摘要 目的:運用網絡藥理學與生物信息學方法探討扶正養(yǎng)心方治療心力衰竭合并糖尿病的作用成分和機制。方法:基于GEO數據庫篩選心力衰竭合并糖尿病與心力衰竭的差異基因;BATMAN-TCM、ETCM數據庫檢索扶正養(yǎng)心方的藥物活性成分和作用靶點,將獲得的疾病基因和藥物成分靶點取交集繪制Venn圖及中藥復方調控網絡。對交集基因進行蛋白-蛋白互作(PPI)分析、基因本體(GO)功能富集分析和京都基因與基因組百科全書(KEGG)通路富集分析。應用分子對接技術驗證扶正養(yǎng)心方和核心靶點之間的關系。結果:共獲得差異表達基因108個;扶正養(yǎng)心方中含有活性成分403個、作用靶點2 346個;交集基因15個。缺口受體蛋白1(NOTCH1)為PPI核心網絡中的關鍵蛋白。GO富集分析包括565個生物過程、13種細胞組分、4個分子功能。KEGG通路富集分析主要包括RAS相關蛋白1(RAP1)信號通路、磷脂酰肌醇3-激酶-蛋白激酶B信號通路、磷脂酶D信號通路、肌動蛋白細胞骨架調節(jié)、絲裂原活化蛋白激酶信號通路等18條信號通路,血小板衍生生長因子受體β(PDGFRB)、凝血因子Ⅱ凝血酶受體(F2R)和KIT原癌基因酪氨酸蛋白激酶(KIT)是通路富集最多的基因。分子對接結果顯示,扶正養(yǎng)心方的核心成分與NOTCH1、PDGFRB、F2R和KIT具有較好的結合力。結論:扶正養(yǎng)心方干預心力衰竭合并糖尿病具有多成分、多靶點、多通路的特點。
關鍵詞 心力衰竭;糖尿?。环稣B(yǎng)心方;網絡藥理學;生物信息學;機制
doi:10.12102/j.issn.1672-1349.2023.16.001
The Mechanism of Fuzheng Yangxin Recipe in the Treatment of Heart Failure Combined with Diabetes Mellitus Based on Network Pharmacology and Bioinformatics
WANG Anzhu, MA Xiaochang
Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, China
Corresponding Author MA Xiaochang, E-mail: maxiaochang@x263.net
Abstract Objective:To explore the" mechanisms of action of Fuzheng Yangxin Recipe in the treatment of heart failure combined with diabetes mellitus based on network pharmacology and bioinformatics.Methods:Based on the GEO database to screen the genes related heart failure combined with diabetes,the BATMAN-TCM and ETCM databases were retrieved for the drug active ingredients and targets action of Fuzheng Yangxin Recipe,and the obtained;disease genes and drug ingredient targets were intersected to draw the Venn diagrams and the regulatory network of the herbal compound.Protein-protein interaction(PPI) analysis,Gene Ontology(GO) functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway enrichment analysis were performed on the intersecting genes.Molecular docking was used to verify the relationship between Fuzheng Yangxin Recipe and its core targets.Results:A total of 108 expressed genes were obtained;there were 403 active ingredients and 2 346 action targets,and 15 intersecting genes.Notch receptor protein 1(NOTCH1) was the key protein in the PPI core network.The GO enrichment analysis included 565 biological processes,13 cellular components,and 4 molecular function.KEGG pathway enrichment analysis mainly obtained 18 signaling pathways,including RAS-associated protein 1(RAP1) signaling pathway,phosphatidylinositol 3-kinase-protein kinase B signaling pathway,phospholipase D signaling pathway,actin cytoskeleton regulation,and mitogen-activated protein kinase signaling pathway.Platelet-derived growth factor receptor β(PDGFRB),coagulation factor Ⅱ thrombin receptor(F2R),and KIT proto-oncogene,receptor tyrosine kinase(KIT) were the most enriched genes with the pathway.The molecular docking results showed that the core components of Fuzheng Yangxin Recipe showed better affinity with NOTCH1,PDGFRB,F2R and KIT.Conclusion:The intervention of Fuzheng Yangxin Recipe in the treatment of heart failure combined with diabetes mellitus was related with multi-component,multi-target and multi-pathway.
