Molecular Modeling to Estimate the Diffusion Coefficients of Drugs and Other Small Molecules
Abstract
:1. Introduction
2. Methods
3. Results and Discussion
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
- Weisz, P.B. Diffusion and chemical transformation. Science 1973, 179, 433–440. [Google Scholar] [CrossRef] [PubMed]
- Srivastava, P.K. Elementary Biophysics; Alpha Science: Oxford, UK, 2005; p. 140. [Google Scholar]
- Sugano, K.; Kansy, M.; Artursson, P.; Avdeef, A.; Bendels, S.; Di, L.; Ecker, G.F.; Faller, B.; Fischer, H.; Gerebtzoff, G.; et al. Coexistence of passive and carrier-mediated processes in drug transport. Nat. Rev. Drug Discov. 2010, 9, 597–614. [Google Scholar] [CrossRef]
- Kaneo, Y.; Morimoto, K. (Eds.) Biopharmaceutics; Hirokawa Publishing Company: Tokyo, Japan, 2008; pp. 16–17. [Google Scholar]
- Nicholson, C. Anomalous diffusion inspires anatomical insights. Biophys. J. 2015, 108, 2091–2093. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Papisov, M.; Belov, V. Solute transport in the cerebrospinal fluid: Physiology and practical implications. In Nervous System Drug Delivery; Lonser, R.R., Sarntinoranont, M., Bankiewicz, K., Eds.; Academic Press: Cambridge, MA, USA, 2019; pp. 251–274. [Google Scholar]
- Shin, T.; Ogata, S.; Iwahara, M.; Ogawa, R.; Akamatsu, T.; Atsuyama, K.; Sakuma, H. Microorganism Culture Apparatus. Japanese Patent 161979 (P2010-161979A), 29 July 2010. [Google Scholar]
- Miyamoto, S.; Atsuyama, K.; Ekino, K.; Shin, T. Estimating the Diffusion Coefficients of Sugars Using Diffusion Experiments in Agar-gel and Computer Simulations. Chem. Pharm. Bull. 2018, 66, 632–636. [Google Scholar] [CrossRef] [Green Version]
- Manabe, S.; Fujioka, R.; Kanai, A. Development of novel apparatus for evaluation of diffusion coefficient under stationary state. Bull. Fac. Hum. Environ. Sci. Fukuoka Womens Univ. 1996, 27, 31–36. [Google Scholar]
- Ribeiro, A.C.F.; Ortona, O.; Simões, S.M.N.; Santos, C.I.A.V.; Prazeres, P.M.R.A.; Valente, A.J.M.; Lobo, V.M.M.; Burrows, H.D. Binary mutual diffusion coefficients of aqueous solutions of sucrose, lactose, glucose, and fructose in the temperature range from (298.15 to 328.15) K. J. Chem. Eng. Data 2006, 51, 1836–1840. [Google Scholar] [CrossRef] [Green Version]
- Carrasco, B.; García de la Torre, J. Hydrodynamic properties of rigid particles: Comparison of different modeling and computational procedures. Biophys. J. 1999, 75, 3044–3057. [Google Scholar] [CrossRef] [Green Version]
- Ortega, A.; García de la Torre, J. Efficient, accurate calculation of rotational diffusion and NMR relaxation of globular proteins from atomic-level structures and approximate hydrodynamic calculations. J. Am. Chem. Soc. 2005, 127, 12764–12765. [Google Scholar] [CrossRef]
- Islam, M.A. Einstein–Smoluchowski diffusion equation: A discussion. Phys. Scr. 2004, 70, 120–125. [Google Scholar] [CrossRef]
- Einstein, A. Motion of suspended particles in stationary liquids required from the molecular kinetic theory of heat. Ann. Phys. 1905, 17, 549–560. [Google Scholar] [CrossRef] [Green Version]
- Edward, J.T. Molecular volumes and the Stokes–Einstein equation. J. Chem. Educ. 1970, 47, 261–270. [Google Scholar] [CrossRef]
- Trovato, F.; Tozzini, V. Diffusion within the cytoplasm: A mesoscale model of interacting macromolecules. Biophy. J. 2014, 107, 2579–2591. [Google Scholar] [CrossRef] [Green Version]
- Chemical Computing Group. Available online: http://www.chemcomp.com/ (accessed on 16 October 2020).
