Journal Article

Evaluation of chirality descriptors derived from SMILES heteroencoders

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

2025

Overview

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. Scientific contribution Our work proposes latent space arithmetic to obtain descriptors of molecular chirality from SMILES heteroencoders. We used this molecular representation to build quantitative structure-enantioselectivity relationships for the prediction of the elution order of enantiomers in chiral chromatography and compared the results with those of circular fingerprints. We showed that delta descriptors of opposite enantiomers enhance the ability of latent space vectors to encode chirality.

• Publisher: Springer International Publishing,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Algorithms / Arithmetic / Artificial intelligence / Chemistry / Chemistry and Materials Science / Chiral HPLC / Chirality / Chromatography / Computational Biology/Bioinformatics / Computer Applications in Chemistry / Datasets / Documentation and Information in Chemistry / Elution / Enantiomers / Fingerprints / High performance liquid chromatography / Learning algorithms / Ligands / Machine learning / Neural network / Neural networks / Quantitative structure-enantioselectivity relationships / Random forest / Representations / Retention / Software / Stereochemistry / Theoretical and Computational Chemistry