A multitask GNN-based interpretable model for discovery of selective JAK inhibitors.

Wang, Yimeng; Gu, Yaxin; Lou, Chaofeng; Gong, Yuning; Wu, Zengrui; Li, Weihua; Tang, Yun; Liu, Guixia

The Janus kinase (JAK) family plays a pivotal role in most cytokine-mediated inflammatory and autoimmune responses via JAK/STAT signaling, and administration of JAK inhibitors is a promising therapeutic strategy for several diseases including COVID-19. However, to screen and design selective JAK inhibitors is a daunting task due to the extremely high homology among four JAK isoforms. In this study, we aimed to simultaneously predict pIC50 values of compounds for all JAK subtypes by constructing an interpretable GNN multitask regression model. The final model performance was positive, with R2 values of 0.96, 0.79 and 0.78 on the training, validation and test sets, respectively. Meanwhile, we calculated and visualized atom weights, followed by the rank sum tests and local mean comparisons to obtain key atoms and substructures that could be fine-tuned to design selective JAK inhibitors. Several successful case studies have demonstrated that our approach is feasible and our model could learn the interactions between proteins and small molecules well, which could provide practitioners with a novel way to discover and design JAK inhibitors with selectivity.

SMALL molecules; GRAPH neural networks; REGRESSION analysis; PROTEIN-protein interactions; INFLAMMATION

Journal of Cheminformatics, 2022, Vol 14, Issue 1, p1

1758-2946

Academic Journal

10.1186/s13321-022-00593-9