Chromatographic\nDetermination of Permeability-Relevant\nLipophilicity Facilitates Rapid Analysis of Macrocyclic Peptide Scaffolds

Hydrocarbon-determined shake-flask measurements have\ndemonstrated\ngreat utility for optimizing lipophilicity during early drug discovery.\nAlternatively, chromatographic methods confer reduced experimental\nerror and improved handling of complex mixtures. In this study, we\ndeveloped a chromatographic approach for estimating hydrocarbon–water\nshake-flask partition coefficients for a variety of macrocyclic peptides\nand other bRo5 molecules including PROTACs. The model accurately predicts\nexperimental shake-flask measurements with high reproducibility across\na wide range of lipophilicities. The chromatographic retention times\nrevealed subtle conformational effects and correlated with the ability\nto sequester hydrogen bond donors in low dielectric media. Estimations\nof shake-flask lipophilicity from our model also accurately predicted\ntrends in MDCK passive cell permeability for a variety of thioether-cyclized\ndecapeptides. This method provides a convenient, high-throughput approach\nfor measuring lipophilic permeability efficiency and predicting passive\ncell permeability in bRo5 compounds that is suitable for multiplexing\npure compounds or investigating the properties of complex library\nmixtures.