Systematic elucidation of the effective constituents and potential mechanisms of Scrophulariae Radix against neoplasm based on LC-MS, network pharmacology, and molecular docking approaches
Scrophulariae Radix is a traditional Chinese medicine used to treat neoplasms in previous publications. Nevertheless, how the Scrophulariae Radix chemical constituents treat neoplasm still needs to be clarified. Herein, we combined the response surface method, UPLC-ESI-MS/MS, network pharmacology, m...
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Frontiers Media S.A.
2025-07-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2025.1615076/full |
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| author | Shu-jie Yu Xiao-bin Kong Xin Jin Meng-yi Shan Gang Cheng Pei-lu Wang Wen-long Li Pei-yuan Zhao Yun-jie Sheng Bing-qian He Qi Shi Hua-qiang Li Qi-ming Zhao Lu-ping Qin Lu-ping Qin Xiong-yu Meng Xiong-yu Meng |
| author_facet | Shu-jie Yu Xiao-bin Kong Xin Jin Meng-yi Shan Gang Cheng Pei-lu Wang Wen-long Li Pei-yuan Zhao Yun-jie Sheng Bing-qian He Qi Shi Hua-qiang Li Qi-ming Zhao Lu-ping Qin Lu-ping Qin Xiong-yu Meng Xiong-yu Meng |
| author_sort | Shu-jie Yu |
| collection | DOAJ |
| description | Scrophulariae Radix is a traditional Chinese medicine used to treat neoplasms in previous publications. Nevertheless, how the Scrophulariae Radix chemical constituents treat neoplasm still needs to be clarified. Herein, we combined the response surface method, UPLC-ESI-MS/MS, network pharmacology, molecular docking, and molecular dynamics (MD) simulation to characterize bioactive constituents in Scrophulariae Radix and further uncover their potential mechanisms against neoplasm. As a result, the material–liquid ratio was significantly reduced from 100 g/mL to 32 g/mL, and the extraction efficiency was 1.332%, which was close to the predicted value of 1.346% in the response surface method, indicating that the algorithm model had a good fit. Next, a total of 738 compounds, including 161 terpenoids, 144 phenolic acids, 51 alkaloids, 24 flavonoids, 34 saccharides, 32 lignans and coumarins, 45 amino acids and derivatives, 23 organic acids, 134 lipids, 22 nucleotides and derivatives, and 59 other ingredients, were characterized from Scrophulariae Radix based on the accurate precursor and product ions, retention time, standards, fragmentation patterns, and previous publications. Subsequently, to screen which constituents were most effective, the network pharmacology was constructed, and 96 active compounds and 488 key neoplasm-related targets were identified, leading to the establishment of the “Drug-Compound-Target” network and PPI network. The top 4 components and targets were selected for the presentation of MD simulation, consisting of cytosporone C, cystomexicone A, mediterraneone, and bestim, with the highest degree related targets carbonic anhydrase 12 (CA12), carbonic anhydrase 2 (CA2), carbonic anhydrase 9 (CA9), and carbonic anhydrase 1 (CA1) being considered as the core compounds and targets. GO pathway analysis was closely related to hormone, protein phosphorylation, and protein kinase activity. KEGG pathway enrichment primarily involved pathways in cancer and the cAMP signaling pathway in cancer. Overall, this integration method provided guiding significance for the exploration of TCM treatment. |
| format | Article |
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| institution | Kabale University |
| issn | 1664-462X |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Plant Science |
| spelling | doaj-art-d7dc67d6e85d41c396f6fc0efee4f5e72025-08-20T03:31:10ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2025-07-011610.3389/fpls.2025.16150761615076Systematic elucidation of the effective constituents and potential mechanisms of Scrophulariae Radix against neoplasm based on LC-MS, network pharmacology, and molecular docking approachesShu-jie Yu0Xiao-bin Kong1Xin Jin2Meng-yi Shan3Gang Cheng4Pei-lu Wang5Wen-long Li6Pei-yuan Zhao7Yun-jie Sheng8Bing-qian He9Qi Shi10Hua-qiang Li11Qi-ming Zhao12Lu-ping Qin13Lu-ping Qin14Xiong-yu Meng15Xiong-yu Meng16School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, ChinaSchool of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, ChinaSchool of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, ChinaSchool of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, ChinaSchool of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, ChinaSchool of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, ChinaSchool of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, ChinaInstitute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, ChinaSchool of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, ChinaAcademy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, ChinaSchool of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, ChinaSchool