Target-family differences in stereochemical discrimination: a same-assay analysis of enantiomer pairs in ChEMBL

Abstract

Chiral molecules can differ substantially in biological potency, yet the extent to which this stereochemical discrimination varies across protein families has not been systematically measured. Here, same-assay enantiomer pairs were extracted from ChEMBL 37 to construct an archive-scale, target-family-stratified distribution of the eudysmic ratio while minimizing variation arising from comparisons across different assays. The analysis identified 18,346 eligible structural pairs, including 12,344 assigned unambiguously to kinases, ion channels, G protein-coupled receptors, nuclear receptors, or proteases. Across all eligible pairs, the median enantiomeric potency difference was approximately threefold; 27.7% exceeded tenfold and 7.5% exceeded 100-fold. Stereochemical discrimination was generally greater among pairs assayed against proteases and nuclear receptors, intermediate for G protein-coupled receptors, and lower for kinases and ion channels. The ordering at the upper end depended on whether chemical series, targets, or individual pairs were weighted, but the broader separation between the higher- and lower-discrimination families was robust to controls for ligand chemistry, stereocenter count, assay type, congeneric-series clustering, selection bias, and recoverable censoring. Aggregation by protein produced a reproducible target-associated index across disjoint chemical series, although uncontrolled assay and ligand-design factors preclude interpreting it as an intrinsic protein property. Target identity explained substantially more variation than protein family, and the eudysmic ratio alone carried little information for predicting family membership. These findings provide the first large-scale, same-assay map of enantiomeric potency differences across major protein families and establish a reproducible framework for investigating the molecular determinants of stereochemical discrimination.