Drug-membrane permeabilities across chemical space

Unraveling the relation between the chemical structure of small drug-like compounds and their rate of passive permeation across lipid membranes is of fundamental importance for pharmaceutical applications. The elucidation of a comprehensive structure-permeability relationship expressed in terms of a few molecular descriptors is unfortunately hampered by the overwhelming number of possible compounds. In this work, we reduce a priori the size and diversity of chemical space to solve an analogous—but smoothed out—structure-property relationship problem. This is achieved by relying on a physics-based coarse-grained model that reduces the size of chemical space, enabling a comprehensive exploration of this space with greatly reduced computational cost. We perform high-throughput coarse-grained (HTCG) simulations to derive a permeability surface in terms of two simple molecular descriptors—bulk partitioning free energy and pka. The surface is constructed by exhaustively simulating all coarse-grained compounds that are representative of small organic molecules (ranging from 30 to 160 Da) in a high-throughput scheme. We provide results for acidic, basic and zwitterionic compounds. Connecting back to the atomic resolution, the HTCG predictions for more than 500,000 compounds allow us to establish a clear connection between specific chemical groups and the resulting permeability coefficient, enabling for the first time an inverse design procedure. Our results have profound implications for drug synthesis: the predominance of commonly-employed chemical moieties narrows down the range of permeabilities.

Menichetti, Kanekal, Bereau, arXiv:1805.10158