of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, ChinaSchool of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, ChinaSchool of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, ChinaZhejiang Key Laboratory of Chinese Medicine Modernization, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, ChinaSchool of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, ChinaZhejiang Key Laboratory of Chinese Medicine Modernization, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, ChinaScrophulariae Radix is a traditional Chinese medicine used to treat neoplasms in previous publications. Nevertheless, how the Scrophulariae Radix chemical constituents treat neoplasm still needs to be clarified. Herein, we combined the response surface method, UPLC-ESI-MS/MS, network pharmacology, molecular docking, and molecular dynamics (MD) simulation to characterize bioactive constituents in Scrophulariae Radix and further uncover their potential mechanisms against neoplasm. As a result, the material–liquid ratio was significantly reduced from 100 g/mL to 32 g/mL, and the extraction efficiency was 1.332%, which was close to the predicted value of 1.346% in the response surface method, indicating that the algorithm model had a good fit. Next, a total of 738 compounds, including 161 terpenoids, 144 phenolic acids, 51 alkaloids, 24 flavonoids, 34 saccharides, 32 lignans and coumarins, 45 amino acids and derivatives, 23 organic acids, 134 lipids, 22 nucleotides and derivatives, and 59 other ingredients, were characterized from Scrophulariae Radix based on the accurate precursor and product ions, retention time, standards, fragmentation patterns, and previous publications. Subsequently, to screen which constituents were most effective, the network pharmacology was constructed, and 96 active compounds and 488 key neoplasm-related targets were identified, leading to the establishment of the “Drug-Compound-Target” network and PPI network. The top 4 components and targets were selected for the presentation of MD simulation, consisting of cytosporone C, cystomexicone A, mediterraneone, and bestim, with the highest degree related targets carbonic anhydrase 12 (CA12), carbonic anhydrase 2 (CA2), carbonic anhydrase 9 (CA9), and carbonic anhydrase 1 (CA1) being considered as the core compounds and targets. GO pathway analysis was closely related to hormone, protein phosphorylation, and protein kinase activity. KEGG pathway enrichment primarily involved pathways in cancer and the cAMP signaling pathway in cancer. Overall, this integration method provided guiding significance for the exploration of TCM treatment.https://www.frontiersin.org/articles/10.3389/fpls.2025.1615076/fullScrophulariae Radixneoplasmresponse surface analysis methodUPLC-ESI-MS/MSnetwork pharmacologymolecular docking |
| spellingShingle | Shu-jie Yu Xiao-bin Kong Xin Jin Meng-yi Shan Gang Cheng Pei-lu Wang Wen-long Li Pei-yuan Zhao Yun-jie Sheng Bing-qian He Qi Shi Hua-qiang Li Qi-ming Zhao Lu-ping Qin Lu-ping Qin Xiong-yu Meng Xiong-yu Meng Systematic elucidation of the effective constituents and potential mechanisms of Scrophulariae Radix against neoplasm based on LC-MS, network pharmacology, and molecular docking approaches Frontiers in Plant Science Scrophulariae Radix neoplasm response surface analysis method UPLC-ESI-MS/MS network pharmacology molecular docking |
| title | Systematic elucidation of the effective constituents and potential mechanisms of Scrophulariae Radix against neoplasm based on LC-MS, network pharmacology, and molecular docking approaches |
| title_full | Systematic elucidation of the effective constituents and potential mechanisms of Scrophulariae Radix against neoplasm based on LC-MS, network pharmacology, and molecular docking approaches |
| title_fullStr | Systematic elucidation of the effective constituents and potential mechanisms of Scrophulariae Radix against neoplasm based on LC-MS, network pharmacology, and molecular docking approaches |
| title_full_unstemmed | Systematic elucidation of the effective constituents and potential mechanisms of Scrophulariae Radix against neoplasm based on LC-MS, network pharmacology, and molecular docking approaches |
| title_short | Systematic elucidation of the effective constituents and potential mechanisms of Scrophulariae Radix against neoplasm based on LC-MS, network pharmacology, and molecular docking approaches |
| title_sort | systematic elucidation of the effective constituents and potential mechanisms of scrophulariae radix against neoplasm based on lc ms network pharmacology and molecular docking approaches |
| topic | Scrophulariae Radix neoplasm response surface analysis method UPLC-ESI-MS/MS network pharmacology molecular docking |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2025.1615076/full |
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