Improving the Prediction of Potential Kinase Inhibitors with Feature Learning on Multisource Knowledge

Abstract

Purpose: The identification of potential kinase inhibitors plays a key role in drug discovery for treating human diseases. Currently, most existing computational methods only extract limited features such as sequence information from kinases and inhibitors. To further enhance the identification of kinase inhibitors, more features need to be leveraged. Hence, it is appealing to develop effective methods to aggregate feature information from multisource knowledge for predicting potential kinase inhibitors. In this paper, we propose a novel computational framework called FLMTS to improve the performance of kinase inhibitor prediction by aggregating multisource knowledge.

Method: FLMTS uses a random walk with restart (RWR) to combine multiscale information in a heterogeneous network. We used the combined information as features of compounds and kinases and input them into random forest (RF) to predict unknown compound-kinase interactions.

Results: Experimental results reveal that FLMTS obtains significant improvement over existing state-of-the-art methods. Case studies demonstrated the reliability of FLMTS, and pathway enrichment analysis demonstrated that FLMTS could also accurately predict signaling pathways in disease treatment.

Conclusion: In conclusion, our computational framework of FLMTS for improving the prediction of potential kinase inhibitors successfully aggregates feature information from multisource knowledge, yielding better prediction performance than existing state-of-the-art methods.

Keywords: Feature learning; Heterogeneous network; Kinase inhibitor; Multisource knowledge.