
Weakly basic small molecule drugs exhibit slow intracellular diffusion and accumulation in lysosomes, which can reduce their cellular activity and efficacy.


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For drugs to be active they have to reach their targets. Within cells this requires free diffusion, distribution, and availability. Here, we explored the intracellular diffusion rates and distribution of a series of small molecular fluorescent drugs, in comparison to proteins, by microscopy and fluorescence recovery after photobleaching (FRAP). While all proteins diffused freely, we found a strong correlation between p K a and the intracellular diffusion and distribution of small molecule drugs. Weakly basic, small-molecule drugs displayed lower fractional recovery after photobleaching and 10-to-20-fold slower diffusion rates in cells than in aqueous solutions. As, more than half of pharmaceutical drugs are weakly basic, they, are protonated at pH 7.4, resulting in their sequestration in the cell cytoplasm. Protonation, facilitates the formation of membrane impermeable ionic form of the weak base small molecules. This results in ion trapping, further reducing diffusion rates of weakly basic small molecule drugs under macromolecular crowding conditions where other nonspecific interactions become more relevant and dominant. Our imaging studies showed that acidic organelles, particularly the lysosome, captured these molecules. Surprisingly, blocking lysosomal import only slightly increased diffusion rates and fractional recovery. Conversely, blocking protonation by N- acetylated analogues, greatly enhanced their diffusion and fractional recovery after FRAP. Based on these results, N -acetylation of small molecule drugs may improve the intracellular availability and distribution of weakly basic, small molecule drugs.

### Competing Interest Statement

The authors have declared no competing interest.

Reversing protonation of weakly basic drugs greatly enhances intracellular diffusion and decreases lysosomal sequestration

slow-intracellular-diffusion-and-lysosomal-sequestration-of-weakly-basic-small-molecule-drugs


Slow Intracellular Diffusion and Lysosomal Sequestration of Weakly Basic Small Molecule Drugs
