Article(id=1190373729671676573, tenantId=1146029695717560320, journalId=1189982191388893191, issueId=1190332325088039709, articleNumber=null, orderNo=null, doi=10.16438/j.0513-4870.2024-1107, pmid=null, cstr=null, oa=null, hot=null, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=research-article, receivedDate=1730995200000, receivedDateStr=2024-11-08, revisedDate=1733587200000, revisedDateStr=2024-12-08, acceptedDate=null, acceptedDateStr=null, onlineDate=1761736813228, onlineDateStr=2025-10-29, pubDate=1746979200000, pubDateStr=2025-05-12, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1761736813228, onlineIssueDateStr=2025-10-29, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1761736813228, creator=13701087609, updateTime=1761736813228, updator=13701087609, issue=Issue{id=1190332325088039709, tenantId=1146029695717560320, journalId=1189982191388893191, year='2025', volume='60', issue='5', pageStart='1183', pageEnd='1572', issueExtLink='null', onlineDate='null', pubDate='null', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=1, specialIssue=null, createTime=1761726941606, creator=13701087609, updateTime=1761813457266, updator=13701087609, preIssue=null, nextIssue=null, ext={EN=IssueExt(id=1190695198163354009, tenantId=1146029695717560320, journalId=1189982191388893191, issueId=1190332325088039709, language=EN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=), CN=IssueExt(id=1190695198163354010, tenantId=1146029695717560320, journalId=1189982191388893191, issueId=1190332325088039709, language=CN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=)}, issueFiles=null}, startPage=1525, endPage=1533, ext={EN=ArticleExt(id=1190373729961083553, articleId=1190373729671676573, tenantId=1146029695717560320, journalId=1189982191388893191, language=EN, title=Artificial intelligence-designing drug-loaded bacterial outer membrane vesicles for in vitro activation of dendritic cells, columnId=1190335348761793317, journalTitle=Acta Pharmaceutica Sinica, columnName=Original Articles, runingTitle=null, highlight=null, articleAbstract=

Dendritic cells (DCs) play a critical role in both innate and adaptive immunity, particularly in regulating antitumor immune responses. However, immunosuppressive cytokines in the tumor microenvironment and lipid peroxidation imbalance within DCs limit their ability to activate tumor-specific T cells effectively. To address this, we developed a novel biomimetic nanodrug delivery platform using artificial intelligence (AI). This platform encapsulates curcumin nanoparticles in bacterial outer membrane vesicles (OMVs) to enhance DCs function through a dual approach: targeted drug delivery and immune activation. In vitro experiments demonstrated that curcumin reduced lipid peroxidation stress in DCs by modulating the IRE1α-XBP1 signaling pathway, thereby restoring their antigen-presenting function. Additionally, OMVs not only acted as efficient drug carriers but also as immune activators, promoting DCs maturation and enhancing tumor-specific immune responses. This study presents a promising strategy for improving antitumor immunotherapy and offers new insights into the application of AI in drug delivery systems.

, correspAuthors=Meng-chi SUN, authorNote=null, correspAuthorsNote=null, copyrightStatement=Copyright ©2025 Acta Pharmaceutica Sinica. All rights reserved., copyrightOwner=null, extLink=null, articleAbsUrl=null, sourceXml=null, magXml=null, pdfUrl=null, pdf=null, pdfFileSize=null, pdfExtLink=null, richHtmlUrl=null, mobilePdfUrl=null, reviewReport=null, pdfFirstPage=null, abstractGraph=null, abstractGraphContent=null, abstractVideo=null, citation=null, cebUrl=null, magXmlContent=null, mapNumber=null, authorCompany=null, fund=null, authors=null, authorsList=Dong-xuan XIE, Yu-hao DONG, Zhong-gui HE, Jin SUN, Meng-chi SUN), CN=ArticleExt(id=1190374098636210856, articleId=1190373729671676573, tenantId=1146029695717560320, journalId=1189982191388893191, language=CN, title=基于人工智能设计的载药细菌外膜囊泡用于体外激活树突状细胞的研究, columnId=1190335348896011050, journalTitle=药学学报, columnName=研究论文, runingTitle=null, highlight=null, articleAbstract=

树突状细胞(dendritic cells, DCs) 在连接先天免疫与适应性免疫中起着关键作用, 尤其在T细胞的活化和肿瘤免疫应答的调控中具有重要功能。然而, 肿瘤微环境中的免疫抑制性细胞因子以及DCs内的脂质过氧化失衡, 极大限制了其有效激活肿瘤特异性T细胞能力。为此, 作者基于人工智能设计了一种纳米仿生药物递送平台, 该平台通过将姜黄素纳米粒装载于细菌外膜囊泡(outer membrane vesicles, OMVs) 中, 旨在通过药物递送与免疫激活双重策略增强DCs功能。体外实验结果表明, 姜黄素通过调控IRE1α-XBP1信号通路显著缓解了DCs的脂质过氧化应激, 从而恢复其抗原呈递功能。此外, OMVs不仅作为高效药物载体, 还作为强大的免疫激活剂, 促进了DCs的成熟并增强了其肿瘤特异性免疫应答能力。本研究提出了一种提升抗肿瘤免疫治疗的新策略, 并为人工智能在药物递送系统中的应用提供了新的研究视角。

, correspAuthors=孙孟驰, authorNote=null, correspAuthorsNote=
*孙孟驰, E-mail:
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#共同第一作者 .

