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Permeation of small molecules through a lipid bilayer: a computer simulation study

Permeation of small molecules through a lipid bilayer: a computer simulation study
Permeation of small molecules through a lipid bilayer: a computer simulation study
To reach their biological target, drugs have to cross cell membranes, and understanding passive membrane permeation is therefore crucial for rational drug design. Molecular dynamics simulations offer a powerful way of studying permeation at the single molecule level, yielding detailed dynamic and thermodynamic data. Biological membranes have a very inhomogeneous character and a highly anisotropic behavior. Starting from a computer model proven to reproduce the physical properties of such a complex system, the permeation of small organic molecules across a lipid bilayer model has been studied. Free energy profiles and diffusion coefficients along the bilayer normal have been calculated for small organic molecules by means of all-atom molecular dynamics (MD) simulations constraining the compounds at chosen depths inside the membrane. These data also allow for the calculation of permeability coefficients, the results for which have been compared with experimental data. The calculated permeability coefficients are generally 1 order of magnitude larger than the equivalent experimental data, but the molecules' relative permeability coefficients are reproduced.
dynamics simulation, surface-area, phospholipid-bilayers, lecithin, bilayers, nonelectrolyte partition, dimyristoyl lecithin, transportphenomena, rapid calculation, solute diffusion, water transport
1089-5647
4875-4884
Bemporad, Daniele
a04810c0-2208-44b7-9bd0-9c0d26861777
Essex, Jonathan W.
1f409cfe-6ba4-42e2-a0ab-a931826314b5
Luttmann, Claude
b628198d-df1f-4478-9b83-fd3bba2e7113
Bemporad, Daniele
a04810c0-2208-44b7-9bd0-9c0d26861777
Essex, Jonathan W.
1f409cfe-6ba4-42e2-a0ab-a931826314b5
Luttmann, Claude
b628198d-df1f-4478-9b83-fd3bba2e7113

Bemporad, Daniele, Essex, Jonathan W. and Luttmann, Claude (2004) Permeation of small molecules through a lipid bilayer: a computer simulation study. Journal of Physical Chemistry B, 108 (15), 4875-4884. (doi:10.1021/jp035260s).

Record type: Article

Abstract

To reach their biological target, drugs have to cross cell membranes, and understanding passive membrane permeation is therefore crucial for rational drug design. Molecular dynamics simulations offer a powerful way of studying permeation at the single molecule level, yielding detailed dynamic and thermodynamic data. Biological membranes have a very inhomogeneous character and a highly anisotropic behavior. Starting from a computer model proven to reproduce the physical properties of such a complex system, the permeation of small organic molecules across a lipid bilayer model has been studied. Free energy profiles and diffusion coefficients along the bilayer normal have been calculated for small organic molecules by means of all-atom molecular dynamics (MD) simulations constraining the compounds at chosen depths inside the membrane. These data also allow for the calculation of permeability coefficients, the results for which have been compared with experimental data. The calculated permeability coefficients are generally 1 order of magnitude larger than the equivalent experimental data, but the molecules' relative permeability coefficients are reproduced.

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More information

Published date: 15 April 2004
Keywords: dynamics simulation, surface-area, phospholipid-bilayers, lecithin, bilayers, nonelectrolyte partition, dimyristoyl lecithin, transportphenomena, rapid calculation, solute diffusion, water transport

Identifiers

Local EPrints ID: 20131
URI: https://eprints.soton.ac.uk/id/eprint/20131
ISSN: 1089-5647
PURE UUID: ed599e9c-c625-4f0d-8e7b-e1f649c4d226
ORCID for Jonathan W. Essex: ORCID iD orcid.org/0000-0003-2639-2746

Catalogue record

Date deposited: 22 Feb 2006
Last modified: 06 Jun 2018 13:07

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