Classification of substances by health hazard using deep neural networks and molecular electron densities

Satnam Singh; Gina Zeh; Jessica Freiherr; Thilo Bauer; Isik Türkmen; Andreas T Grasskamp

doi:10.1186/s13321-024-00835-y

Classification of substances by health hazard using deep neural networks and molecular electron densities

J Cheminform. 2024 Apr 16;16(1):45. doi: 10.1186/s13321-024-00835-y.

Authors

Satnam Singh^{1

2}, Gina Zeh¹, Jessica Freiherr^{1

2}, Thilo Bauer³, Isik Türkmen¹, Andreas T Grasskamp⁴

Affiliations

¹ Department of Sensory Analytics and Technologies, Fraunhofer Institute for Process Engineering and Packaging IVV, Giggenhauser Str. 35, 85354, Freising, Germany.
² Department of Psychiatry and Psychotherapy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Schwabachanlage 6, 91054, Erlangen, Germany.
³ Computer Chemistry Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstr. 25, 91052, Erlangen, Germany.
⁴ Department of Sensory Analytics and Technologies, Fraunhofer Institute for Process Engineering and Packaging IVV, Giggenhauser Str. 35, 85354, Freising, Germany. andreas.grasskamp@ivv.fraunhofer.de.

PMID: 38627862
DOI: 10.1186/s13321-024-00835-y

Abstract

In this paper we present a method that allows leveraging 3D electron density information to train a deep neural network pipeline to segment regions of high, medium and low electronegativity and classify substances as health hazardous or non-hazardous. We show that this can be used for use-cases such as cosmetics and food products. For this purpose, we first generate 3D electron density cubes using semiempirical molecular calculations for a custom European Chemicals Agency (ECHA) subset consisting of substances labelled as hazardous and non-hazardous for cosmetic usage. Together with their 3-class electronegativity maps we train a modified 3D-UNet with electron density cubes to segment reactive sites in molecules and classify substances with an accuracy of 78.1%. We perform the same process on a custom food dataset (CompFood) consisting of hazardous and non-hazardous substances compiled from European Food Safety Authority (EFSA) OpenFoodTox, Food and Drug Administration (FDA) Generally Recognized as Safe (GRAS) and FooDB datasets to achieve a classification accuracy of 64.1%. Our results show that 3D electron densities and particularly masked electron densities, calculated by taking a product of original electron densities and regions of high and low electronegativity can be used to classify molecules for different use-cases and thus serve not only to guide safe-by-design product development but also aid in regulatory decisions. SCIENTIFIC CONTRIBUTION: We aim to contribute to the diverse 3D molecular representations used for training machine learning algorithms by showing that a deep learning network can be trained on 3D electron density representation of molecules. This approach has previously not been used to train machine learning models and it allows utilization of the true spatial domain of the molecule for prediction of properties such as their suitability for usage in cosmetics and food products and in future, to other molecular properties. The data and code used for training is accessible at https://github.com/s-singh-ivv/eDen-Substances .

Keywords: 3D-UNet; Computational chemistry; Electron density; Health hazard; Machine learning.