- Halgren, T. Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94. J. Comp. Chem. 1996, 17, 490–519. [Google Scholar] [CrossRef]
- Ihnat, M.; Goring, D.A.I. Shape of the cellodextrins in aqueous solution at 25 °C. Can. J. Chem. 1967, 45, 2353–2361. [Google Scholar] [CrossRef] [Green Version]
- Hartley, G.S.; Robinson, C. Atomic models. Trans Faraday Soc. 1952, 48, 847–853. [Google Scholar]
- Isbell, H.S.; Pigman, W. The oxidation of alpha and beta glucose and a study of the isomeric forms of the sugar in solution. J. Res. Natl. Bur. Stand. 1937, 18, 337–364. [Google Scholar] [CrossRef]
- Lipinski, C.A.; Lombardo, F.; Dominy, B.W.; Feeney, P.J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Delivery Rev. 1997, 23, 4–25. [Google Scholar] [CrossRef]
- Veber, D.F.; Johnson, S.R.; Cheng, H.-Y.; Smith, B.R.; Ward, K.W.; Kopple, K.D. Molecular Properties That Influence the Oral Bioavailability of Drug Candidates. J. Med. Chem. 2002, 45, 2615–2623. [Google Scholar] [CrossRef]
- Uedaira, H.; Uedaira, H. Diffusion coefficients of xylose and maltose in aqueous solution. Bull. Chem. Soc. Jpn. 1969, 42, 2140–2142. [Google Scholar] [CrossRef]
- Uedaira, H.; Uedaira, H. Translational frictional coefficients of molecules in aqueous solution. J. Phys. Chem. 1970, 74, 2211–2214. [Google Scholar] [CrossRef]
- Gosting, L.J.; Morris, M.S. Diffusion studies on dilute aqueous sucrose solutions at 1 and 25° with the Gouy interference method. J. Am. Chem. Soc. 1949, 71, 1998–2006. [Google Scholar] [CrossRef]
Molecule | MW b | NoC c | Radius (Å) | Diffusion Coefficient (×106 cm2/s) | ||||||
---|---|---|---|---|---|---|---|---|---|---|
Estimated | Literature | Deviation | ||||||||
rs | re | Ds | De | D0d | DCi | Ds − D0 | De − D0 | |||
xylose | 150 | 14 | 3.09 | 3.39 | 7.94 | 7.24 | 7.50 e | 6.78 | 0.44 | −0.26 |
fructose | 180 | 4 | 3.27 | 3.59 | 7.50 | 6.84 | 6.93 f | 6.63 | 0.57 | −0.09 |
galactose | 180 | 6 | 3.27 | 3.62 | 7.50 | 6.77 | (6.90) | 6.25 | 0.60 | −0.13 |
glucose | 180 | 10 | 3.28 | 3.69 | 7.48 | 6.65 | 6.79 g | 5.77 | 0.69 | −0.14 |
sucrose | 342 | 15 | 4.03 | 4.84 | 6.09 | 5.07 | 5.23 h | 4.93 | 0.86 | −0.16 |
lactose | 342 | 27 | 4.03 | 4.89 | 6.09 | 5.02 | 5.66 f | 4.59 | 0.43 | −0.64 |
trehalose | 342 | 10 | 4.04 | 5.04 | 6.07 | 4.89 | (5.35) | 4.70 | 0.72 | −0.46 |
maltose | 342 | 24 | 4.04 | 5.01 | 6.07 | 4.89 | 5.20 e | 4.71 | 0.87 | −0.31 |
alanine | 89 | 1 | 2.72 | 2.91 | 9.01 | 8.42 | (9.86) | 9.21 | −0.85 | −1.44 |
proline | 115 | 2 | 2.97 | 3.18 | 8.25 | 7.71 | (8.39) | 7.74 | −0.14 | −0.68 |
threonine | 119 | 2 | 2.95 | 3.24 | 8.31 | 7.56 | (8.64) | 7.99 | −0.33 | −1.08 |
leucine | 131 | 7 | 3.20 | 3.51 | 7.66 | 6.75 | (7.65) | 7.00 | 0.01 | −0.9 |
aspartic acid | 133 | 2 | 2.92 | 3.19 | 8.39 | 7.70 | (8.55) | 7.90 | −0.16 | −0.85 |
arginine | 174 | 2 | 3.41 | 4.10 | 7.19 | 5.98 | (7.45) | 6.80 | −0.26 | −1.47 |
aspirin | 179 | 4 | 3.37 | 3.98 | 7.27 | 6.16 | (7.63) | 6.98 | −0.36 | −1.47 |
salbutamol | 239 | 6 | 3.91 | 5.03 | 6.27 | 4.85 | (6.66) | 6.01 | −0.39 | −1.81 |
Loxoprofen a | 246 | 8 c | 3.89 | 5.17 | 6.30 | 4.77 | (6.56) | 5.91 | −0.26 | −1.79 |
Fast Green | 763 | 30 | 5.41 | 7.30 | 4.54 | 3.36 | (4.30) | 3.65 | 0.24 | −0.94 |
Sample Availability: Samples of the compounds are not available from the authors. | |
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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
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
APA StyleMiyamoto, S., & Shimono, K. (2020). Molecular Modeling to Estimate the Diffusion Coefficients of Drugs and Other Small Molecules. Molecules, 25(22), 5340. https://doi.org/10.3390/molecules25225340