Keywords heart failure; diabetes mellitus; Fuzheng Yangxin Recipe; network pharmacology; bioinformatics; mechanism
心力衰竭是目前主要的公共衛(wèi)生問題之一,2017年全球疾病負擔研究顯示,心力衰竭患病人數約6 434萬例[1]。2019年美國發(fā)布的數據顯示,年齡>20歲人群中約620萬例患有心力衰竭,預計到2030年,心力衰竭患病率約增加46%[2]。2015年全球20~79歲的成年人中每11例病人中1例病人患有糖尿病;預計到2040年,約有6.42億例糖尿病病人[3]。2型糖尿?。╰ype 2 diabetes mellitus,T2DM)占所有糖尿病病人90%以上[4]。隨著人口老齡化加劇,心力衰竭合并糖尿病患病率持續(xù)增加。針對T2DM病人的臨床試驗中,基線時心力衰竭患病率為10%~30%[5-7]。慢性心力衰竭病人的臨床試驗中,無論心力衰竭的表型如何,T2DM患病率約為30%[8-10]。北美和歐洲住院的心力衰竭病人數據顯示,T2DM患病率為40%~45%[11-12]。血糖的控制可能無法將心血管疾病風險恢復至非糖尿病水平。有研究表明,強化血糖控制可將T2DM病人的糖化血紅蛋白(glycated hemoglobin,HbA1c)降低至6.5%以下,但對主要大血管事件、全因死亡無顯著影響[13]。將HbA1c目標定為6%的試驗表明,強化降糖未顯著減少主要心血管事件,反而增加了死亡率[14]。雖然心力衰竭不是這些研究的主要終點,薈萃分析表明,強化降糖未降低在某些情況下可能增加心力衰竭發(fā)病率和住院風險[15]。除糖尿病引起的心肌病發(fā)生結構和功能變化外,同時存在復雜的潛在和相互關聯的病理生理學導致糖尿病背景下心力衰竭發(fā)生[16]。因此,心力衰竭合并糖尿病病人的藥物治療是臨床關注的焦點。
中醫(yī)學無心力衰竭這一名詞,但在2000多年前的典籍中已有關于心力衰竭臨床癥狀的描述。中醫(yī)認為心力衰竭的發(fā)病與心陽氣虛有關,中醫(yī)藥可廣泛用于心力衰竭病人的治療[17]。扶正養(yǎng)心方是在陳可冀院士活血化瘀思想指導下,總結多年收治心力衰竭病人臨床診療經驗組合而成的方藥,由人參、附子、黃芪、麥冬、當歸、生地、紅景天、三七8味中藥組成的中醫(yī)復方。臨床實踐發(fā)現中醫(yī)藥應用于心力衰竭合并糖尿病病人有較好的療效,但關于其治療的潛在機制尚未明確。
網絡藥理學是以系統(tǒng)生物學和多向藥理學為基礎,選取特定節(jié)點采用生物分子網絡分析方法對藥物進行分子設計和靶點分析的一門學科[18]。該方法從系統(tǒng)生物學角度構建“疾病-基因-靶點-成分-藥物”網絡,具有動態(tài)性、系統(tǒng)性、互作性特點,與中醫(yī)藥、整體觀念、辨證施治的疾病觀念一致[19]。本研究基于網絡藥理學探討扶正養(yǎng)心方治療心力衰竭合并糖尿病的作用機制,以期為扶正養(yǎng)心方的治療提供依據。
1 資料與方法
1.1 基于GEO數據庫分析基因芯片篩選差異基因
從GEO數據庫(https://www.ncbi.nlm.nih.gov/geo/)檢索“heart failure”“diabetes mellitus”基因表達譜,選擇“Homo sapiens”人類樣本。通過閱讀摘要,選擇需要的結果并下載其矩陣文件和注釋平臺文件。使用R包(“BiocManager”“Limma” “Pheatmap”)對芯片數據進行二次分析,設定logFC>0.5,adj P value<0.05作為明顯差異基因的篩選條件。選取上調、下調的前20個基因繪制熱圖。繪制火山圖時,adj P value<0.05,logFC>0.5,表示該基因上調,用“紅色”表示;adjP value<0.05,logFC<0.5,表示該基因下調,用“綠色”表示。無差異基因用“黑色”表示。
1.2 扶正養(yǎng)心方有效成分篩選和靶標預測
利用BATMAN-TCM數據庫[20](http://bionet.ncpsb.org/batman-tcm/)、ETCM數據庫[21](http://www.tcmip.cn/ETCM/index.php/Home/)對每味中藥有效成分進行篩選,使用BATMAN-TCM數據庫時,設定adj P value=0.05、Score cutoff=20。將獲得成分輸入PubChem(https://pubchem.ncbi.nlm.nih.gov/)中獲得CID號碼。
