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Biophysical Journal 87:1-13 (2004)
© 2004 The Biophysical Society

Computer Simulation of Small Molecule Permeation across a Lipid Bilayer: Dependence on Bilayer Properties and Solute Volume, Size, and Cross-Sectional Area

D. Bemporad *, C. Luttmann {dagger} and J. W. Essex *

* School of Chemistry, University of Southampton, Highfield, Southampton, United Kingdom; and {dagger} Aventis Pharma SA, Vitry sur Seine, France

Correspondence: Address reprint requests to J. W. Essex, School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK. Tel.: 44 (0) 23-8059-2794; Fax: 44 (0) 23-8059-3781; E-mail: jwel{at}soton.ac.uk.

Cell membrane permeation is required for most drugs to reach their biological target, and understanding this process is therefore crucial for rational drug design. Recent molecular dynamics simulations have studied the permeation of eight small molecules through a phospholipid bilayer. Unlike experiments, atomistic simulations allow the direct calculation of diffusion and partition coefficients of solutes at different depths inside a lipid membrane. Further analyses of the simulations suggest that solute diffusion is less size-dependent and solute partitioning more size-dependent than was commonly thought.




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