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The partitioning of small molecules in cell membranes—a key parameter for pharmaceutical applications—typically relies on experimentally available bulk partitioning coefficients. Computer simulations provide a structural resolution of the insertion thermodynamics via the potential of mean force but require significant sampling at the atomistic level. Here, we introduce high-throughput coarse-grained molecular dynamics simulations to screen thermodynamic properties. This application of physics-based models in a large-scale study of small molecules establishes linear relationships between partitioning coefficients and key features of the potential of mean force. This allows us to predict the structure of the insertion from bulk experimental measurements for more than 400 000 compounds. The potential of mean force hereby becomes an easily accessible quantity—already recognized for its high predictability of certain properties, e.g., passive permeation. Further, we demonstrate how coarse graining helps reduce the size of chemical space, enabling a hierarchical approach to screening small molecules. [ABSTRACT FROM AUTHOR]

We compare different coarse-grained single-blob models for star polymers. We find that phenomenological models inspired by the Daoud-Cotton theory reproduce quite poorly the thermodynamics of these systems, even if the potential is assumed to be density dependent, as done in the analysis of experimental results. Using the numerically determined coarse-grained potential, we also determine the minimum value fc of the functionality of the star polymer for which a fluid-solid transition occurs. By applying the Hansen-Verlet criterion we find 35 < fc <= 40. This result is confirmed by an analysis that uses the modified (reference) hypernetted chain method and is qualitatively consistent with previous work. [ABSTRACT FROM AUTHOR]

The permeation of small-molecule drugs across a phospholipid membrane bears much interest both in the pharmaceutical sciences and in physical chemistry. Connecting the chemistry of the drug and the lipids to the resulting thermodynamic properties remains of immediate importance. Here we report molecular dynamics (MD) simulation trajectories using the coarse-grained (CG) Martini force field. A wide, representative coverage of chemistry is provided: across solutes—exhaustively enumerating all 105 CG dimers—and across six phospholipids. For each combination, umbrella-sampling simulations provide detailed structural information of the solute at all depths from the bilayer midplane to bulk water, allowing a precise reconstruction of the potential of mean force. Overall, the present database contains trajectories from 15,120 MD simulations. This database may serve the further identification of structure-property relationships between compound chemistry and drug permeability. Measurement(s) molecular dynamics trajectories Technology Type(s) computational modeling technique • molecular dynamics simulation Factor Type(s) Small organic molecules • phospholipid Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.11733504 [ABSTRACT FROM AUTHOR]