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基于文献增强知识图谱嵌入的肝纤维化候选分子重定位研究

Literature-Augmented Knowledge Graph Embedding for Repurposing Candidate Molecules in Hepatic FibrosisYAN Yiyun*

  • 摘要: 目的:本研究旨在通过构建疾病特异性知识图谱并结合多种知识图谱嵌入模型,筛选出具有潜力的肝纤维化药物重定位候选分子。方法: 整合DRKG肝纤维化子图与PubMed文献摘要,利用大语言模型抽取SPO三元组,经实体标准化、关系归一化及节点重分类后,构建含122 775个节点、292 711条边的知识图谱。采用TransE、RotatE、RGCN和CompGCN四种嵌入模型进行链接预测训练,并联合多模型归一化评分、实体类型约束、非分子实体排除、规范名去重及精细分类策略,从24 211个原始候选中筛选主榜。结果: 最终确定5 041个候选分子,Top候选包括姜黄素、吡非尼酮、白藜芦醇等,均具备L1_direct级证据。14个预设阳性对照全部检出,其中13个进入主榜、12个进入Top-30、14个进入Top-200,显示良好的阳性富集能力。对主榜第10位芹菜素与FAK(PDB: 2J0L)的分子对接显示最佳结合能为−7.51 kcal/mol,全部9个构象均低于−5.0 kcal/mol。结论: 本研究为肝纤维化药物重定位的候选分子筛选和实验验证提供了计算策略与数据支撑。

     

    Abstract: Objective This study aims to construct a diseasespecific knowledge graph and apply multiple knowledge graph embedding models to prioritize candidate molecules with experimental validation potential for hepatic fibrosis drug repurposing. Methods The DRKG hepatic fibrosis subgraph was integrated with PubMed literature abstracts, and a large language model (LLM) was used to extract subjectpredicateobject (SPO) triples. After entity normalization, relation standardization, and nodetype reclassification, a literatureaugmented knowledge graph was built, containing 122 775 nodes, 292 711 edges, 7 entity types, and 19 standardized relation types. Four KGE models—TransE, RotatE, RGCN, and CompGCN—were trained as internal baselines for link prediction. Combined with multimodel normalized scoring, entitytype constraints, nonmolecular entity exclusion, canonical name deduplication, and finegrained classification strategies, a final ranked list of candidates was generated from an initial pool of 24 211 candidates. Results A total of 5 041 experimentally verifiable candidate molecules were identified. Top candidates include curcumin, pirfenidone, resveratrol, quercetin, berberine, salvianolic acid B, EGCG, taurine, astragaloside IV, and apigenin, all supported by L1_direct evidence in the knowledge graph. Knownpositive recovery analysis detected all 14 positive controls, with 13 in the main list, 12 in Top30, and 14 in Top200, indicating strong internal positive enrichment. Molecular docking of apigenin (ranked #10) against FAK (PDB: 2J0L) yielded a best binding energy of −7.51 kcal/mol, with all 9 conformations below the −5.0 kcal/mol threshold. Conclusions This study provides interpretable candidate prioritization and mechanistic moleculartargetpathway clues for hepatic fibrosis drug repurposing, preliminarily validates the physical binding feasibility of knowledgegraphprioritized candidates, and offers computational strategies and data support for subsequent candidate screening and experimental validation.

     

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