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肝纤维化药物重定位候选分子的知识图谱预测与分子对接验证

Knowledge graph prediction and molecular docking validation of drug repositioning candidates for hepatic fibrosis

  • 摘要: 肝纤维化是多种慢性肝病进展至肝硬化、肝细胞癌的关键病理环节,目前尚缺乏经监管机构批准的特异性抗纤维化药物。本研究旨在构建文献增强知识图谱并结合多种知识图谱嵌入(KGE)模型,系统性筛选具有抗肝纤维化潜力的药物重定位候选分子,并通过分子对接验证其结合可行性。通过整合DRKG肝纤维化子图与PubMed文献摘要,利用DeepSeek大语言模型API抽取“头实体−关系−尾实体”(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124 327个节点、292 533条边的知识图谱。采用TransE、RotatE、RGCN和CompGCN 4种嵌入模型进行链接预测训练,并联合多模型Z-score归一化集成评分、实体类型约束及精细分类策略进行候选排序。对排名靠前的候选分子进行证据层级验证和分子对接模拟。结果显示,集成KGE模型达到AUC-ROC 0.9487的预测性能,最终确定5 041个候选分子。Top-10候选以天然产物和已上市药物为主,包括琥珀酸(succinate)、槲皮素(quercetin)、葛根素(puerarin)等,均具备L1_direct级(候选分子在训练图谱中存在与肝纤维化目标疾病节点的直接治疗边)证据支持。14个预设阳性对照全部检出(回收率100%),14个全部进入主榜。分子对接结果显示,柚皮素(Top-10)与芹菜素(Top-20)针对FAK(PDB: 2J0L)的最佳结合能为−7.28 与−7.51 kcal/mol(1 kcal=4.184 kJ),均低于 - 5.0 kcal/mol阈值,非键相互作用分析揭示了氢键及疏水作用等关键结合驱动力。本研究为肝纤维化药物重定位提供了从文献知识整合、多模型候选排序到结构生物学验证的完整计算策略,所鉴定的候选分子(尤其是柚皮素和芹菜素)展现出良好的治疗潜力,为后续实验验证提供了明确的数据指向。

     

    Abstract: Hepatic fibrosis is a critical pathological link in the progression of various chronic liver diseases to cirrhosis and hepatocellular carcinoma, yet no specifically approved anti-fibrotic drug is currently available. This study aims to construct a literature-augmented knowledge graph and integrate multiple knowledge graph embedding (KGE) models to systematically screen drug repositioning candidates with potential anti-hepatic fibrosis activity, and to validate their binding feasibility through molecular docking. We integrated the DRKG hepatic fibrosis subgraph with PubMed literature abstracts, and employed the DeepSeek large language model API to extract SPO triples. After entity standardization, relation normalization, and node reclassification, a knowledge graph comprising 124 327 nodes and 292 533 edges was constructed. Four embedding models—TransE, RotatE, RGCN, and CompGCN—were adopted for link prediction training, followed by candidate ranking integrated with multi-model Z-score normalized ensemble scoring, entity type constraints, and fine-grained classification strategies. Top-ranked candidate molecules underwent evidence-level validation and molecular docking simulations. The ensemble KGE model achieved a predictive performance of AUC-ROC 0.9487, ultimately identifying 5 041 candidate molecules. The Top-10 candidates were predominantly natural products and already-marketed drugs, including succinate, quercetin, and puerarin, all of which were supported by L1_direct-level (candidate molecules have direct therapeutic edges to the target disease node of liver fibrosis in the training graph) evidence. All 14 preset positive controls were detected (100% recall rate), with 14 entering the main ranking list. Molecular docking results showed that the best binding energy of naringenin (Top-10) with FAK (PDB: 2J0L) was −7.28 kcal/mol (1 kcal=4.184 kJ), and that of apigenin (Top-20) with FAK (PDB: 2J0L) was −7.51 kcal/mol, both below −5.0 kcal/mol threshold. Non-bonded interaction analysis revealed key binding driving forces including hydrogen bonds and hydrophobic interactions. This study provides a comprehensive computational strategy for hepatic fibrosis drug repositioning, spanning from literature knowledge integration and multi-model candidate ranking to structural biology validation. The identified candidate molecules, particularly naringenin and apigenin, demonstrate favorable therapeutic potential and offer clear data directions for subsequent experimental validation.

     

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