Graphormer-Integrated Interaction Network Construction and Action Prediction of Major Bupleurum Chinense Compounds and Targets
Main Article Content
Abstract
To address the low accuracy of multi-component-multi-target interaction prediction in Bupleurum chinense caused by complex molecular structures and limited target associations, this paper employs advanced graph models combined with biological network topology information. The same graph-based representation strategy is relevant to materials informatics, including the screening of molecular or polymer structures for electromagnetic sensing, dielectric response, and functional coating design. Specifically, RDKit is used to construct chemically defined molecular graphs, with atoms as nodes and covalent bonds as edges, and to encode multidimensional atomic features. These graphs are directly input into Graphormer. Graphormer then incorporates a fully connected attention mechanism that integrates topological distances and spatial geometric information from RDKit graphs to extract higher-order molecular representations. Node2Vec is used to embed the protein-protein interaction network in a low-dimensional space and identify potential target pathways. Finally, compound and protein embeddings are concatenated and fed into a two-channel neural network to predict interaction probabilities. With negative sampling for training, the method achieves stable average AUROC values of 0.91-0.93 and AUPRC values of 0.88-0.90. Even when only 10% of targets are visible, the F1-score reaches 0.683±0.021 and Coverage Rate@50 reaches 76.4%, indicating strong inductive reasoning under sparse knowledge conditions.
Downloads
Article Details
This work is licensed under a Creative Commons Attribution 4.0 International License.
Authors who publish with this journal agree to the following terms:
- Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
- Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
- Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).
References
C. Sui, W. J. Han, C. R. Zhu, and J. H. Wei, “Recent progress in saikosaponin biosynthesis in Bupleurum,” Current Pharmaceutical Biotechnology, vol. 22, no. 3, pp. 329-340, 2021, doi: 10.2174/1389201021999200918101248.
E. Hamzaoğlu, “A new variety of the Bupleurum (Apiaceae) from Türkiye,” Anatolian Journal of Botany, vol. 7, no. 1, pp. 46-49, 2023, doi: 10.30616/ajb.1249583.
A. V. Myagchilov, P. G. Gorovoi, and L. I. Sokolova, “Flavonoids of the Far Eastern species of the genus Bupleurum L,” Russian Journal of Bioorganic Chemistry, vol. 50, no. 7, pp. 2884-2889, 2024, doi: 10.1134/S1068162024070227.
S. Hou, R. Zhang, C. Zhang, L. Wang, H. Wang, and X. X. Wang, “Role of vermicompost and biochar in soil quality improvement by promoting Bupleurum falcatum L,” nutrient absorption. Soil Use and Management, vol. 39, no. 4, pp. 1600-1617, 2023, doi: 10.1111/sum.12955.
J. Ghosh and M. Bhaumik, “Typification of nine names of the genus Bupleurum (Apiaceae),” Feddes Repertorium, vol. 136, no. 2, pp. 114-127, 2025, doi: 10.1002/fedr.70010.
D. Mu and Q. Ma, “A review of antidepressant effects and mechanisms of three common herbal medicines: Panax ginseng, Bupleurum chinense, and Gastrodia elata,” CNS & Neurological Disorders - Drug Targets-CNS & Neurological Disorders, vol. 22, no. 8, pp. 1164-1175, 2023, doi: 10.2174/1871527322666221116164836.
W. Han, J. Xu, H. Wan, L. Zhou, B. Wu, J. Gao, et al., “Overexpression of BcERF3 increases the biosynthesis of saikosaponins in Bupleurum chinense,” FEBS Open Bio, vol. 12, no. 7, pp. 1344-1352, 2022, doi: 10.1002/2211-5463.13412.
M. Gao, X. Huo, L. Lu, M. Liu, and G. Zhang, “Analysis of codon usage patterns in Bupleurum falcatum chloroplast genome,” Chinese Herbal Medicines, vol. 15, no. 2, pp. 284-290, 2023, doi: 10.1016/j.chmed.2022.08.007.
G. Zhang, H. Wang, J. Jiang, Q. Wang, B. Li, L. Shi, et al., “The complete chloroplast genome of Bupleurum marginatum var,” stenophyllum (H. Wolff) Shan & Yin Li (Apiaceae), a new substitution for Chinese medicinal material, Bupleuri Radix (Chai hu). Mitochondrial DNA Part B, vol. 6, no. 2, pp. 441-443, 2021, doi: 10.1080/23802359.2020.1870899.
Z. W. Li, J. T. Wu, Y. Bi, M. M. Li, A. Naseem, J. Pan, et al., “A new triterpenoid saponin and a new natural saponin from the roots of Bupleurum scorzonerifolium Willd,” Natural Product Research, vol. 39, no. 15, pp. -4346, 2025, doi: 10.1080/14786419.2024.2338827.
S. Khaled, M. Benahmed, S. Akkal, and H. Laouer, “Experimental and theoretical approaches to examine the effects of Bupleurum montanum extracts as corrosion inhibitors on carbon steel in an acidic solution,” Chemical Papers, vol. 79, no. 3, pp. 1707-1737, 2025, doi: 10.1007/s11696-025-03884-1.
X. Zou, Y. Sui, X. Y. Tang, R. Zhang, Q. Shu, T. Gong, et al., “Mechanism of Bupleurum scorzonerifolium and Paeonia lactiflora herbal pair against liver cancer: An exploration based on UPLC-Q-TOF-MS combined with network pharmacology,” Zhongguo Zhongyao Zazhi (China Journal of Chinese Materia Medica), vol. 47, no. 13, pp. 3597-3608, 2022, doi: 10.19540/j.cnki.cjcmm.20220110.402.