Exploring experimental and computational markers of cyclic peptides: Charting islands of permeability

Abstract

An increasing number of macrocyclic peptides that cross biological membranes are being reported, suggesting that it might be possible to develop peptides into orally bioavailable therapeutics; however, current understanding of what makes macrocyclic peptides cell permeable is still limited. Here, we synthesized 62 cyclic hexapeptides and characterized their permeability using in vitro assays commonly used to predict in vivo absorption rates, i.e. the Caco-2 and PAMPA assays. We correlated permeability with experimentally measured parameters of peptide conformation obtained using rapid methods based on chromatography and nuclear magnetic resonance spectroscopy. Based on these correlations, we propose a model describing the interplay between peptide permeability, lipophilicity and hydrogen bonding potential. Specifically, peptides with very high permeability have high lipophilicity and few solvent hydrogen bond interactions, whereas peptides with very low permeability have low lipophilicity or many solvent interactions. Our model is supported by molecular dynamics simulations of the cyclic peptides calculated in explicit solvent, providing a structural basis for the observed correlations. This prospective exploration into biomarkers of peptide permeability has the potential to unlock wider opportunities for development of peptides into drugs.3

Nonclassical Size Dependence of Permeation Defines Bounds for Passive Adsorption of Large Drug Molecules

“…18–20 However, there is a lack of consensus as to whether this decrease in permeability at higher A log P values is due to poor solubility or sequestration into the PAMPA membrane, and the phenomenon may depend on the particular system involved. 20,21 …”

Intramolecular hydrogen bonding: An opportunity for improved design in medicinal chemistry

“…Wang et al synthetized 62 peptides, measured their permeability in the PAMPA and Caco‐2 cell system and performed chromatographic and NMR experiments. Then the authors correlated permeability with the logarithm of the capacity factor and the NMR amide temperature coefficients, which was considered a convenient overall measure of the hydrogen bonding potential of a peptide.…”

Leveraging chromatography based physicochemical properties for efficient drug design

“…Notably, HBD has hardly changed (increased by only 1 count) highlighting the significance of limiting HBD exposure for oral absorption of large molecules. Wang et al [37] observed a correlation of RP HPLC log k' with passive permeability determined by human colorectal adenocarcinoma cells (Caco-2) and the parallel artificial membrane permeability assay (PAMPA) for a set of macrocyclic peptides. Bockus et al used Elog D (5.5 to 7.5) to study macrocycles.…”