Chromatographic Determination of Permeability-Relevant Lipophilicity Facilitates Rapid Analysis of Macrocyclic Peptide Scaffolds

Hydrocarbon-determined shake-flask measurements have
demonstrated
great utility for optimizing lipophilicity during early drug discovery.
Alternatively, chromatographic methods confer reduced experimental
error and improved handling of complex mixtures. In this study, we
developed a chromatographic approach for estimating hydrocarbon–water
shake-flask partition coefficients for a variety of macrocyclic peptides
and other bRo5 molecules including PROTACs. The model accurately predicts
experimental shake-flask measurements with high reproducibility across
a wide range of lipophilicities. The chromatographic retention times
revealed subtle conformational effects and correlated with the ability
to sequester hydrogen bond donors in low dielectric media. Estimations
of shake-flask lipophilicity from our model also accurately predicted
trends in MDCK passive cell permeability for a variety of thioether-cyclized
decapeptides. This method provides a convenient, high-throughput approach
for measuring lipophilic permeability efficiency and predicting passive
cell permeability in bRo5 compounds that is suitable for multiplexing
pure compounds or investigating the properties of complex library
mixtures.