Abstract
BACKGROUND: The blood-brain barrier (BBB) paracellular permeability must be evaluated in various contexts in vitro and in vivo, including pharmacological evaluation of drug candidates, investigations of pathological changes in disease and model development. However, most available paracellular marker substances are either radioactive, lack sensitivity and thereby require large sample volumes, or they can influence the BBB themselves via osmotic pressure. Moreover, in drug permeability studies, an adequate paracellular marker should be detectable in the same sample as the compound being tested, ideally applying the same analytical technology. METHODS: We rationally designed a novel permeability marker to be highly sensitively measurable with ultra-performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS); to be not a potential substrate of solute carriers or transporters; stable against enzymatic digestion and well tolerated. We evaluated this novel permeability marker in vitro in Transwell(®) models with four different cell types (MDCK II, hCMEC/D3, primary and from induced pluripotent stem cells derived brain capillary endothelial cells) and cross-validated these results with known fluorescence markers. We further analyzed its in vivo pharmacokinetics and brain-to-plasma ratio in healthy Swiss mice. Possible interactions with LAT-1 and PepT1 were evaluated with uptake and/or inhibition assays. RESULTS: Based on non-canonical and ᴅ-dipeptide structure, the developed marker ᴅ-methyl-tyrosinyl-ᴅ-ornithine (ᴅ-Tyr(Me)Orn) is hydrophilic and with low molecular weight (309 Da), it enables a low endogenous background and is readily available through peptide synthesis, also as isotopically labeled derivative. The developed UPLC-MS/MS quantification assay allows a highly sensitive measurement in different matrices (lower limit of quantification: 0.05 ng/mL cell medium, lysed cells, 0.1 ng/mL mouse plasma; 3 ng/g, mouse brain). In the well-known MDCK II Transwell(®) model, it revealed a suitable P(app) of 5.13 ± 1.08 × 10(− 7) cm/s. Using the marker ᴅ-Tyr(Me)Orn it was further possible to compare the tightness of three brain capillary endothelial cell models. The time dependent distribution and in vivo pharmacokinetics was determined in healthy Swiss mice and revealed a constantly low brain concentration and brain-to-plasma ratio. CONCLUSION: We developed a highly feasible new paracellular marker, easily adaptable in various experimental designs. GRAPHICAL ABSTRACT: [Image: see text] SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12987-026-00806-5.