Abstract
The expression of the drug efflux pump ABCB1 correlates negatively with cancer survival, making the transporter an attractive target for therapeutic inhibition. In order to identify new inhibitors of ABCB1, we have exploited the cryo-EM structure of the protein to develop a pharmacophore model derived from the best docked conformations of a structurally diverse range of known inhibitors. The pharmacophore model was used to screen the Chembridge compound library. We identified six new potential inhibitors with distinct chemistry compared to the third-generation inhibitor tariquidar and with favourable lipophilic efficiency (LipE) and lipophilicity (CLogP) characteristics, suggesting oral bioavailability. These were evaluated experimentally for efficacy and potency using a fluorescent drug transport assay in live cells. The half-maximal inhibitory concentrations (IC(50)) of four of the compounds were in the low nanomolar range (1.35 to 26.4 nM). The two most promising compounds were also able to resensitise ABCB1-expressing cells to taxol. This study demonstrates the utility of cryo-electron microscopy structure determination for drug identification and design.