Conformational Flexibility, Internal Hydrogen Bonding, and Passive Membrane Permeability: Successful in Silico Prediction of the Relative Permeabilities of Cyclic Peptides

We report an atomistic physical model for the passive membrane permeability of cyclic peptides.
The computational modeling was performed in advance of the experiments and did not involve the use of
“training data”. The model explicitly treats the conformational flexibility of the peptides by extensive
conformational sampling in low (membrane) and high (water) dielectric environments. The passive membrane
permeabilities of 11 cyclic peptides were obtained experimentally using a parallel artificial membrane
permeability assay (PAMPA) and showed a linear correlation with the computational results with R2 =
0.96. In general, the results support the hypothesis, already well established in the literature, that the ability
to form internal hydrogen bonds is critical for passive membrane permeability and can be the distinguishing
factor among closely related compounds, such as those studied here. However, we have found that the
number of internal hydrogen bonds that can form in the membrane and the solvent-exposed polar surface
area correlate more poorly with PAMPA permeability than our model, which quantitatively estimates the
solvation free energy losses upon moving from high-dielectric water to the low-dielectric interior of a
membrane.