SYSTCM: A systemic web platform for objective identification of pharmacological effects based on interplay of “traditional Chinese Medicine-components-targets”

Mechanism analysis is essential for the use and promotion of Traditional Chinese Medicine (TCM). Traditional methods of network analysis relying on expert experience lack an explanatory framework, prompting the application of deep learning and machine learning for objective identification of TCM pharmacological effects. A dataset was used to construct an interacted network graph between 424 molecular descriptors and 465 pharmacological targets to represent the relationship between components and pharmacological effects. Subsequently, the optimal identification model of pharmacological effects (IPE) was established through convolution neural networks of GoogLeNet structure. The AUC values are greater than 0.8, MCC values are greater than 0.7, and ACC values are greater than 0.85 across various test datasets. Subsequently, 18 recognition models of TCM efficacy (RTE) were created using support vector machines (SVM). Integration of pharmacological effects and efficacies led to the development of the systemic web platform for identification of pharmacological effects (SYSTCM). The platform, comprising 70,961 terms, including 636 Traditional Chinese Medicines (TCMs), 8190 components, 40 pharmacological effects, and 18 efficacies. Through the SYSTCM platform, (1) Total 100 components were predicted from TCMs with anti-inflammatory pharmacological effects. (2) The pharmacological effects of complete constituents were predicted from Coptidis Rhizoma (Huang Lian). (3) The principal components, pharmacological effects, and efficacies were elucidated from Salviae Miltiorrhizae radix et rhizome (Dan Shen). SYSTCM addresses subjectivity in pharmacological effect determination, offering a potential avenue for advancing TCM drug development and clinical applications. Access SYSTCM at http://systcm.cn. •We created SYSTCM, a platform to identify pharmacological effects of 636 herbs, 8190 components, covering 40 effects and 18 efficacies.•SYSTCM applied to case studies demonstrated components with anti-inflammatory, Huang Lian's key effects and Dan Shen's role in blood circulation.•IPE and RTE use GoogLeNet and ML, designed around TCM features, to predict pharmacological effects and efficacies.