1.3 構建“藥物-疾病”交集靶基因數據庫并建立中藥復方調控網絡
將獲得的差異基因與扶正養(yǎng)心方靶點基因取交集,采用R包(“Venn Diagram”)繪制Venn圖。使用Cytoscape 3.8.2軟件構建中藥名稱、交集基因和藥物有效成分為節(jié)點的中藥復方調控網絡。
1.4 蛋白-蛋白互作(PPI)網絡分析
采用Cytoscape 3.8.2中的“BisoGenet”[22],基于6個主要的人類PPI數據庫Biological General Repository for Interaction Datasets(BioGRID)、Biomolecular Interaction Network Database(BIND)、Molecular Interaction Database(MINT)、Human Protein Reference Database(HPRD)、Database of Interacting Proteins(DIP)和intAct對交集基因進行PPI網絡分析,構建基因-蛋白質-蛋白質可視化生物學網絡;采用CytoNCA插件對網絡進行拓撲分析[23],通過度中心性(degree centrality,DC)≥20%、接近中心性(between centrality,BC)≥20%作為核心節(jié)點的篩選條件,獲得的關鍵節(jié)點,即在“藥物-靶基因”信息傳遞過程中具有重要、高效信息傳遞的關鍵蛋白。
1.5 功能富集分析
基因本體(Gene Ontology,GO)分別從生物過程(biological process,BP)、細胞組分(cellular component,CC)、分子功能(molecular function,MF)3方面對基因進行功能注釋。采用京都基因與基因組百科全書(Kyoto Encyclopedia of Genes and Genomes,KEGG)對基因涉及的信號通路進行分析。利用R包(“org.Hs.eg.db”)“DOSE”“clusterProfiler”“enrichplot”“colorspace”“stringi”“ggplot2”完成GO和KEGG富集分析可視化,根據富集數目和顯著程度(P value cutoff<0.05,Q value cutoff<0.05)分別輸出富集后氣泡圖,將得到的KEGG通路導入Cytoscape 3.8.2,根據度值大小繪制通路-基因網絡圖。
1.6 分子對接
將PPI網絡的關鍵靶點和通路-基因網絡圖中的核心基因與扶正養(yǎng)心方的主要成分進行分子對接。通過Protein Data Bank(https://www.rcsb.org/)下載核心靶點的蛋白3D格式[24],借助PyMOL 2.5軟件對蛋白進行去水、加氫、提取配體等操作,AutoDock Vina 1.1.2軟件進行分子對接。
2 結 果
2.1 基于GEO數據庫心力衰竭差異基因分析
GEO數據庫下載GSE26887芯片與平臺文件,獲取12個心力衰竭與7個心力衰竭合并糖尿病的樣本數據。利用R及其相關軟件包對數據進行過濾及標準化,篩選差異基因。得到心力衰竭與心力衰竭合并糖尿病差異基因108個(上調73個、下調35個),分別取上調和下調最明顯的前20個基因,分析并繪制熱圖與火山圖。詳見圖1。
2.2 扶正養(yǎng)心方有效成分和靶點
經過數據庫篩選獲得活性成分,人參158個,附子52個,黃芪31個,麥冬39個,當歸97個,生地13個,紅景天4個,三七79個,去重后獲得403個活性成分。經過數據庫篩選獲得作用靶點,人參1 793個,附子304個,黃芪640個,麥冬487個,當歸1 267個,生地487個,紅景天124個,三七1206個,去重后獲得2 364個作用靶點。詳見表1。
2.3 構建藥物-疾病交集靶基因數據庫并建立中藥復方調控網絡
將獲得的扶正養(yǎng)心方靶基因與疾病基因取交集,共獲得15個交集基因(見圖2),以Cytoscape 3.8.2軟件構建“有效成分-交集基因”中藥復方調控網絡圖,包含120個節(jié)點(15個基因、105個成分)和124條邊。節(jié)點之間的連接代表這些節(jié)點的功能關系。詳見圖3。連接節(jié)點數量越多提示目標或化合物在該網絡中的作用越重要。使用網絡分析功能計算網絡度。度數較多的活性成分包括豆甾醇、山柰酚、槲皮素、熊竹素等。
2.4 PPI網絡及其拓撲分析
采用BisoGenet對15個交集基因進行PPI網絡構建,包括651個節(jié)點和7 208條邊。通過CytoNCA軟件包篩選最終得到27個關鍵節(jié)點和181條邊,篩選策略見圖4。基于核心網絡,將NOTCH1蛋白定義為PPI核心網絡中的關鍵蛋白。
