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Ren Q, Qu N, Sun J, Zhou J, Liu J, Ni L, Tong X, Zhang Z, Kong X, Wen Y, Wang Y, Wang D, Luo X, Zhang S, Zheng M, Li X. KinomeMETA: meta-learning enhanced kinome-wide polypharmacology profiling. Brief Bioinform 2023; 25:bbad461. [PMID: 38113075 PMCID: PMC10729787 DOI: 10.1093/bib/bbad461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 11/08/2023] [Accepted: 11/22/2023] [Indexed: 12/21/2023] Open
Abstract
Kinase inhibitors are crucial in cancer treatment, but drug resistance and side effects hinder the development of effective drugs. To address these challenges, it is essential to analyze the polypharmacology of kinase inhibitor and identify compound with high selectivity profile. This study presents KinomeMETA, a framework for profiling the activity of small molecule kinase inhibitors across a panel of 661 kinases. By training a meta-learner based on a graph neural network and fine-tuning it to create kinase-specific learners, KinomeMETA outperforms benchmark multi-task models and other kinase profiling models. It provides higher accuracy for understudied kinases with limited known data and broader coverage of kinase types, including important mutant kinases. Case studies on the discovery of new scaffold inhibitors for membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase and selective inhibitors for fibroblast growth factor receptors demonstrate the role of KinomeMETA in virtual screening and kinome-wide activity profiling. Overall, KinomeMETA has the potential to accelerate kinase drug discovery by more effectively exploring the kinase polypharmacology landscape.
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Affiliation(s)
- Qun Ren
- Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Ning Qu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Jingjing Sun
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Jingyi Zhou
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Lingang Laboratory, Shanghai 200031, China
| | - Jin Liu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Lin Ni
- Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Xiaochu Tong
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Zimei Zhang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Xiangtai Kong
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Yiming Wen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Yitian Wang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Dingyan Wang
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, Hangzhou 330106, China
| | - Xiaomin Luo
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Sulin Zhang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Mingyue Zheng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
- Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xutong Li
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
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