Consensus screening for a challenging target: the quest for P-glycoprotein inhibitors

08 November 2023, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


ATP-binding cassette (ABC) transporters are a large family of proteins involved in membrane transport of a wide variety of substrates. Among them, ABCB1, also known as MDR-1 or P-glycoprotein (P-gp), is the most characterized. By exporting xenobiotics out of the cell, P-gp activity can affect the ADME properties of several drugs. Moreover, P-gp has been found to mediate multidrug resistance in cancer cells. Thus, the inhibition of P-gp activity may lead to increased absorption and/or intracellular accumulation of co-administered drugs, enhancing their effectiveness. Using the human cryoEM 3D structure of the P-gp in the inhibitor-bound intermediate form (PDBID: 6qee), approximately 200'000 commercially available natural compounds from the ZINC database were virtually screened. To build a model able to discriminate between substrate and inhibitors, two datasets of compounds with known activity, including P-gp inhibitors, substrates, and inactive molecules were also docked. The best docking pose of selected substrates and inhibitors were used to generate 3D common feature pharmacophoric models that were combined with the Autodock Vina binding energy values to prioritize compounds for visual inspection. With this consensus approach, 13 potential candidates were identified and then tested for their ability to inhibit P-gp, using zosuquidar, a P-gp inhibitor of clinical use, as a reference drug. Eight compounds were found to be active with 6 of them having an IC50 lower than 5 µM in a membrane-based ATPase activity assay. Moreover, the P-gp inhibitory activity was also confirmed by two different cell-based in vitro methods. These results demonstrate the ability of the combined structure-based pharmacophore modeling and docking-based virtual screening approach to predict novel hit compounds with inhibitory activity toward P-gp. The resulting chemical scaffolds could serve as inspiration for the optimization of novel and more potent P-gp inhibitors.


Molecular docking
Pharmacophore modeling
Virtual screening
Consensus scoring

Supplementary materials

Figure S1
P-gp binding site (A) and best docked pose of compounds 2 (B), 4 (C), 13 (D), 14 (E), 17 (F), and 29 (G) in the binding site of P-gp. Compounds are shown in sticks, while Trp232, Tyr307, Tyr310, and Asn721 are colored in green. Hydrogen bonds are shown as yellow dashed lines. For comparison, the experimental binding pose of the two copies of zosuquidar is also shown in grey.


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