Modeling the Effect of Hydrophobicity on the Passive Permeation of Solutes across a Bacterial Model Membrane

Passive diffusion across biomembranes is an important mechanism of permeation for multiple drugs, including antibiotics. However, this process is frequently neglected while studying drug uptake and, in our view, warrants further investigation. Here, we apply molecular dynamics simulations to investigate the impact of changes in molecular hydrophobicity on the permeability of a series of inhibitors of the quorum sensing of Pseudomonas aeruginosa, previously discovered by us, across a membrane model. Overall, we show that permeation across this membrane model does not correlate with the molecule's hydrophobicity. We demonstrate that using a simple model for permeation, based on the difference between the maximum and minimum of the free energy profile, outperforms the inhomogeneous solubility-diffusion model, yielding a permeability ranking that better agrees with the experimental results, especially for hydrophobic permeants. The calculated differences in permeability could not explain differences in in bacterio activity. Nevertheless, substantial differences in molecular orientation along the permeation pathway correlate with the in bacterio activity, emphasizing the importance of analyzing, at an atomistic level, the permeation pathway of these solutes.

Automated summary

Passive diffusion across biomembranes is an important permeation mechanism for drugs, including antibiotics, but it is often overlooked in drug uptake studies and requires further investigation. In this study, molecular dynamics simulations were used to investigate the influence of changes in molecular hydrophobicity on the permeability of a series of inhibitors of Pseudomonas aeruginosa's quorum sensing. The findings show that permeation across a membrane model is not correlated with the molecule's hydrophobicity. A simple model based on the difference in free energy profile outperforms the inhomogeneous solubility-diffusion model in predicting permeability, especially for hydrophobic molecules. The calculated differences in permeability do not explain differences in bacterio activity, but substantial differences in molecular orientation along the permeation pathway correlate with bacterio activity.