Classifying Transportable vs. Non-Transportable Compounds Through Fundamental Energy Constraints

Predicting whether a compound is subject to active transport is crucial in drug development. We propose a simple threshold for passive membrane permeability Pm, derived from the cell’s energy limitation, to identify compounds unlikely to be actively effluxed. For MDCK cells, this threshold—normalized to the applied compound concentration (Cext)—was determined to be log(Pm*Cext / [cm/s*µM] ) = -1.7. To derive this threshold, we conducted an extensive analysis of literature-reported efflux ratios (ER) in MDCKII-MDR1, MDCK-BCRP, and MDCK-MRP2 cells (294 datapoints across 136 unique compounds). Concentration-dependent measurements for Amprenavir, Eletriptan, Loperamide, and Quinidine enabled the most accurate determination of the threshold. Literature ER values were re-evaluated through the experimental determination of reliable Pm values, as well as newly measured ER values with MDCK efflux assays. The results of these assays and the re-evaluation allowed us to reclassify all but three outliers (compounds with ER > 2.5 and log(Pm*Cext) > −1.7). In contrast, more than 60% of the compounds analyzed without significant ER values (123 compounds) fell above the threshold, in strong agreement with our theory of an energy limitation to active transport. This permeability threshold thus provides a simple and broadly applicable criterion to identify compounds for which active efflux is energetically not feasible, offering a practical tool for early drug discovery and optimization.