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Molecular mechanisms of T‐cell receptor and costimulatory molecule ligation/blockade in autoimmune disease therapy [J]. Immunol Rev, 2009, 229: 337-355., articleTitle=null, refAbstract=null)], funds=[Fund(id=1190694640778097108, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1190373729671676573, awardId=82372111, language=CN, fundingSource=国家自然科学基金资助项目(82372111), fundOrder=null, country=null)], companyList=[AuthorCompany(id=1190694632460792179, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1190373729671676573, xref=null, ext=[AuthorCompanyExt(id=1190694632469180788, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1190373729671676573, companyId=1190694632460792179, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=1. 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Joint International Research Laboratory of Intelligent Drug Delivery Systems, Ministry of Education, Shenyang 110016, China), AuthorCompanyExt(id=1190694632876028287, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1190373729671676573, companyId=1190694632842473853, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=3.智能药物递送系统国际合作联合实验室, 辽宁 沈阳 110016)])], figs=[ArticleFig(id=1190694638165045700, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1190373729671676573, language=EN, label=null, caption=null, figureFileSmall=eOVkTSJ3p81QGt5zZ3FYKA==, figureFileBig=HSB42gaMa3j9xs0ae//yqQ==, tableContent=null), ArticleFig(id=1190694638462841286, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1190373729671676573, language=CN, label=Figure 1, caption= The strategy of Cur-NPs@OMVs in alleviating lipid peroxidation stress and promoting dendritic cell (DC) activation for enhanced immunotherapy. A: The preparation process of Cur-NPs@OMVs; B: The strategy of Cur-NPs@OMVs in alleviating lipid peroxidation stress and promoting DC activation for enhanced immunotherapy. Cur: Curcumin; NPs: Nanoparticles; LVS: Luxurians virulent salmonella; OMVs: Outer membrance vesicles , figureFileSmall=eOVkTSJ3p81QGt5zZ3FYKA==, figureFileBig=HSB42gaMa3j9xs0ae//yqQ==, tableContent=null), ArticleFig(id=1190694638563504584, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1190373729671676573, language=EN, label=null, caption=null, figureFileSmall=12RSi1/XtOW/4xNfXcwS/Q==, figureFileBig=Hsddsxp0GFiQMuGpjHDaLA==, tableContent=null), ArticleFig(id=1190694638639002058, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1190373729671676573, language=CN, label=Figure 2, caption= Analysis of machine learning models, molecular docking, and molecular dynamics simulation results. A: SHAP summary plot for the Random Forest model; B: SHAP summary plot for the Decision Tree model; C: SHAP summary plot for the SVM model; D: Accuracy plot for the Random Forest model across different datasets; E: Accuracy plot for the Decision Tree model; F: Accuracy plot for the SVM model: G: Selection results from the Random Forest model applied to the TCM library, with likelihood on the y-axis and ranking on the x-axis; H: 3D molecular docking representation of Cur with the METTL3 protein; I: 2D molecular docking representation of Cur with METTL3; J: RMSD plot of the Cur-METTL3 protein complex; K-M: Bar chart quantifying interactions (K), detailed depiction of interactions (L), and time-lapse graph of interactions (M) between METTL3 and Cur; N: Analysis of bond rotation in Cur; O: Chemical structure and properties of Cur influencing biological activity and protein interactions , figureFileSmall=12RSi1/XtOW/4xNfXcwS/Q==, figureFileBig=Hsddsxp0GFiQMuGpjHDaLA==, tableContent=null), ArticleFig(id=1190694638852911564, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1190373729671676573, language=EN, label=null, caption=null, figureFileSmall=SCKbtRyS/D8ZrGjBqm1GLQ==, figureFileBig=beIEmOTpIl8I1RtHKHD62w==, tableContent=null), ArticleFig(id=1190694639003906510, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1190373729671676573, language=CN, label=Figure 3, caption= Preparation and characterization of Cur-NPs@OMVs. A, B: Chemical structures of curcumin and toyocamycin (Toy); C: Schematic representation of the preparation process; D-F: TEM and size distribution images of Cur-NPs, OMVs, and Cur-NPs@OMVs (scale bar = 100 nm); G: CLSM images of Cur-NPs@OMVs, where OMVs were stained with DiI dye (red) and curcumin naturally fluoresces green (scale