Molecular Insight into Affinities of Drugs and Their Metabolites to Lipid Bilayers Marke ́ ta Paloncy ́ ova ́ , Karel Berka,* and Michal Otyepka* Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky ́ University Olomouc, tr ̌ . 17. listopadu 12, 771 46, Olomouc, Czech Republic * S Supporting Information ABSTRACT: The penetration properties of drug-like mole- cules on human cell membranes are crucial for understanding the metabolism of xenobiotics and overall drug distribution in the human body. Here, we analyze partitioning of substrates of cytochrome P450s (caffeine, chlorzoxazone, coumarin, ibupro- fen, and debrisoquine) and their metabolites (paraxanthine, 6- hydroxychlorzoxazone, 7-hydroxycoumarin, 3-hydroxyibupro- fen, and 4-hydroxydebrisoquine) on two model membranes: dioleoylphosphatidylcholine (DOPC) and palmitoyloleoyl- phophatidylglycerol (POPG). We calculated the free energy profiles of these molecules and the distribution coefficients on the model membranes. The drugs were usually located deeper in the membrane than the corresponding metabolites and also had a higher affinity to the membranes. Moreover, the behavior of the molecules on the membranes differed, as they seemed to have a higher affinity to the DOPC membrane than to POPG, implying they have different modes of action in human (mostly PC) and bacterial (mostly PG) cells. As the xenobiotics need to pass through lipid membranes on their way through the body and the effect of some drugs might depend on their accumulation on membranes, we believe that detailed information of penetration phenomenon is important for understanding the overall metabolism of xenobiotics. ■ INTRODUCTION The interaction of drugs with cell membranes dictates their pharmacological properties because it affects the drug distribution, transport, accumulation, partitioning, and metab- olism. 1-5 A drug must be passively 6 or actively 7-9 transported across the cell membrane before it can reach its target and perform its biological role. Passive transport depends on membrane structure, dynamics, 10 and its permeability for a particular substance. 6 Recently, we suggested that the position- ing of drugs on lipid bilayers might also affect their interaction with drug metabolizing cytochrome P450 (CYP) enzymes, 4 which are anchored to the membrane of the endoplasmic reticulum, 11 and as a consequence affect the metabolism of drugs. In addition, the positioning on and affinity to a membrane may play an important role in other biologically significant processes, such as antioxidant inhibition of lipid peroxidation. 12 The importance of drug-membrane inter- actions in biology, pharmacology, and medicine has called for extensive research in this field, which is rather challenging due to the complexity of biological membranes. Many experimental and theoretical techniques have been developed to study various aspects of drug membrane interactions. 1,13-16 Cell membranes form a protective wall around the cellular interior against an external environment, and separate cytosolic and noncytosolic sides of organelles. 17,18 The membranes are predominantly composed of lipids, which form a lipid bilayer. Lipid bilayers are widely used as a membrane model in both experiments and theoretical calculations. The membrane compositions of various cell structures differ, and their properties are mostly determined by their lipid composition, 19 which is highly variable and includes numerous lipid types. However, by careful choice of lipid, a bilayer composed of one lipid type can mimic the key physicochemical features of a particular membrane. 1 In the present work, we chose to use a dioleoylphosphatidylcholine (DOPC) bilayer because phospha- tidylcholine makes up about 40% of the human endoplasmic reticulum membrane mass, 19 where the drug metabolizing CYP enzymes are mostly located. 20 The other model, a palmitoy- loleoylphosphatidylglycerol (POPG) lipid bilayer, was chosen as an example of a negatively charged membrane, which is typically present in bacteria. 21 Both bilayers differ in headgroup charge, density, thickness, and many other properties (Figure 1). Knowledge of the differences in cell membrane compositions among organelles or various organisms (e.g., between host and pathogen) can be used in rational drug targeting. 1 However, to exploit such information, the nature of drug-membrane interaction needs to be understood in detail. Molecular dynamics (MD) simulation is a unique technique used in recent years for studying the dynamics of biological systems, simultaneously enabling fine space (atomistic) and Received: November 30, 2012 Revised: February 6, 2013 Published: February 6, 2013 Article pubs.acs.org/JPCB © 2013 American Chemical Society 2403 dx.doi.org/10.1021/jp311802x | J. Phys. Chem. B 2013, 117, 2403-2410