clearly show that quercetin competitively inhibits the binding of MC-LR to its respective targets.