Diffusion of small molecule drugs is affected by surface interactions and crowder proteins

Dey, Debabrata; Nunes-Alves, Ariane; Wade, Rebecca C.; Schreiber, Gideon

doi:10.1016/j.isci.2022.105088

Cited by 14 publications

(32 citation statements)

References 68 publications

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“…In previous work, we have shown that fluorescein diffusion is slowed by adding proteins, even at relatively low concentrations. 13 Here, we measured the diffusion coefficients of fluorescein in the cytoplasm of live HeLa cells, observing almost complete recovery from photobleaching within 1s (Figure 2A-C). Dconfocal of 56 µm 2 s -1 in PBS was reduced to Dconfocal 38 µm 2 s -1 in the crowded cellular cytoplasm of HeLa cells (Figure 2B).…”

Section: Resultsmentioning

confidence: 84%

“…The GSK3 inhibitor SB216763 (M.W.=371 Da, Figure 1) aggregates when dissolved in PBS buffer, which can be reversed by adding BSA. 13 Comparative FRAP profiles and Dconfocal rates of SB216763 in different mediums are shown in Figure 3A-C. For comparison to live cell cytoplasm, we used 100 mg/mL of BSA or DMEM media.…”

Section: Resultsmentioning

confidence: 99%

“…In previous work, we studied the diffusion behavior of fluorescent drug molecules under crowding conditions constituting proteins and polymers, thus, mimicking the cellular environment. 13 However, the cellular cytoplasm of eukaryotic cells is by far more complex than can be mimicked in vitro. 14 This relates to the presence of intracellular membranes, multiple organelles, 15,16 and large diversity of macromolecules, in terms of size, charge and hydrophobicity of the cellular milieu.…”

Section: Introductionmentioning

confidence: 99%

“…[24][25][26] Monitoring diffusion behavior is a good proxy for predicting intracellular drug delivery and other processes, such as non-specific binding or aggregation. 13 The primary tool for measuring cellular diffusion is fluorescence recovery after the photobleaching (FRAP), which inherently requires all studied molecules to be fluorescent. FRAP under a confocal microscope is a sensitive versatile method that is suitable for measurement of weakly fluorescent molecules, as opposed to single molecules fluorescence correlation spectroscopy.…”

Section: Introductionmentioning

confidence: 99%

“…FRAP under a confocal microscope is a sensitive versatile method that is suitable for measurement of weakly fluorescent molecules, as opposed to single molecules fluorescence correlation spectroscopy. 13,27,28 In this work, we investigated intracellular diffusion of a series of fluorescent dyes and drugs (Figure 1 and Table 1) by FRAP. For most measurements we used Line-FRAP, which has a much lower death time and faster data accumulation in comparison to standard FRAP (800 Hz versus 50 Hz, for detailed…”

Section: Introductionmentioning

confidence: 99%

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

Dey

Marciano

Poryvai

et al. 2023

Preprint

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Drug efficacy depends not only on delivery but also on intracellular diffusion, distribution and availability. Yet, more than a half of pharmaceutical drugs are weakly basic and thus, protonated and sequestered at intracellular pH. Protonation reduces their diffusion rates due to macromolecular crowding and nonspecific interactions, and subcellular sequestration prevents them from reaching their target due to ion trapping. Here, we explored the intracellular diffusion rates of a series of small molecular fluorescent drugs by fluorescence recovery after the photobleaching (FRAP). We found a strong correlation between drug pKaand intracellular diffusion and distribution. Weakly basic, small-molecule drugs displayed slower fraction recovery after photobleaching and 10-to-20-fold lower diffusion rates in cells than in aqueous solutions, suggesting sequestration. But while our imaging studies showed that acidic organelles, particularly the lysosome, captured these molecules, blocking lysosomal import did not improve diffusion. Instead, blocking protonation enhanced their diffusion, as shown by theirN-acetylated analogues. Moreover, co-administration with basic quinacrine, which is accumulated in lysozymes, prevented the sequestration of the anti-cancer drug mitoxantrone, thereby improving its biodistribution. Based on these results, combiningN-acetylation with co-administration may improve the intracellular diffusion and distribution of weakly basic, small molecule drugs.

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Section: Resultsmentioning

confidence: 84%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

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

Dey

Marciano

Poryvai

et al. 2023

Preprint

Self Cite

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Brownian dynamics simulations of biomolecular diffusional association processes

Muñiz‐Chicharro

Votapka

Amaro

et al. 2022

WIREs Comput Mol Sci

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Brownian dynamics (BD) is a computational method to simulate molecular diffusion processes. Although the BD method has been developed over several decades and is well established, new methodological developments are improving its accuracy, widening its scope, and increasing its application. In biological applications, BD is used to investigate the diffusive behavior of molecules subject to forces due to intermolecular interactions or interactions with material surfaces. BD can be used to compute rate constants for diffusional association, generate structures of encounter complexes for molecular binding partners, and examine the transport properties of geometrically complex molecules. Often, a series of simulations is performed, for example, for different protein mutants or environmental conditions, so that the effects of the changes on diffusional properties can be estimated. While biomolecules are commonly described at atomic resolution and internal molecular motions are typically neglected, coarse‐graining and the treatment of conformational flexibility are increasingly employed. Software packages for BD simulations of biomolecules are growing in capabilities, with several new packages providing novel features that expand the range of questions that can be addressed. These advances, when used in concert with experiment or other simulation methods, such as molecular dynamics, open new opportunities for application to biochemical and biological systems. Here, we review some of the latest developments in the theory, methods, software, and applications of BD simulations to study biomolecular diffusional association processes and provide a perspective on their future use and application to outstanding challenges in biology, bioengineering, and biomedicine. This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics Molecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo Methods Software > Simulation Methods

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Utility of Brownian dynamics simulations in chemistry and biology: A comprehensive review

ElSawy

2025

Biochimica et Biophysica Acta (BBA) - General Subjects

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Diffusion of small molecule drugs is affected by surface interactions and crowder proteins

Cited by 14 publications

References 68 publications

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

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

Brownian dynamics simulations of biomolecular diffusional association processes

Utility of Brownian dynamics simulations in chemistry and biology: A comprehensive review

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