Structure–Permeability Relationship of Semipeptidic Macrocycles—Understanding and Optimizing Passive Permeability and Efflux Ratio
Antoine Le Roux, Émilie Blaise, Pierre‐Luc Boudreault, Christian Comeau, Annie Doucet, M.A. Giarrusso, Marie-Pierre L. Collin, Thomas Neubauer, Florian Kölling, Andreas H. Göller, Lea Seep, Dieudonné Tshitenge Tshitenge, Matthias Wittwer, Maximilian Kullmann, Alexander Hillisch, Joachim Mittendorf, Éric Marsault
Abstract
We herein report the first thorough analysis of the structure-permeability relationship of semipeptidic macrocycles. In total, 47 macrocycles were synthesized using a hybrid solid-phase/solution strategy, and then their passive and cellular permeability was assessed using the parallel artificial membrane permeability assay (PAMPA) and Caco-2 assay, respectively. The results indicate that semipeptidic macrocycles generally possess high passive permeability based on the PAMPA, yet their cellular permeability is governed by efflux, as reported in the Caco-2 assay. Structural variations led to tractable structure-permeability and structure-efflux relationships, wherein the linker length, stereoinversion, N-methylation, and peptoids site-specifically impact the permeability and efflux. Extensive nuclear magnetic resonance, molecular dynamics, and ensemble-based three-dimensional polar surface area (3D-PSA) studies showed that ensemble-based 3D-PSA is a good predictor of passive permeability.