bar = 100 μm); H: Size distribution of Cur-NPs and Cur-NPs@OMVs; I: Zeta potential of Cur-NPs and Cur-NPs@OMVs , figureFileSmall=SCKbtRyS/D8ZrGjBqm1GLQ==, figureFileBig=beIEmOTpIl8I1RtHKHD62w==, tableContent=null), ArticleFig(id=1190694639209427408, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1190373729671676573, language=EN, label=null, caption=null, figureFileSmall=UrENGAMUMg/C1kcrHaGGzA==, figureFileBig=WlE81FkmFS2Wg5Mf63Ru9w==, tableContent=null), ArticleFig(id=1190694640249614802, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1190373729671676573, language=CN, label=Figure 4, caption= <i>In vitro</i> cell-culture experiments of Cur-NPs@OMVs. A: Schematic illustration of the co-culture system experiment; B: Analysis of the advantages of Cur-NPs@OMVs; C, D: Quantified histograms of cell viability at 24 h (C) and 48 h (D) (<i>n</i> = 6, $\bar{x} \pm s$); E: Flow cytometry results of CD80 + CD86 + DCs <i>in vitro</i>; F: Proportions of CD80 + CD86 + cells across the four groups (<i>n</i> = 3); G: Schematic representation of Cur-NPs@OMVs facilitating ER inhibition, leading to enhanced T cell-mediated anti-tumor immune responses; H-J: Average flow cytometry intensity for different treatments (<i>n</i> = 3); K: Flow cytometry analysis of CD80 + CD86 + DCs after treatment with varying concentrations of Cur-NPs@OMVs; L: Proportions of CD80 + CD86 + cells across the Cur-NPs@OMVs concentration groups; M: Heatmap of cytokine secretion from DC2.4 cells after different treatments (<i>n</i> = 3); N-Q: Release levels of TNF-<i>α</i> (N), IL-6 (O), IL-12 (P), and IL-10 (Q) from DCs activated by the four groups (<i>n</i> = 3). 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基于人工智能设计的载药细菌外膜囊泡用于体外激活树突状细胞的研究
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谢东轩 1, # , 东玉灏 2, # , 何仲贵 1, 3 , 孙进 1, 3 , 孙孟驰 2, 3, *
药学学报 | 研究论文 2025,60(5): 1525-1533
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药学学报 | 研究论文 2025, 60(5): 1525-1533
基于人工智能设计的载药细菌外膜囊泡用于体外激活树突状细胞的研究
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谢东轩1, #, 东玉灏2, #, 何仲贵1, 3, 孙进1, 3, 孙孟驰2, 3, *
作者信息
  • 1.沈阳药科大学无涯创新学院, 辽宁 沈阳 110016
  • 2.沈阳药科大学药学院, 辽宁 沈阳 110016
  • 3.智能药物递送系统国际合作联合实验室, 辽宁 沈阳 110016

通讯作者:

*孙孟驰, E-mail:
Artificial intelligence-designing drug-loaded bacterial outer membrane vesicles for in vitro activation of dendritic cells
Dong-xuan XIE1, Yu-hao DONG2, Zhong-gui HE1, 3, Jin SUN1, 3, Meng-chi SUN2, 3, *
Affiliations
  • 1. Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
  • 2. School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, China
  • 3. Joint International Research Laboratory of Intelligent Drug Delivery Systems, Ministry of Education, Shenyang 110016, China
出版时间: 2025-05-12 doi: 10.16438/j.0513-4870.2024-1107
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树突状细胞(dendritic cells, DCs) 在连接先天免疫与适应性免疫中起着关键作用, 尤其在T细胞的活化和肿瘤免疫应答的调控中具有重要功能。然而, 肿瘤微环境中的免疫抑制性细胞因子以及DCs内的脂质过氧化失衡, 极大限制了其有效激活肿瘤特异性T细胞能力。为此, 作者基于人工智能设计了一种纳米仿生药物递送平台, 该平台通过将姜黄素纳米粒装载于细菌外膜囊泡(outer membrane vesicles, OMVs) 中, 旨在通过药物递送与免疫激活双重策略增强DCs功能。体外实验结果表明, 姜黄素通过调控IRE1α-XBP1信号通路显著缓解了DCs的脂质过氧化应激, 从而恢复其抗原呈递功能。此外, OMVs不仅作为高效药物载体, 还作为强大的免疫激活剂, 促进了DCs的成熟并增强了其肿瘤特异性免疫应答能力。本研究提出了一种提升抗肿瘤免疫治疗的新策略, 并为人工智能在药物递送系统中的应用提供了新的研究视角。

人工智能  /  姜黄素  /  免疫抑制  /  树突状细胞  /  细菌外膜囊泡

Dendritic cells (DCs) play a critical role in both innate and adaptive immunity, particularly in regulating antitumor immune responses. However, immunosuppressive cytokines in the tumor microenvironment and lipid peroxidation imbalance within DCs limit their ability to activate tumor-specific T cells effectively. To address this, we developed a novel biomimetic nanodrug delivery platform using artificial intelligence (AI). This platform encapsulates curcumin nanoparticles in bacterial outer membrane vesicles (OMVs) to enhance DCs function through a dual approach: targeted drug delivery and immune activation. In vitro experiments demonstrated that curcumin reduced lipid peroxidation stress in DCs by modulating the IRE1α-XBP1 signaling pathway, thereby restoring their antigen-presenting function. Additionally, OMVs not only acted as efficient drug carriers but also as immune activators, promoting DCs maturation and enhancing tumor-specific immune responses. This study presents a promising strategy for improving antitumor immunotherapy and offers new insights into the application of AI in drug delivery systems.

