The impact of assay recovery on the apparent permeability, a function of lysosomal trapping.

permeability assessment tools, like PAMPA, Caco-2, and MDCK, are frequently used to assess permeability and provide input in to various classification systems. Frequently, the measured recovery values in permeability assays are poor. Poor recovery may be a result of lysosomal trapping of compound. It was hypothesized that a relationship existed between diminished assay recovery of compound due to lysosomal trapping and underestimation of the P value.To examine this hypothesis, a series of experiments were conducted measuring cellular accumulation, percent recovery, and permeability in the absence or presence of an inhibitor of the V-type H-ATPase, bafilomycin A1, to determine if a quantifiable relationship between lysosomal trapping, recovery, and permeability existed.Displacing compounds from lysosomes using bafilomycin A1 resulted in an improved compound recovery in the assay and a corresponding elevated permeability, where for each 10% loss in recovery, a P underestimate of ∼2.2 × 10 cm/s was observed. The findings highlight the potential for compound misclassification in various classification systems when assay recovery is not considered. Consideration of lysosomal trapping in the context of permeability assays may yield permeability values more reflective of the intrinsic permeability and the appropriate permeability classification.