Partition coefficients (logP) for small molecules are important for understanding the lipophilicity or membrane permeability of the compound and are routinely calculated during small molecule drug discovery projects. Most of the logP tools used in the industry are based on QSAR models. In this work, we used YANK software from John Chodera lab to calculate logP values using alchemical hydration free energies for two different solvent systems - 1-octanol/water and hexadecane/water. Our results have acceptable RMSE errors, demonstrating the applicability of these calculations for non-traditional systems - QSAR-based logP calculators are not designed for hexadecane/water systems. We also present cases where we are getting large RMSE errors, possibly due to poor force field parameters.

Calculating 1-octanol/water and hexadecane/water partition coefficients for small molecules

2019 Fall National Meeting

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