文章链接：https://link.springer.com/epdf/10.1007/s10822-025-00741-x?sharing_token=V68CfOs1WoXdoVlhXbCCbve4RwlQNchNByi7wbcMAY5EsdfynNbQpsJarEbpPadBkiHrCRAqh4X36jJDzBmbEhwo-LUSCW3uEOJNSlRZW3wOyl63ksNW0esSNGngq4oTsQuuf2YET2Z7yzFIok_nmjcZh_nacXui1MuddGzp6W0%3D

Klebsiella pneumoniae (K. pneumoniae), a multidrug-resistant Gram-negative bacillus, represents a significant global health threat due to its role in hospital-acquired infections and the emergence of carbapenem-resistant hypervirulent strains. This study integrates the Drug Repurposing Knowledge Graph (DRKG) with molecular dynamics (MD) simulations to identify and validate stable structural segments of the KPHS_11890 gene, which encodes a membrane fusion protein of the AcrAB-TolC efflux pump that is critical for antibiotic resistance in K. pneumoniae. Using the PyKEEN framework, a knowledge graph embedding model was trained on a comprehensive dataset combining DrugBank, K. pneumoniae strain sequences, and NCBI databases, identifying KPHS_11890 as a top-ranked candidate (Hits@10 = 0.1602). The structural reliability of the target was first confirmed via rigorous quality assessment (Ramachandran plot, ERRAT, and ProSA), followed by triplicate 100-ns molecular dynamics simulations using GROMACS 2025. The integrated analysis of essential dynamics and free energy landscapes (FEL) revealed a thermodynamically stable core domain (residues 18–342) and a critical functional hinge region near residue 115. The structural rigidity of the core suggests minimized entropic penalties for inhibitor binding, while the identified hinge motion presents a specific mechanical vulnerability for allosteric locking. This integrated DRKG-MD approach not only efficiently pinpoints high-potential targets but also elucidates their biophysical mechanisms, providing a robust structural basis for designing novel inhibitors to overcome efflux pump-mediated resistance.

肺炎克雷伯菌是一种多重耐药革兰阴性杆菌，因其在医院获得性感染中的作用以及碳青霉烯类耐药高毒力菌株的出现，已成为全球重大健康威胁。本研究将药物重定位知识图谱与分子动力学模拟相结合，旨在识别并验证KPHS_11890基因的稳定结构片段。该基因编码AcrAB-TolC外排泵的膜融合蛋白，对肺炎克雷伯菌的抗生素耐药性至关重要。
通过PyKEEN框架，整合DrugBank、肺炎克雷伯菌株序列及NCBI数据库的全面数据集，训练知识图谱嵌入模型，最终确定KPHS_11890为高潜力候选靶点（Hits@10 = 0.1602）。首先通过严格的质量评估（拉氏图、ERRAT和ProSA分析）确认目标结构的可靠性，随后使用GROMACS 2025进行三次重复的100纳秒分子动力学模拟。
结合基本动力学分析与自由能景观研究发现，该蛋白存在一个热力学稳定的核心结构域（残基18–342）及位于残基115附近的关键功能性铰链区。核心区的结构刚性表明其结合抑制剂时的熵罚效应较小，而铰链区的动态运动特征揭示了可通过变构锁定作用的机械脆弱位点。这种DRKG-MD整合策略不仅能高效定位高潜力靶点，还可阐明其生物物理机制，为设计新型抑制剂以克服外排泵介导的耐药性提供了坚实的结构基础。