artificial intelligence  /  curcumin  /  immunosuppression  /  dendritic cell  /  outer membrane vesicle
谢东轩, 东玉灏, 何仲贵, 孙进, 孙孟驰. 基于人工智能设计的载药细菌外膜囊泡用于体外激活树突状细胞的研究. 药学学报, 2025 , 60 (5) : 1525 -1533 . DOI: 10.16438/j.0513-4870.2024-1107
Dong-xuan XIE, Yu-hao DONG, Zhong-gui HE, Jin SUN, Meng-chi SUN. Artificial intelligence-designing drug-loaded bacterial outer membrane vesicles for in vitro activation of dendritic cells[J]. Acta Pharmaceutica Sinica, 2025 , 60 (5) : 1525 -1533 . DOI: 10.16438/j.0513-4870.2024-1107
免疫系统是维持体内稳态的复杂防御网络, 通过精准识别并清除异常细胞或病原体来发挥保护作用。近年来, 肿瘤免疫治疗, 特别是通过激活宿主免疫系统对抗肿瘤的策略, 展现了巨大的潜力[1-3]。尽管多种免疫治疗策略已开发并能诱导免疫反应, 但在临床中仅部分患者能够显著受益[4], 这突显了免疫治疗的复杂性与挑战, 亟需更有效的免疫激活策略。树突状细胞(dendritic cells, DCs) 作为免疫系统的核心调节者, 在肿瘤免疫反应中扮演关键角色[5-8]。肿瘤微环境中的树突状细胞往往因脂质代谢紊乱而功能受损, 内质网应激与其下游的IRE1α-XBP1通路在此过程中起着重要作用[9]。这种代谢异常不仅削弱了DCs的功能, 还减少了其主要组织相容性复合体(major histocompatibility complex, MHC)表达, 进而抑制了T细胞介导的抗肿瘤免疫反应[10]。因此, 靶向调节DCs的脂质代谢紊乱以恢复其正常功能, 成为提升免疫治疗效果的关键策略。
随着生物信息学和人工智能(artificial intelligence, AI) 技术的迅猛发展, 新的研究方法不断涌现, 为药物靶点发现和制剂设计提供了新的视野与机遇[11]。AI技术在解读复杂生物数据和识别潜在药物靶点方面展现出显著优势, 能够提高药物研发的效率和成功率[12]。本文构建了一套潜在调控IRE1α-XBP1通路的药物筛选数据库, 以识别如姜黄素(curcumin, Cur)、决明子素、红景天苷及银杏内酯等具有该靶点结合能力的有效成分。
细菌外膜囊泡(outer membrane vesicles, OMVs) 作为一种新兴生物材料, 其在激活宿主免疫系统方面的潜力日益受到关注[13, 14]。OMVs是革兰阴性细菌在正常生长过程中自发产生的纳米级(20~250 nm) 脂质双层结构[15]。这些囊泡富含多种来自细菌外膜的免疫原性成分, 包括脂多糖(lipopolysaccharide, LPS)16]、肽聚糖[17]和鞭毛蛋白[18]等病原相关分子模式(pathogen-associated molecular patterns, PAMPs) 及特异性抗原[19]。因此, OMVs能够有效模拟其亲代病原体, 从而激活宿主的先天性和适应性免疫反应[20]。此外, 由于OMVs不具备活体细菌的感染与复制能力, 被认为是一种更安全且有效的药物递送载体与免疫激活策略。
本研究开发了一种新型纳米仿生药物递送平台, 旨在重塑肿瘤微环境中DCs的功能(图 1)。作者通过筛选确定姜黄素为调控IRE1α-XBP1信号通路的有效候选药物。并将其封装于聚乳酸-羟基乙酸共聚物[poly(lactic-co-glycolic acid), PLGA] 纳米粒子中, 进一步通过减毒沙门氏菌(live-attenuated salmonella, LVS) 代谢产生的OMVs进行包覆, 形成Cur-NPs@OMVs复合体系。体外实验表明, 该系统显著增强了DCs的功能, 减轻了脂质过氧化应激。本研究为基于AI的药物发现和递送技术提供了新的视角, 突出了靶向DCs脂质代谢在提升肿瘤免疫治疗效果中的重要性。希望本研究能为恶性肿瘤的免疫治疗提供新的策略与方向, 并展示AI技术在药物研发中的广泛应用前景。
仪器与试剂  聚乙烯醇(PVA, 上海阿拉丁生化科技股份有限公司); 聚乳酸-羟基乙酸共聚物(上海舜纳生物科技有限公司); 姜黄素(上海麦克林生化科技股份有限公司); 丰加霉素(toyocamycin, Toy, MCE, 美国); 鼠源树突状细胞(DC2.4); RPMI-1640培养基(大连美仑生物技术有限公司); 胎牛血清、青霉素-链霉素双抗溶液、四甲基偶氮唑蓝(MTT)、PE-CD80、APC-CD86、Cell Staining Buffer (BioLegend, 美国); 酶联免疫吸附测定试剂盒(上海通蔚生物有限公司)。
Python编程环境(如scikit-learn、RDKit、PyTorch); Maestro 9.7软件; BT-25S电子分析天平(上海赛多利斯科学仪器有限公司); 超声波细胞破碎仪(宁波新芝生物科技股份有限公司); TCS SP2/AOBS激光共聚焦显微镜(confocal laser scanning microscopy, CLSM, 尼康公司, 日本); 超速离心机(日立公司, 日本); 40B1自动立式压力蒸气灭菌器(上海申安医疗器械厂); LF-1脂质体挤出器(奥维斯丁公司, 加拿大); 激光粒度分析仪(马尔文公司, 英国); JEOL 100CX Ⅱ透射电子显微镜(transmission electron microscopy, TEM, 日立电子株式会社, 日本); CO2细胞培养箱(赛默飞公司, 美国); SW-CJ-1F超净工作台(江苏苏净安泰公司); 倒置生物显微镜(重庆奥特光学公司); SYNERGY酶标仪(BioTek公司, 美国); FACS Calibur流式细胞仪(Becton Dickinson公司, 美国)。
