Bioisostere Effects on the EPSA of Common Permeability-Limiting Groups

16 March 2022, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


Polar molecular surface area provides a valuable metric when optimizing properties as varied as membrane permeability and efflux susceptibility. The EPSA method to measure this quantity has had a substantial impact in medicinal chemistry, providing insight into the conformational and stereoelectronic features that govern the polarity of small molecules, targeted protein degraders, and macrocyclic peptides. Recognizing the value of bioisosteres in replacing permeation-limiting polar groups, we determined the effects of common amide, carboxylic acid, and phenol bioisosteres on EPSA, using matched molecular pairs within the Merck compound collection. Our findings highlight bioisosteres within each class that are particularly effective in lowering EPSA and others which, despite widespread use, offer little to no such benefit. Our method for matched-pair identification is generalizable across large compound collections and thus may constitute a flexible platform to study the effects of bioisosterism both in EPSA and other in vitro assays.


matched molecular pairs
polar surface area
medicinal chemistry

Supplementary materials

Supporting Information File
Contains information on: Substructure queries and reaction schemes used in MMP identification Clustering by 3D similarity and compound selection Similarity distributions of MMPs included in the analysis Effect of amidine pKa on amide-to-amidine EPSA changes Statistical deconvolution of structural elements affecting amide-to-carbamate EPSA changes Calculation of Boltzmann-weighted Dipole, HBA basicity, and HBD acidity properties


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