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Molecular Modeling to Estimate the Diffusion Coefficients of Drugs and Other Small Molecules.

ABSTRACT: Diffusion is a spontaneous process and one of the physicochemical phenomena responsible for molecular transport, the rate of which is governed mainly by the diffusion coefficient; however, few coefficients are available because the measurement of diffusion rates is not straightforward. The translational diffusion coefficient is related by the Stokes-Einstein equation to the approximate radius of the diffusing molecule. Therefore, the stable conformations of small molecules were first calculated by molecular modeling. A simple radius rs and an effective radius re were then proposed and estimated using the stable conformers with the van der Waals radii of atoms. The diffusion coefficients were finally calculated with the Stokes-Einstein equation. The results showed that, for the molecules with strong hydration ability, the diffusion coefficients are best given by re and for other compounds, rs provided the best coefficients, with a reasonably small deviation of ~0.3 × 10-6 cm2/s from the experimental data. This demonstrates the effectiveness of the theoretical estimation approach, suggesting that diffusion coefficients have potential use as an additional molecular property in drug screening.

SUBMITTER: Miyamoto S

PROVIDER: S-EPMC7709040 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

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Molecular Modeling to Estimate the Diffusion Coefficients of Drugs and Other Small Molecules.

Miyamoto Shuichi S Shimono Kazumi K

Molecules (Basel, Switzerland) 20201116 22

Diffusion is a spontaneous process and one of the physicochemical phenomena responsible for molecular transport, the rate of which is governed mainly by the diffusion coefficient; however, few coefficients are available because the measurement of diffusion rates is not straightforward. The translational diffusion coefficient is related by the Stokes-Einstein equation to the approximate radius of the diffusing molecule. Therefore, the stable conformations of small molecules were first calculated ...[more]

PMID: 33207661

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Project description:BackgroundApplications of electric-field-induced permeabilization of cells range from cancer therapy to wastewater treatment. A unified understanding of the underlying mechanisms of membrane electropermeabilization, however, has not been achieved. Protocols are empirical, and models are descriptive rather than predictive, which hampers the optimization and expansion of electroporation-based technologies. A common feature of existing models is the assumption that the permeabilized membrane is passive, and that transport through it is entirely diffusive. To demonstrate the necessity to go beyond that assumption, we present here a quantitative analysis of the post-permeabilization transport of three small molecules commonly used in electroporation research - YO-PRO-1, propidium, and calcein - after exposure of cells to minimally perturbing, 6 ns electric pulses.ResultsInflux of YO-PRO-1 from the external medium into the cell exceeds that of propidium, consistent with many published studies. Both are much greater than the influx of calcein. In contrast, the normalized molar efflux of calcein from pre-loaded cells into the medium after electropermeabilization is roughly equivalent to the influx of YO-PRO-1 and propidium. These relative transport rates are correlated not with molecular size or cross-section, but rather with molecular charge polarity.ConclusionsThis comparison of the kinetics of molecular transport of three small, charged molecules across electropermeabilized cell membranes reveals a component of the mechanism of electroporation that is customarily taken into account only for the time during electric pulse delivery. The large differences between the influx rates of propidium and YO-PRO-1 (cations) and calcein (anion), and between the influx and efflux of calcein, suggest a significant role for the post-pulse transmembrane potential in the migration of ions and charged small molecules across permeabilized cell membranes, which has been largely neglected in models of electroporation.

Dataset Information

Molecular Modeling to Estimate the Diffusion Coefficients of Drugs and Other Small Molecules.

Publications

Molecular Modeling to Estimate the Diffusion Coefficients of Drugs and Other Small Molecules.

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