人工智能的筛选和模拟  采用基于机器学习的人工智能算法对潜在药物进行筛选。首先构建包含FDA批准药物的数据库, 并通过RDKit提取分子指纹和分子描述符。接着, 作者采用随机森林模型, 并通过网格搜索优化超参数, 预测候选药物与IRE1α-XBP1信号通路相互作用的可能性。在完成模型训练和验证后, 姜黄素凭借其在通路调控中的最高预测评分被选为首要候选药物。具体的算法原理和模型参数可参考作者在GitHub上的源代码。
机器学习与深度学习筛选  m6A是最丰富的mRNA修饰, 由甲基转移酶复合物催化, 其中METTL3是唯一的催化亚基, 其可以通过催化IRE1α的m6A进而激活细胞的IRE1α-XBP1通路, 来实现DCs的活化, 从而产生抗癌的作用[21]。应用机器学习与深度学习方法筛选可能与METTL3蛋白相互作用的药物分子, 为相关疾病治疗提供新思路。实验步骤首先包括Python编程环境的搭建及必要库的安装, 如scikit-learn、RDKit和PyTorch, 支持后续图神经网络分析。通过ZINC数据库下载中药成分库(Traditional Chinese Medicine, TCM), 并使用Maestro 9.7进行分子对接模拟。
在数据集构建阶段, 使用spide工具对PubMed进行高级搜索, 关键词包括“METTL3蛋白”、“抑制剂”和“配体”, 系统阅读文献并提取相关活性物质信息。重点比较不同活性物质的分子特征(如分子质量、苯环位置、疏水/亲水键分布), 确保所选化合物与METTL3蛋白的相互作用。最终构建METTL3蛋白药物数据集, 并记录EC50值和血药浓度, 排除低活性化合物。在特征选择与数据集划分阶段, 使用pandas导入药物数据集, 结合RDKit从SMILES文件中提取分子描述符与指纹信息, 构建特征列表并进行优化。通过多次训练模型, 选择最佳分子描述符, 去除冗余特征, 提升模型性能。数据集随机划分为训练集(80%) 和测试集(20%)。在机器学习模型训练阶段, 分别引入随机森林、支持向量机和决策树模型, 采用交叉验证优化超参数, 确保最佳预测准确率。通过计算特征重要性并使用SHAP进行可视化, 评估模型准确率及ROC-AUC等指标, 验证模型有效性。在药物筛选阶段, 将TCM药物SMILES文件库导入训练模型, 筛选可能与METTL3蛋白相互作用的候选药物, 并根据模型预测的概率, 优先选择可能性较高的分子进行后续实验。通过对不同模型筛选结果的对比, 分析一致性与差异性, 最终选择预测一致性强且综合可能性高的药物分子进行实验验证。
分子对接及分子模拟  首先, 从RCSB数据库检索METTL3蛋白结构, 选择5 311种结构中相对偏差较小的样本。利用计算机模拟技术对蛋白质进行建模, 并通过分子动力学模拟研究其在溶液中的动态行为, 揭示其纳米尺度上的构象变化。在虚拟筛选部分, 导入METTL3的PDB文件至Maestro 9.7, 使用“protein prepare”功能修正蛋白结构; 接着, 利用Glide模块的“Receptor Grid Generation”功能生成格点文件, 设置配体为空间中心, 并将格点空间调整至20 Å, 将格点文件导入虚拟筛选工作流, 并结合FDA化合物数据库筛选药物分子, 最终获得候选药物; 通过Maestro进行分子对接, 使用“Induced Fit Docking”功能对候选配体进行结合预测, 评估其与METTL3的相互作用。本研究采用半柔性对接, 允许蛋白质与药物分子在对接过程中发生构象变化。在分子动力学模拟环节, 保存对接后的蛋白质结构为PDB文件, 并利用“System Builder”构建完整体系。通过“Minimization”功能进行能量最小化, 去除因位阻等因素引起的潜在能量。最后, 在温度300 K、压强1.013 bar的NPT系统中, 进行100 ns的分子动力学模拟, 以观察配体与METTL3的结合稳定性。
制剂学制备与表征  采用羧基修饰的PLGA[22]制备载药纳米粒子, 并筛选出最佳制剂条件。随后, 依据该条件制备了Cur-NPs、Cur-NPs@OMVs及Toy-NPs@OMVs, 供后续细胞实验使用。
Cur-NPs的制备与表征  采用超声乳化法制备Cur-NPs。首先, 将PLGA溶解于甲醇和二氯甲烷(1∶3, v/v) 混合溶液中, 然后加入2 mg姜黄素于4 mL油相中, 充分溶解并混合, 为了确保药物与载体充分混合, 在室温下使用混匀仪振荡至澄清溶液; 接着, 缓慢加入预冷的2.5% PVA水溶液, 形成初乳, 将乳液置于超声波细胞破碎仪中, 在冰浴条件下以350 W功率超声乳化15 min, 形成复乳; 之后, 使用旋转蒸发仪去除有机溶剂, 将乳液在4 ℃、10 000 ×g离心30 min, 收集沉淀并用超纯水洗涤3次以去除残余PVA和未包裹的姜黄素; 然后, 测定粒径、PDI和表面电位, 每个样品测定3次以确保结果的准确性; 最终, 取10 μL样品滴加至碳膜铜网上, 静置30 s后用滤纸吸干, 使用1%磷钨酸负染, 最后在电镜下观察。