2.5 GO富集分析結果
對15個交集關鍵基因進行GO功能分析,結果以P<0.05篩選。富集結果包括565個BP、13個CC、4個MF。BP主要涉及細胞趨化(cell chemotaxis)、趨化調節(jié)(regulation of chemotaxis)、離子轉運(regulation of metal ion transport)、傷口愈合的正向調節(jié)(positive regulation of wound healing)等方面;CC主要涉及離子通道(ion channel complex)、跨膜轉運體(transmembrane transporter complex)、轉運體(transporter complex)、外側質膜(external side of plasma membrane)、富含膠原的細胞外基質(collagen-containing extracellular matrix)、細胞連接(cell-cell junction)、血小板α顆粒(platelet alpha granule lumen)等;MF涉及細胞因子結合(cytokine binding)、跨膜受體蛋白酪氨酸激酶活性(transmembrane receptor protein tyrosine kinase activity)、膠原連接(collagen binding)、跨膜受體蛋白激酶活性(transmembrane receptor protein kinase activity)。BP和CC的前10項及MF的4項見圖5。
2.6 KEGG富集分析結果
KEGG通路富集分析共獲得18條信號通路。KEGG富集分析結果提示扶正養(yǎng)心方作用機制可能與RAS相關蛋白1信號通路(RAS-associated protein 1,Rap1 signaling pathway)、磷脂酰肌醇3-激酶(phosphatidylinositol 3 kinase,PI3K)-蛋白激酶B(protein kinase B,AKT)信號通路、磷脂酶D信號通路(phospholipase D signaling pathway)、肌動蛋白細胞骨架調節(jié)(regulation of actin cytoskeleton)、鈣信號通路(calcium signaling pathway)、絲裂原活化蛋白激酶(mitogen-activated protein kinase,MAPK)信號通路、p53信號通路(p53 signaling pathway)有關。采用Cytoscape 3.8.2構建“通路-基因”網絡,詳見圖6。結果顯示在15個關鍵基因中血小板衍生生長因子受體β(platelet-derived growth factor receptor β,PDGFRB)、凝血因子Ⅱ凝血酶受體(coagulation factor Ⅱ thrombin receptor,F2R)和KIT原癌基因酪氨酸蛋白激酶(KIT proto-oncogene,receptor tyrosine kinase,KIT)為富集最多的基因,提示這些基因與扶正養(yǎng)心方作用機制高度相關。詳見圖7。
2.7 分子對接
將豆甾醇、山柰酚、槲皮素、熊竹素作為小分子配體,合并基因缺口受體蛋白1(notch receptor 1,NOTCH1)、PDGFRB、F2R和KIT作為蛋白受體進行分子對接,并獲得其結合能。結合能<0提示配體和受體可自發(fā)結合,對接結果的親和力值越小,目標與活性成分之間的相互作用越穩(wěn)定(見表2)。通過分子對接發(fā)現,上述4個重要靶點與4個主要活性成分具有良好的結合活性。選取前10個的對接結果進行可視化分析。詳見圖8。
(A為山柰酚與KIT結合模式;B為槲皮素與中KIT結合模式;C為豆甾醇與F2R結合模式;D為熊竹素與F2R結合模式;E山柰酚為與F2R結合模式;F為槲皮素與F2R結合模式;G為豆甾醇與NOTCH1結合模式;H為山柰酚與NOTCH1結合模式;I為熊竹素與NOTCH1結合模式;J為槲皮素與NOTCH1結合模式。圖中虛線為氫鍵,數值為鍵長)
3 討 論
心力衰竭合并糖尿病是臨床常見的問題,病理機制復雜,可能與能量代謝紊亂、晚期糖基化終產物形成增加,影響細胞外基質、胰島素抵抗、線粒體質量下降、炎癥和氧化應激有關[25]。
