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Scaffold and SAR studies on c-MET inhibitors using machine learning approaches

摘要Numerous c-mesenchymal-epithelial transition(c-MET)inhibitors have been reported as potential anticancer agents.However,most fail to enter clinical trials owing to poor efficacy or drug resistance.To date,the scaffold-based chemical space of small-molecule c-MET inhibitors has not been analyzed.In this study,we constructed the largest c-MET dataset,which included 2,278 molecules with different struc-tures,by inhibiting the half maximal inhibitory concentration(IC50)of kinase activity.No significant differences in drug-like properties were observed between active molecules(1,228)and inactive mol-ecules(1,050),including chemical space coverage,physicochemical properties,and absorption,distri-bution,metabolism,excretion,and toxicity(ADMET)profiles.The higher chemical diversity of the active molecules was downscaled using t-distributed stochastic neighbor embedding(t-SNE)high-dimensional data.Further clustering and chemical space networks(CSNs)analyses revealed commonly used scaffolds for c-MET inhibitors,such as M5,M7,and M8.Activity cliffs and structural alerts were used to reveal"dead ends"and"safe bets"for c-MET,as well as dominant structural fragments consisting of pyr-idazinones,triazoles,and pyrazines.Finally,the decision tree model precisely indicated the key structural features required to constitute active c-MET inhibitor molecules,including at least three aromatic het-erocycles,five aromatic nitrogen atoms,and eight nitrogen-oxygen atoms.Overall,our analyses revealed potential structure-activity relationship(SAR)patterns for c-MET inhibitors,which can inform the screening of new compounds and guide future optimization efforts.

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作者 Jing Zhang [1] Mingming Zhang [2] Weiran Huang [3] Changjie Liang [4] Wei Xu [5] Jinghua Zhang [5] Jun Tu [2] Innocent Okohi Agida [2] Jinke Cheng [2] Dong-Qing Wei [6] Buyong Ma [3] Yanjing Wang [3] Hongsheng Tan [7] 学术成果认领
作者单位 Clinical Research Institute & School of Public Health,Shanghai Jiao Tong University School of Medicine,Shanghai,200025,China;Department of Biochemistry and Molecular Cell Biology,Shanghai Key Laboratory for Tumor Microenvironment and Inflammation,Shanghai Jiao Tong University School of Medicine,Shanghai,200025,China;Academy of Integrative Medicine,Shanghai University of Traditional Chinese Medicine,Shanghai,201203,China [1] Department of Biochemistry and Molecular Cell Biology,Shanghai Key Laboratory for Tumor Microenvironment and Inflammation,Shanghai Jiao Tong University School of Medicine,Shanghai,200025,China [2] Engineering Research Center of Cell & Therapeutic Antibody,School of Pharmacy,Shanghai Jiao Tong University,Shanghai,200240,China [3] Academy of Integrative Medicine,Shanghai University of Traditional Chinese Medicine,Shanghai,201203,China [4] Core Facility of Basic Medical Sciences,Shanghai Jiao Tong University School of Medicine,Shanghai,200025,China [5] School of Life Sciences and Biotechnology,Shanghai Jiao Tong University,Shanghai,200030,China [6] Clinical Research Institute & School of Public Health,Shanghai Jiao Tong University School of Medicine,Shanghai,200025,China [7]
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DOI 10.1016/j.jpha.2025.101303
发布时间 2025-09-30(万方平台首次上网日期,不代表论文的发表时间)
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药物分析学报(英文版)

药物分析学报(英文版)

2025年15卷6期

1321-1333页

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