细菌外膜囊泡的制备与表征  LB培养基的配方为胰蛋白胨(10 g·L-1)、酵母提取物(10 g·L-1) 和NaCl (5 g·L-1), 在超声波处理后, 121 ℃高压灭菌30 min备用。从-80 ℃冷冻库中取出减毒沙门氏菌, 在37 ℃水浴中快速解冻。将10 μL细菌接种于4 mL LB培养基中, 于37 ℃、250 r·min-1下培养10 h, 随后转接至100 mL LB培养基中, 继续培养至吸光度值(A600) 达到0.8, 作为OMVs的来源。细菌培养达到预定光密度后, 室温静置24 h, 将培养液在4 ℃、4 000 ×g离心35 min, 收集上清液并通过0.45 μm滤膜过滤。使用100 kDa超滤浓缩管在4 ℃、200 000 ×g超速离心2 h, 收集沉淀并用PBS重悬, 洗涤两次后, 0.45 μm滤膜再次过滤, 以纯化OMVs, 并储存于-20 ℃。将OMVs稀释至1 mg·mL-1, 进一步稀释至25倍后, 使用DLS测定其粒径、PDI及zeta电位。同上在电镜下观察形貌特征。
Cur-NPs@OMVs的制备与表征  Cur-NPs@OMVs采用挤出法制备。将制备好的Cur-NPs与OMVs按比例混合, 在冰浴条件下以80 W功率超声乳化3 min (2 s工作/3 s间歇), 然后通过220 nm聚碳酸酯膜挤出7次, 随后以3 000 ×g离心10 min去除未结合的OMVs, 弃去上清液并用PBS洗涤3次, 所得Cur-NPs@OMVs储存于4 ℃备用。将Cur-NPs@OMVs样品稀释25倍后, 测定其粒径和zeta电位。同上在电镜下观察形貌特征。
Cur-NPs@OMVs共定位效果考察  OMVs用DiI荧光染料标记, 将2 mg·mL-1 OMVs与5 μg·mL-1 DiI按1∶1比例混合, 室温孵育2 h, 随后以200 000 ×g超速离心2 h, 去除未结合的DiI。标记后的OMVs经220 nm挤出器挤出7次, 再以3 000 ×g离心10 min去除多余OMVs, PBS洗涤3次。通过CLSM观察Cur-NPs与DiI标记OMVs的共定位情况。
树突状细胞的培养  选用小鼠来源的DC2.4细胞进行体外激活实验。细胞在RPMI-1640培养基中生长, 补充10% FBS和1%青霉素-链霉素双抗溶液。培养条件为37 ℃、5% CO₂。当细胞融合度达到80%~90%时, 进行传代。对数生长期的DC2.4细胞使用PBS进行消化, 消化后用培养基重悬以终止反应, 并继续培养。
细胞毒性实验  在96孔板中接种1×104个DC2.4细胞, 分别培养24和48 h以确保细胞充分贴壁。随后, 吸除培养基并用PBS洗涤细胞4次, 然后添加含有Cur-NPs、Cur-NPs@OMVs和Toy-NPs@OMVs的无血清培养基。细胞在培养箱中继续孵育指定时间。孵育结束后, 再次吸除培养基, 在避光条件下向每孔加入10 μL质量浓度为5 mg·mL-1的MTT溶液, 并在37 ℃下孵育4 h。随后, 小心去除MTT溶液, 加入150 μL DMSO以完全溶解形成的紫色晶体, 并在振荡器上轻轻振荡10 min。最后, 使用酶标仪在490 nm波长下测定各孔的吸光度值, 根据公式(1) 计算细胞存活率。
$ \mathrm{细}\mathrm{胞}\mathrm{存}\mathrm{活}\mathrm{率}\left(\mathrm{\%}\right)=\frac{({A}_{\mathrm{样}\mathrm{品}\mathrm{组}}-{A}_{\mathrm{空}\mathrm{白}\mathrm{组}})}{({A}_{\mathrm{对}\mathrm{照}\mathrm{组}}-{A}_{\mathrm{空}\mathrm{白}\mathrm{组}})}\times 100\mathrm{\%} $
其中, A样品组A空白组A对照组分别为样品组、空白组和对照组在在490 nm波长的吸光度值。
树突状细胞激活实验  在12孔培养板中接种1×105个DC2.4细胞, 每孔加入1 mL RPMI-1640培养基, 在37 ℃、5% CO₂条件下培养24 h, 以确保细胞充分贴壁。培养结束后, 轻轻吸出旧培养基, 用PBS洗涤细胞1次, 以去除浮游细胞和残留物。随后, 添加1 mL不含FBS的RPMI-1640培养基。在各实验组中, 分别加入质量浓度为10~100 μg·mL-1的Cur-NPs、Cur-NPs@OMVs及Toy-NPs@OMVs, 孵育24 h。孵育结束后, 采用流式细胞术分析细胞表面标志物的表达。用PBS洗涤细胞4次, 以去除未结合的纳米颗粒。使用PBS轻微消化细胞30 s后, 加入完全培养基以终止消化。随后以600 ×g离心3 min, 弃去上清, 加入PBS重悬细胞。细胞悬液与1%小鼠血清封闭液以1∶1体积比混合, 在室温下孵育30 min, 以减少非特异性结合。接着, 加入PE标记的CD80和APC标记的CD86抗体, 避光孵育30 min。最后, 用Cell Staining Buffer洗涤后悬混均匀, 过筛至流式管中, 使用流式细胞仪检测DC2.4细胞表面CD80及CD86的表达。
此外, 为了评估制剂对DC2.4细胞因子分泌的影响, 需收集培养上清液, 并使用ELISA试剂盒定量检测TNF-α、IL-6、IL-12和IL-10的分泌情况。
统计学分析  统计分析使用GraphPad Prism 10.2.1软件。单因素方差分析(ANOVA) 评估组间差异的显著性, Tukey的HSD事后检验用于多组比较以控制组间变量。数据以均值±标准差(SD) 表示, 并以相对值(实验组与对照组比值) 呈现。统计显著性水平设定为*P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.000 1。
