Behaviour of small solutes and large drugs in a lipid bilayer from computer simulationsIntroductionMaterials and methodsSimulation protocolResults and discussionFour region modelSolute flexibilityPopulation of dihedral torsionsHydrogen bondsH-bonds for the small solutesDrug external H-bondsDrug internal H-bondsOrientationOverall orientation of small solutesPolar group orientation in small solutesDrug head orientationDrug vector: up and down orientationsDrug vector: parallel or perpendicular to bilayer normalOrientational timesSmall solute orientational timesDrug head orientational timesDrug vector orientational timesConclusionsAcknowledgementsReferencesBehaviour of small solutes and large drugs in a lipid bilayerfrom computer simulationsD. Bemporada, C. Luttmannb, J.W. Essexa,*aSchool of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UKbAventis Pharma S.A., 13 quai Jules Guesde, F-94403 Vitry sur Seine cedex, FranceReceived 2 August 2004; received in revised form 14 July 2005; accepted 14 July 2005Available online 9 August 2005AbstractTo reach their biological target, drugs have to cross cell membranes, and understanding passive membrane permeation is therefore crucialfor rational drug design. Molecular dynamics simulations offer a powerful way of studying permeation at the single molecule level. Startingfrom a computer model proven to be able to reproduce the physical properties of a biological membrane, the behaviour of small solutes andlarge drugs in a lipid bilayer has been studied. Analysis of dihedral angles shows that a few nanosesconds are sufficient for the simulations toconverge towards common values for those angles, even if the starting structures belong to different conformations. Results clearly show that,despite their difference in size, small solutes and large drugs tend to lie parallel to the bilayer normal and that, when moving from watersolution into biomembranes, permeants lose degrees of freedom. This explains the experimental observation that partitioning and permeationare highly affected by entropic effects and are size-dependent. Tilted orientations, however, occur when they make possible the formation ofhydrogen bonds. This helps to understand the reason why hydrogen bonding possibilities are an important parameter in cruder approacheswhich predict drug absorption after administration. Interestingly, hydration is found to occur even in the membrane core, which is usuallyconsidered an almost hydrophobic region. Simulations suggest the possibility for highly polar compounds like acetic acid to cross biologicalmembranes while hydrated. These simulations prove useful for drug design in rationalising experimental observations and predicting solutebehaviour in biomembranes.D 2005 Elsevier B.V. All rights reserved.Keywords: Molecular dynamics simulation; Constraint; h-blockers; DPPC membrane; Permeability1. IntroductionFor most of the routes of administration, cell membranepermeation is required for a drug molecule to reach thegeneral circulation. Even after direct injection or even if thedrug can permeate via the paracellul ar route in theextracellular space, it soon encounters cell membranes tobe crossed in order to reach its biological target which isusually represented by a protein inside the cell cytoplasm.Most drugs cross cell membranes by passive permeationwithout the help of protein carriers, unless they areanalogues of physiological substrates. An understanding ofsolute behaviour inside biological membranes is then crucialfor subcellular pharmacokinetics and rational drug design[1].Functional cell membranes are flui d mosaics of proteinswithin a lipid bilayer matrix [2]. Experimental andtheoretical models for biological membranes, especiallywhen studying solute permeation, are therefore phospho-lipid bilayers. Among them, extensive data have beencollected for the dipalmitoylphosphatidylcholine (DPPC)bilayer. Recently, several ns-long all-atom MD simulationshave been performed in our laboratory [3,4] investigatingthe permeation process of eight small organic compoundsin a DPPC membrane. The eight solutes represent the mostcommon chemical funct ional groups: acetamide, aceticacid, benzene, ethane, methanol, methylacetate, methyla-0005-2736/$ - see front matter D 2005 Elsevier B.V. All rights reserved.doi:10.1016/j.bbamem.2005.07.009* Corresponding author. Tel.: +44 23 8059 2794; fax: +44 23 8059 3781.E-mail address: [email protected] (J.W. Essex).Biochimica et Biophysica Acta 1718 (2005) 1 – 21http://www.elsevier.com/locate/bbamine, water. Simulation results show in general a goodcorrelation between the free energy in the centre of themembrane with the experimental free energy of partition-ing for the solutes between water and hexadecane. Thenotable exception to this rule is for benzene, which,because of its size, is sensitive to the lateral packing in thelipid bilayers, supporting the view that biomembranes donot always behave like bulk solvents. With the exceptionof water, the diffusion coefficients of the molecules arebroadly similar. Surprisingly, calculated diffusion coeffi-cients inside the bilayer are dependent on solute size to alesser extent than in water and the size dependence shownby permeability is instead to be ascribed to the solutepartitioning. Continuing those studies, the permeation ofthree real drugs across the DPPC bilayer has also beensimulated [5]. The drugs are alprenolol, atenolol andpindolol, belonging to the class of h-adrenoreceptorsantagonists. The simulations perfectly reproduce theexperimental ranking of the permeability coefficients, andfree energy calculations show that partition coefficientsbetween water and 1-octanol overestimate the drug abilityto dissolve into the membrane.The advantage of MD simulations over conventionalexperiments is that the contributions from the differentregions of the lipid bilayer, that is free energy, diffusion andlocal resistance as a function of depth, can be studied at amolecular level, whereas experimental models can onlyapproximate the membrane as a uniform barrier slab.Further analyses of the simulat ions mentioned above arepresented here. While the previous articles [3–5] focused onthe calculation of the relevant physical properties, the aim ofthis paper is to investigate the behaviour of the drugs andthe small organic compounds inside the membrane withatomistic detail. Therefore, flexibility, mean orientation, re-orientational correlation times and hydrogen