title: A novel approach to the investigation of passive molecular permeation through lipid bilayers from atomistic simulations.
abstract: Predicting the permeability coefficient (P) of drugs permeating through the cell membrane is of paramount importance in drug discovery. We here propose an approach for calculating P based on bias-exchange metadynamics. The approach allows constructing from atomistic simulations a model of permeation taking explicitly into account not only the "trivial" reaction coordinate, the position of the drug along the direction normal to the lipid membrane plane, but also other degrees of freedom, for example, the torsional angles of the permeating molecule, or variables describing its solvation/desolvation. This allows deriving an accurate picture of the permeation process, and constructing a detailed molecular model of the transition state, making a rational control of permeation properties possible. We benchmarked this approach on the permeation of ethanol molecules through a POPC membrane, showing that the value of P calculated with our model agrees with the one calculated by a long unbiased molecular dynamics of the same system.
authors.affiliation: SISSA-Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, 34136 Trieste, Italy.
authors.forename: Zhaleh
authors.initials: Z
authors.lastname: Ghaemi
authors.forename: Manuela
authors.initials: M
authors.lastname: Minozzi
authors.forename: Paolo
authors.initials: P
authors.lastname: Carloni
authors.forename: Alessandro
authors.initials: A
authors.lastname: Laio
mesh_terms: D002462:Cell Membrane / Q000378:metabolism; D000431:Ethanol / Q000493:pharmacokinetics*; D007700:Kinetics; D008051:Lipid Bilayers / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D010539:Permeability; D010713:Phosphatidylcholines / Q000378:metabolism*; D013816:Thermodynamics
chemical_list: D008051:Lipid Bilayers; D010713:Phosphatidylcholines; D000431:Ethanol; C028694:1-palmitoyl-2-oleoylphosphatidylcholine