结合机器学习、分子对接及分子动力学模拟, 以深入探讨姜黄素作为潜在药物的机制。首先, 利用smiles.csv数据集进行模型训练, 并通过网格搜索优化参数, 评估了随机森林、决策树和支持向量机模型对不同特征的影响力。结果显示, bit_743、bit_2、bit_8、bit_1和descriptor_6对药物活性影响显著, 并且这些特征主要与药物分子与靶点的相互作用相关(图 2A~C)。具体而言, bit_743、bit_2、bit_8和bit_1分别表示羟基、酚羟基和酯基等含氧基团, 而descriptor_6反映了分子中苯环的数量。由于数据集规模较小, 支持向量机在训练集和测试集中的准确性均达到100% (图 2D~F), 这可能导致模型缺乏广泛适用性。相较而言, 随机森林和决策树在训练集中的准确性均为100%, 在测试集中为93%, 表明这两种模型在某些方面具有一致性, 且均能训练出高质量的模型。随后, 利用随机森林模型对TCM库进行了筛选, 结果显示姜黄素的潜在活性排名第一(图 2G)。相比之下, 决策树和支持向量机模型的筛选结果均显示药物分子的活性为100%, 这一结果与实际情况相差甚远, 因此未被采纳。
在分子对接实验中, 观察了姜黄素与5IL2蛋白的结合结果(图 2H), 发现姜黄素的苯环部分嵌入蛋白的空穴结构。相互作用图(图 2I) 显示, 姜黄素与5IL2主要通过苯环上的羟基与ASP形成氢键, 并与PHE通过π-π堆积作用进行相互作用。对接评分为6.89, 表明姜黄素能够有效结合5IL2蛋白。结合物的RMSD图(图 2J) 显示, 姜黄素与5IL2的结合在绝大多数时间内的RMSD值小于2.5, 表明姜黄素与5IL2之间的结合稳定。进一步分析姜黄素与5IL2的相互作用柱状图(图 2K), 横坐标为参与作用的氨基酸残基, 纵坐标为作用持续时间占动力学过程的比例, 绿色表示氢键作用, 蓝色为水桥作用, 紫色为疏水作用, 红色为离子作用。结果显示, 5IL2主要通过氢键(ASP377、ILE378、ASP395) 和疏水键(TYR406、PHE534) 与姜黄素相互作用。时间轴分析(图 2M) 进一步确认ASP377、ILE378、ASP395和PHE534在相互作用中发挥了重要作用。从相互作用图(图 2L) 中可观察到, ASP395与姜黄素的苯环相互作用达97%的时间, ASP377与苯环的氢键相互作用达92%, ILE378则有83%的时间与苯环形成氢键, 而PHE534与苯环的π-π堆积相互作用同样显著。
最后, 观察分子动力学过程中的可旋转键(图 2N), 姜黄素的可旋转键旋转情况较为集中, 表明其与蛋白的结合状态较为牢固。此外, 配体特征图(图 2O) 显示, 姜黄素在分子动力学过程中无分子内氢键, 且所有性质均保持稳定, 进一步验证了姜黄素与5IL2的强结合稳定性。
为制备仿生纳米药物递送平台(Cur-NPs@OMVs), 选择了羧基封端的PLGA聚合物(PLGA-COOH) 通过超声乳化法成功制备Cur-NPs, 并使Cur-NPs与OMVs之间达到理想的锚定效率(图 3C)。Cur-NPs@OMVs的制备优化基于Cur∶PLGA配比、油水相比例及Cur-NPs与OMVs的共载比例。首先, 在不同的Cur∶PLGA配比(1∶10、1∶30、1∶50、1∶70、1∶100) 中, 1∶30配比下, Cur-NPs粒径最小(3 nm), 且zeta电位为-18 mV (图 3I), 表明其具有良好的稳定性, 因此选择1∶30作为最佳配比。接着, 考察了油水相比例对粒径和zeta电位的影响, 结果表明, 1∶1的油水相比例下粒径最小且具有较好的稳定性(图 3H)。最后, 在Cur-NPs与OMVs的不同共载比例中, 1∶2比例下Cur-NPs@OMVs粒径为243.3 nm (图 3H), zeta电位为-19 mV (图 3I), 表现出最佳的稳定性和分散性。因此, 1∶30的Cur∶PLGA配比、1∶1的油水相比例以及1∶2的Cur-NPs与OMVs比例被确定为最佳制备条件。通过以上筛选条件, 成功制备了具有理想粒径(243.3 nm)、良好分散性及稳定性的Cur-NPs@OMVs。同时, TEM和共聚焦荧光成像验证了Cur-NPs的成功包裹(图 3D~G), 且共载效率随着配比变化得到了有效验证。通过优化Cur与PLGA的比例、油水相比例以及Cur-NPs与OMVs的比例, 筛选出了最佳的Cur-NPs@OMVs制备条件。成功制备的纳米载体不仅具有良好的结构均一性和形态特征, 为后续的体外DCs激活实验提供了可靠的制剂基础。
在24和48 h的培养时间内, 所有组别的细胞存活率均超过80% (图 4CD), 表明这些实验制剂具有良好的安全性, 为后续的体外激活实验奠定了基础。Cur-NPs组与Toy-NPs组相比, 虽然两者的细胞毒性均较小, 但Toy-NPs组在48 h后的存活率显著低于Cur-NPs组, 提示Toy的成分可能对细胞存活产生一定的负面影响。针对Toy成分及其潜在的细胞毒机制的深入研究将值得注意, 尽管OMVs作为药物递送平台具有增强免疫反应的潜力, 但其生物相容性及免疫反应仍需进一步评估。OMVs中的PAMPs (如LPS、DNA) 通过激活Toll样受体可能引发免疫反应, 增强抗肿瘤免疫, 但也可能导致免疫细胞的毒性, 甚至引发过度免疫反应。因此, 优化OMVs的提取工艺、精确控制PAMPs含量, 并研究其免疫毒性是未来的重点。此外, 探索OMVs在体内的代谢途径及免疫细胞相互作用将有助于理解其清除机制, 为临床应用提供理论支持。最后, OMVs在临床大规模生产中的挑战包括保持粒径、纯度和生物活性, 未来应优化生产工艺, 确保治疗效果和安全性。
