Molecular Modeling to Estimate the Diffusion Coefficients of Drugs and Other Small Molecules
Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan
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Academic Editors: Pilar Cossio, Claudio Cavasotto and Mattia Sturlese
Molecules 2020, 25(22), 5340; https://doi.org/10.3390/molecules25225340
Received: 20 October 2020
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Revised: 13 November 2020
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Accepted: 14 November 2020
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Published: 16 November 2020
(This article belongs to the Special Issue Integrative Computational Strategies for Drug Screening)
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.
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MDPI and ACS Style
Miyamoto, S.; Shimono, K. Molecular Modeling to Estimate the Diffusion Coefficients of Drugs and Other Small Molecules. Molecules 2020, 25, 5340. https://doi.org/10.3390/molecules25225340
AMA Style
Miyamoto S, Shimono K. Molecular Modeling to Estimate the Diffusion Coefficients of Drugs and Other Small Molecules. Molecules. 2020; 25(22):5340. https://doi.org/10.3390/molecules25225340
Chicago/Turabian StyleMiyamoto, Shuichi, and Kazumi Shimono. 2020. "Molecular Modeling to Estimate the Diffusion Coefficients of Drugs and Other Small Molecules" Molecules 25, no. 22: 5340. https://doi.org/10.3390/molecules25225340
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