Modelling P-gp efflux may help us design better molecules


Figure2 POM Dec comp chem

In order to treat disorders of the central nervous system (CNS), it is essential to design molecules that can cross the blood-brain barrier (BBB), a layer of tightly packed endothelial cells rich in P-glycoprotein (P-gp) efflux pumps that protect the CNS from circulatory chemicals. Designing drugs that can permeate the BBB is a significant challenge that usually involves reducing molecular size and increasing hydrophobicity to promote passive membrane diffusion. A second challenge is then to evade the efflux of the molecules back into the blood by P-gp, a promiscuous transmembrane pump that has over 300 known substrates. BBB-penetration is notoriously difficult to predict for novel molecular series, so enriching our mechanistic understanding of the process is a step towards improving our ability to design CNS drugs.

In this computational chemistry paper of the month, Jorgensen et al. report a molecular dynamics (MD) study of rhodamine, a known P-gp substrate, penetrating lipid bilayers and interacting with P-gp. Although the timescales necessary to sample membrane penetration and P-gp binding using unbiased atomistic MD are computationally inaccessible, the authors were able to increase sampling by flooding the system with rhodamine and performing simulations at enhanced temperatures. The authors also utilised a geometric model of the hinge-shaped pump and a kinetic model to infer mechanistic detail about the efflux process. Importantly, they modelled 2 pathways for P-gp efflux: one that involves the passive diffusion of rhodamine across the luminal membrane into the cell cytosol, before entering the inner volume of P-gp and diffusing into the central binding cavity; and another that involves passive diffusion into the luminal membrane and lateral diffusion through the membrane into the P-gp central binding cavity. The modelling suggests that the latter pathway only accounts for about 5% of the efflux events. The study also revealed that there is no specific binding site for rhodamine in the P-gp binding cavity, consistent with the experimental observation that P-gp is not substrate-specific, and that only 1 rhodamine molecule can fit in the cavity at a time, suggesting that efflux events involve only a single substrate molecule.

Jorgensen C. et al. Modeling Substrate Entry into the P‐Glycoprotein Efflux Pump at the Blood−Brain Barrier. J. Med. Chem. 2023.