Evaluation of chirality descriptors derived from SMILES heteroencoders.

Authors

Natalia Baimacheva, Xinyue Gao, Joao Aires-de-Sousa

Published in

Journal of cheminformatics. Volume 17. Issue 1. Pages 137. Aug 31, 2025. Epub Aug 31, 2025.

Abstract

Molecular representations of chirality, derived from latent space vectors (LSVs) of SMILES heteroencoders, were explored to train machine learning models to predict chiral properties, and were compared to conventional circular fingerprints. Latent space arithmetic was applied to enhance the representation of chirality, by calculating differences between the original descriptor of a molecule and the descriptor of its enantiomer, or the difference between the original descriptor and the descriptor obtained with the stereochemistry-depleted SMILES string. Machine learning was performed with the Random Forest algorithm applied to a dataset of 3858 molecules extracted from the literature (1929 pairs of enantiomers) to predict the elution order observed on the Chiralpak® AD-H column, as well as intrinsic structural chirality labels (R/S or canonical SMILES @/@@). The descriptors derived from the heteroencoders achieved an accuracy of up to 0.75 in the prediction of the elution order, and the fingerprints were superior (0.82). A better predictive ability was observed with the difference LSV descriptors than with the original descriptors.

PMID:
40887592
Bibliographic data and abstract were imported from PubMed on 01 Sep 2025.

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