在CD80和CD86激活实验中, 通过流式细胞术评估了不同递送平台对DCs的激活效果。结果显示, Cur-NPs@OMVs组的CD80 + CD86 + DCs比例显著高于阴性对照组, 仅次于ToyNPs@OMVs组(图 4EFIJ)。Cur在制剂中的浓度与CD80 + CD86 + DCs的比例呈正相关(图 4KL), 表明Cur-NPs@OMVs在激活DCs方面具有显著作用。与Cur-NPs相比, Cur-NPs@OMVs组在激活DCs方面表现更加突出, 提示OMVs对Cur递送效率的提升起到了关键作用(图 4EFHI)。尽管Cur-NPs在CD86的激活上表现较强, 但对CD80的激活作用相对有限(图 4H), 这可能与Cur对不同共刺激分子的选择性激活有关。具体而言, CD86主要参与T细胞的早期激活, 而CD80则在T细胞的完全激活中起更重要作用[23, 24]。此外, 姜黄素的递送效率对其在DCs中的激活效果至关重要。Cur-NPs在体外实验中表现出较好的递送效率, 特别是在与OMVs联合使用时, Cur-NPs@OMVs显著增强了DCs的CD80和CD86激活能力。这表明OMVs在提高姜黄素递送效率并增强免疫效果方面发挥了重要作用。因此, 优化姜黄素的递送平台将对提高肿瘤免疫治疗效果具有重要意义。
在细胞因子释放方面, ELISA检测结果显示, Cur-NPs@OMVs组TNF-α、IL-6、IL-12的分泌水平显著高于阴性对照组(图 4N~P), 分别为462.70 (对照组为362.08)、419.77 (对照组为138.75) 和37.21 pg·mL-1 (对照组为27.60 pg·mL-1), 而IL-10的分泌水平则明显低于对照组(图 4Q)。具体而言, TNF-α和IL-6是促炎性细胞因子, 参与机体的免疫反应与炎症反应。TNF-α能够促进T细胞的活化和增殖, 从而增强抗肿瘤免疫反应; 而IL-6则在调节T细胞和B细胞活性方面发挥重要作用。此外, IL-12是关键的免疫调节因子, 能够诱导细胞毒性T淋巴细胞的生成, 提高其对肿瘤细胞的杀伤能力。相反, IL-10的分泌水平在Cur-NPs@OMVs组中低于对照组。IL-10是一种具有免疫抑制作用的细胞因子, 通常会抑制促炎细胞因子的产生, 从而抑制免疫反应。IL-10的相对低水平表明, Cur-NPs@OMVs能够有效减弱免疫抑制信号, 促进免疫系统的激活。这种现象与DCs的抗原呈递能力的增强密切相关, 说明Cur-NPs@OMVs不仅能够激活DCs的功能, 还能通过降低IL-10的分泌来提高抗肿瘤免疫的强度。因此, Cur-NPs@OMVs通过显著增强促炎细胞因子的分泌并抑制免疫抑制因子的产生, 为树突状细胞提供了强有力的免疫刺激。
尽管近年来免疫疗法显示出良好的前景, 但肿瘤微环境中的抑制因素仍然阻碍有效的抗肿瘤免疫反应。作者将研究重点从单一免疫疗法拓展至多项激活策略, 开发了基于AI的载姜黄素细菌外膜囊泡纳米仿生平台, 并评估了其体外免疫激活能力。结果表明, 该平台通过调控IRE1α-XBP1信号通路, 有效抑制了DCs的脂质过氧化应激, 并促进其活化。此平台有望增强T细胞介导的抗肿瘤免疫反应, 不仅展现了AI技术在个性化药物筛选中的潜力, 也为仿生纳米免疫疗法的开发提供了新思路和方法支持。
作者贡献: 谢东轩负责制剂的制备与表征、细胞实验、数据处理及初稿撰写; 东玉灏负责人工智能实验; 指导教师孙孟驰全程参与课题的规划、设计和指导, 并提供资金支持, 同时对论文进行审阅; 孙进、何仲贵老师对本文也提出了修改意见。
利益冲突: 本文所有作者声明不存在利益冲突关系。
  • 国家自然科学基金资助项目(82372111)
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doi: 10.16438/j.0513-4870.2024-1107
  • 接收时间:2024-11-08
  • 首发时间:2025-10-29
  • 出版时间:2025-05-12
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  • 收稿日期:2024-11-08
  • 修回日期:2024-12-08
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国家自然科学基金资助项目(82372111)
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    1.沈阳药科大学无涯创新学院, 辽宁 沈阳 110016
    2.沈阳药科大学药学院, 辽宁 沈阳 110016
    3.智能药物递送系统国际合作联合实验室, 辽宁 沈阳 110016

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2种不同金属材料的力学参数

Family
属数
Number of
genus
种数
Number of
species
占总种数比例
Percentage of
total species (%)

Genus
种数
Number of
species
占总种数比例
Percentage of total
species (%)
鹅膏菌科Amanitaceae 2 11 5.26 鹅膏菌属 Amanita 10 4.78
小菇科 Mycenaceae 2 12 5.74 丝盖伞属 Inocybe 5 2.39
多孔菌科 Polyporaceae 8 14 6.70 蜡蘑属 Laccaria 5 2.39
红菇科 Russulaceae 3 23 11.00 小皮伞属 Marasmius 6 2.87
小菇属 Mycena 11 5.26
光柄菇属 Pluteus 5 2.39
红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
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