Amphiphilic Drug-Like Molecules Accumulate in a Membrane below the Head Group Region Marke ́ ta Paloncy ́ ova ́ , † Russell DeVane, ‡ Bruce Murch, ‡ Karel Berka,* ,† and Michal Otyepka* ,† † Department of Physical Chemistry, Faculty of Science, Regional Centre of Advanced Technologies and Materials, Palacky ́ University Olomouc, tr ̌ . 17. listopadu 12, 771 46 Olomouc, Czech Republic ‡ Corporate Modeling & Simulation, Procter & Gamble, 8611 Beckett Road, West Chester, Ohio 45069, United States * S Supporting Information ABSTRACT: The partitioning behavior of drug-like molecules into biomembranes has a crucial impact on the design and efficacy of therapeutic drugs. Thermodynamic properties connected with the interaction of molecules with membranes can be evaluated by calculating free-energy profiles normal to the membrane surface. We calculated the free-energy profiles of 25 drug-like molecules in a 1,2-dioleoyl-sn- glycero-3-phosphocholine (DOPC) membrane and free energies of solvation in water and heptane using two methods, molecular dynamics (MD) simulations with the Berger lipid force field and COSMOmic, based on a continuum conductor-like screening model for realistic solvation (COSMO-RS). The biased MD simulations (in total ∼22 μs long) were relatively computationally expensive, whereas the COSMOmic approach offered a significantly less expensive alternative. Both methods provided similar results and showed that the studied amphiphilic drug-like molecules accumulate in the membrane, with the majority localized below the head group region. The MD simulations were more lipophilic and gave free-energy profiles that were systematically deeper than those calculated by COSMOmic. To investigate the physical nature of the increased lipophilicity, we analyzed a water/heptane system and identified that it is most likely caused by overestimation of the attractive term of the Lennard-Jones potential in lipid tails. We concluded that COSMOmic can be successfully used for high-throughput computations of global thermodynamic properties, for example, partition coefficients and energy barrier heights, in phosphocholine membranes. In contrast, MD is better for investigating local properties like molecular positioning and orientation in the membrane because they more accurately reflect the complex structure of lipid bilayers. MD is also useful for studies of highly complex systems, for example, drug-membrane-protein interactions. ■ INTRODUCTION Molecular insight into the interactions of drugs (generally any xenobiotic) with biomembranes broadens our understanding of drug disposition in the human body and, in turn, absorption, distribution, metabolism, and excretion (ADME) processes. Absorption is influenced by the ability of a drug to cross the skin (in the case of a transdermal pathway) or the intestine wall (oral pathway). The distribution depends on the penetration of the drug through cell membranes. Metabolism of the drug is affected by the position and concentration of the drug in the relevant membrane, whereas its excretion depends on the penetration properties of the resulting metabolites and possible accumulation of drugs or metabolites in tissues. As biomem- branes form barriers between environments with different properties, the thermodynamic and kinetic properties of drugs interacting with membranes is of particular interest. 1-8 Several experimental techniques have been employed for estimating partition and penetration properties of drug-like molecules. 9-11 Commonly used techniques for partition measurements include, among others, ultracentrifugation, solid phase microextraction, and equilibrium dialysis. 12 Caco2 cells and skin penetration 13 measurements are commonly used to estimate penetration rates. These experimental techniques allow estimation of penetration and partitioning properties and their dependence on concentration, temperature, pressure, and so forth. However, they do not provide a detailed molecular- level understanding of drug-membrane interactions. A considerable effort has been invested in developing in silico methods that can assess partitioning and permeation of drugs in membranes. 5,14-19 The partitioning of a drug in a membrane can be rationalized by a free-energy profile along the lipid bilayer normal. The free-energy profile can be reconstructed from biased molecular dynamics (MD) simulations, typically from constraint simulations, umbrella sampling, metadynamics, or flooding. 4,20-22 It is worth noting that MD simulations can accurately describe the complex structure of a lipid bilayer 23,24 and simultaneously enable fine space (atomic) and time (sub- picosecond) resolutions. In addition, MD simulations can be used for dynamical studies of even more complex systems, for example, drug-membrane-protein interactions. 25 On the Received: November 14, 2013 Revised: January 12, 2014 Published: January 13, 2014 Article pubs.acs.org/JPCB © 2014 American Chemical Society 1030 dx.doi.org/10.1021/jp4112052 | J. Phys. Chem. B 2014, 118, 1030-1039