Identification and Empiric Evaluation of New Inhibitors of the Multidrug Transporter P-Glycoprotein (ABCB1)

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 (IC50) 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.

Molecular Modeling Studies to Probe the Binding Hypothesis of Novel Lead Compounds against Multidrug Resistance Protein ABCB1

“…Overexpression of ABCB1 is a common cause of chemotherapy failure [21,53]. Inhibition of the transporter can readily re-sensitize cell lines to therapeutic drugs in the laboratory; however, translation to the clinical setting so far has failed due to off-target toxicity, lack of selectivity and tissue damage [12].…”

“…Inhibition of the transporter can readily re-sensitize cell lines to therapeutic drugs in the laboratory; however, translation to the clinical setting so far has failed due to off-target toxicity, lack of selectivity and tissue damage [12]. However, the design of more potent and selective inhibitors remains an attractive strategy to overcome recalcitrant multidrug resistance [12,21,52]. To overcome the obstacles associated with toxicity and off-target effects, we have identified dynamically stable inhibitors through the application of molecular docking and molecular dynamic simulations followed by lipophilic efficiency profiling and pharmacokinetic analyses.…”

“…Four recently identified novel lead compounds [21] with biological activity ranging from 0.001 to 0.019 µM were used to probe the binding hypothesis within ABCB1. An additional dataset of 54 structurally diverse compounds that are purportedly selective compounds for inhibition of P-gp/ABCB1 (over ABCG2 and ABCC1) was obtained from the literature [22][23][24] for the comparison of the binding hypothesis.…”

“…The binding region was delineated by those amino acids that were residing within a radius of 30 Å from X = 171, Y = 166 and Z = 169, which comprises the whole transmembrane domain region. A comparative analysis of the protein-ligand interaction of the four lead compounds [21] with the docking results of 54 selective compounds [22,23,25,41] was followed by PLIF and SAR-directed pose analysis. All four lead compounds 'A', 'D', 'E' and 'F' docked in the transmembrane region and mostly formed hydrophobic interactions with Phe-303, Tyr-307, Phe-343, Met-986 and Gln-990, π-π interactions with Trp-232 and hydrogen bonding with Gln-990, as visualized in Figure 3.…”

“…Previous structural optimization of ABCB1 inhibitors suggests that high molecular weight, lipophilic efficiency (LipE), large logP values, longer skeletal structure and the accumulation of more hydrophobic groups increase the binding affinity of inhibitors [20]. We have also applied structure/activity analyses to identify novel lead compounds denoted as 'A', 'D', 'E' and 'F' (Figure 1) [21]. Their potency and efficacy were proven by their ability to re-sensitize ABCB1-expressing cells to the anticancer drug taxol.…”