Combining graph neural networks and transformers for few-shot nuclear receptor binding activity prediction

• Published in: Journal of cheminformatics 2024-09, Vol.16 (1), p.109-19, Article 109
• Main Authors: Torres, Luis H. M., Arrais, Joel P., Ribeiro, Bernardete
• Format: Article
• Language: English
• Subjects: Annotations; Binding; Biological activity; Chemistry; Chemistry and Materials Science; Complementarity; Computational Biology/Bioinformatics; Computational linguistics; Computer Applications in Chemistry; Documentation and Information in Chemistry; Drug development; Drug Discovery; Drugs; Effectiveness; Electric transformers; Endocrine disruptors; Few-shot Learning; Graph Neural Network; Graph neural networks; Knowledge management; Language processing; Learning; Meta-Learning; Molecular structure; Natural language interfaces; Neural networks; Nuclear Receptor Binding Activity Prediction; Nuclear receptors; Parameter identification; Predictions; Receptor mechanisms; Receptors; Semantics; Structured data; Theoretical and Computational Chemistry; Transformer
• ISSN: 1758-2946; 1758-2946
• DOI: 10.1186/s13321-024-00902-4

Nuclear receptors (NRs) play a crucial role as biological targets in drug discovery. However, determining which compounds can act as endocrine disruptors and modulate the function of NRs with a reduced amount of candidate drugs is a challenging task. Moreover, the computational methods for NR-binding activity prediction mostly focus on a single receptor at a time, which may limit their effectiveness. Hence, the transfer of learned knowledge among multiple NRs can improve the performance of molecular predictors and lead to the development of more effective drugs. In this research, we integrate graph neural networks (GNNs) and Transformers to introduce a few-shot GNN-Transformer, Meta-GTNRP to predict the binding activity of compounds using the combined information of different NRs and identify potential NR-modulators with limited data. The Meta-GTNRP model captures the local information in graph-structured data and preserves the global-semantic structure of molecular graph embeddings for NR-binding activity prediction. Furthermore, a few-shot meta-learning approach is proposed to optimize model parameters for different NR-binding tasks and leverage the complementarity among multiple NR-specific tasks to predict binding activity of compounds for each NR with just a few labeled molecules. Experiments with a compound database containing annotations on the binding activity for 11 NRs shows that Meta-GTNRP outperforms other graph-based approaches. The data and code are available at: https://github.com/ltorres97/Meta-GTNRP . Scientific contribution The proposed few-shot GNN-Transformer model, Meta-GTNRP captures the local structure of molecular graphs and preserves the global-semantic information of graph embeddings to predict the NR-binding activity of compounds with limited available data; A few-shot meta-learning framework adapts model parameters across NR-specific tasks for different NRs in a joint learning procedure to predict the binding activity of compounds for each NR with just a few labeled molecules in highly imbalanced data scenarios; Meta-GTNRP is a data-efficient approach that combines the strengths of GNNs and Transformers to predict the NR-binding properties of compounds through an optimized meta-learning procedure and deliver robust results valuable to identify potential NR-based drug candidates.