Lipophilicity prediction of peptides and peptide derivatives by consensus machine learning

Lipophilicity prediction is routinely applied to small molecules and presents a working alternative to experimental logP or logD determination. For compounds outside the domain of classical medicinal chemistry these predictions lack accuracy, advocating the development of bespoke in silico approaches. Peptides and their derivatives and mimetics fill the structural gap between small synthetic drugs and genetically engineered macromolecules. Here, we present a data-driven machine learning method for peptide logD(7.4) prediction. A model for estimating the lipophilicity of short linear peptides consisting of natural amino acids was developed. In a prospective test, we obtained accurate predictions for a set of newly synthesized linear tri- to hexapeptides. Further model development focused on more complex peptide mimetics from the AstraZeneca compound collection. The results obtained demonstrate the applicability of the new prediction model to peptides and peptide derivatives in a logD(7.4) range of approximately -3 to 5, with superior accuracy to established lipophilicity models for small molecules.