An Interpretable Multitask Framework BiLAT Enables Accurate Prediction of Cyclin-Dependent Protein Kinase Inhibitors

• Published in: Journal of chemical information and modeling 2023-06, Vol.63 (11), p.3350-3368
• Main Authors: Qian, Xu, Dai, Xiaowen, Luo, Lin, Lin, Mingde, Xu, Yuan, Zhao, Yang, Huang, Dingfang, Qiu, Haodi, Liang, Li, Liu, Haichun, Liu, Yingbo, Gu, Lingxi, Lu, Tao, Chen, Yadong, Zhang, Yanmin
• Format: Article
• Language: English
• Subjects: Algorithms; Cell cycle; Chemical Information; Datasets; Deep learning; Enumeration; Kinases; Machine learning; Performance enhancement; Prediction models; Proteins
• ISSN: 1549-9596; 1549-960X
• DOI: 10.1021/acs.jcim.3c00473

The cyclin-dependent protein kinases (CDKs) are protein-serine/threonine kinases with crucial effects on the regulation of cell cycle and transcription. CDKs can be a hallmark of cancer since their excessive expression could lead to impaired cell proliferation. However, the selectivity profile of most developed CDK inhibitors is not enough, which have hindered the therapeutic use of CDK inhibitors. In this study, we propose a multitask deep learning framework called BiLAT based on SMILES representation for the prediction of the inhibitory activity of molecules on eight CDK subtypes (CDK1, 2, 4–9). The framework is mainly composed of an improved bidirectional long short-term memory module BiLSTM and the encode layer of the Transformer framework. Additionally, the data enhancement method of SMILES enumeration is applied to improve the performance of the model. Compared with baseline predictive models based on three conventional machine learning methods and two multitask deep learning algorithms, BiLAT achieves the best performance with the highest average AUC, ACC, F1-score, and MCC values of 0.938, 0.894, 0.911, and 0.715 for the test set. Moreover, we constructed a targeted external data set CDK-Dec for the CDK family, which mainly contains bait values screened by 3D similarity with active compounds. This dataset was utilized in the subsequent evaluation of our model. It is worth mentioning that the BiLAT model is interpretable and can be used by chemists to design and synthesize compounds with improved activity. To further verify the generalization ability of the multitask BiLAT model, we also conducted another evaluation on three public datasets (Tox21, ClinTox, and SIDER). Compared with several currently popular models, BiLAT shows the best performance on two datasets. These results indicate that BiLAT is an effective tool for accelerating drug discovery.