扶正養(yǎng)心方是在陳可冀院士活血化瘀思想指導下總結臨床多年收治心力衰竭病人診療經驗組合而成的方藥,臨床改善心力衰竭辨證為陰血不足、陽氣虛弱、心脈失養(yǎng)的病人療效顯著。扶正養(yǎng)心方治療心力衰竭合并糖尿病與中醫(yī)提倡的“異病同治”理論符合,但內在作用機制尚未明確。方中附子溫陽,人參、黃芪、紅景天補氣,麥冬、生地滋陰,當歸、三七養(yǎng)血活血,共奏溫陽益氣、滋陰養(yǎng)血之效。
應用網絡藥理學和生物信息學結合進一步探討扶正養(yǎng)心方的作用機制,結果表明,活性成分共403種,與治療心力衰竭合并糖尿病的有105種,包括豆甾醇、山柰酚、槲皮素、熊竹素等。這些成分的作用已有研究報道,豆甾醇可增加葡萄糖轉運蛋白4(glucose transporter type 4,GLUT4)易位和表達[26]。山柰酚通過介導kappa B抑制因子激酶(inhibitor of kappa B kinase,IKK)下調并抑制核因子-kappa B(nuclear factor kappa-B,NF-κB)通路激活,抑制肝臟炎癥病變,減輕胰島素抵抗[27];山柰酚通過減少晚期糖基化終產物(advanced glycation end product,AGE)-晚期糖基化終產物受體(receptor for advanced glycation end product,RAGE)/MAPK誘導的氧化應激和炎癥,減輕糖尿病大鼠的心肌缺血再灌注損傷[28];抑制 NF-κB和核因子E2相關因子2(nuclear factor erythroid 2-related factor 2,Nrf-2)激活,抑制糖尿病誘導的心臟纖維化和細胞凋亡[29]。糖尿病大鼠給予槲皮素干預后,空腹血糖和心臟損傷標志物水平降低,胰島素水平升高,氧化應激、炎癥和細胞凋亡水平降低[30]。
將扶正養(yǎng)心方的靶基因與GEO數據庫的疾病基因取交集,獲得15個交集基因。進一步的PPI網絡分析發(fā)現,NOTCH1蛋白是PPI核心網絡中的關鍵蛋白。NOTCH1是NOTCH受體家族中研究廣泛的Ⅰ型跨膜蛋白,可介導生長發(fā)育過程中重要的細胞通信。NOTCH1從核糖體翻譯出來,在內質網中發(fā)生折疊、修飾,轉移到高爾基體中進一步切割。當NOTCH1到達細胞膜,與相鄰細胞上的配體結合,4種主要的典型配體包括Delta樣典型Notch配體1(Delta like canonical Notch ligand 1,DLL1)、Delta樣典型Notch配體4(DLL4)、鋸齒狀典型Notch配體1(jagged canonical Notch ligand 1,JAG1)和鋸齒狀典型Notch配體2(JAG2)[31]。抑制NOTCH1可破壞血糖穩(wěn)態(tài),減少體內和體外的胰島素分泌及胰島β細胞質量[32],與糖尿病的發(fā)展密切相關。NOTCH1通過改善線粒體質量,提供心肌保護[33],JAG1的細胞內結構域在調節(jié)心臟生理和病理性肥大中發(fā)揮著重要作用[34]。
KEGG通路富集分析結果共獲得18條信號通路。Rap1是保守的端粒相互作用蛋白,除在細胞核內維持端粒功能的作用外,與代謝、炎癥和氧化應激相關的各種生理和病理條件下功能相關[35]。NF-κB和過氧化物酶體增殖物激活受體-α(peroxisome proliferators-activated receptor α,PPAR-α)已成為Rap1信號通路的下游效應器。NF-κB激活導致細胞因子激活,引起心肌細胞死亡,進而觸發(fā)慢性炎癥[36],PPARα與調節(jié)心臟能量代謝、心血管健康和疾病相關的各種細胞信號通路有關[37]。PI3K/AKT信號通路是經典的細胞內信號轉導通路,可響應細胞外信號,促進代謝、增殖、細胞存活、生長和血管生成。激活PI3K/AKT信號通路可減輕氧化應激和內質網應激誘導的細胞凋亡,從而保護心肌缺血再灌注損傷[38];糖尿病病人心血管病理變化通過PI3K/AKT信號通路被選擇性抑制[39]。磷脂酶D可水解磷脂酰膽堿產生磷脂酸,磷脂酸是影響心臟肥大、缺血性心臟病和充血性心力衰竭等多種心臟功能的重要磷脂信號分子[40]。肌動蛋白細胞骨架是細胞的中央骨架,細胞結構變化常伴隨肌動蛋白變化,激動蛋白變化又引起細胞結構變化[41]。肌動蛋白細胞骨架響應心肌細胞外基質的機械變化,發(fā)生重新排列,并參與成纖維細胞-肌成纖維細胞分化,進而影響心臟重塑[42]。細胞外基質的變化除與機械信號有關外,也受化學信號的影響,MAPK信號通路是化學和機械應力信號激活成纖維細胞向成纖維細胞狀態(tài)轉變的中心調節(jié)劑[43]。PDGFRB是與通路富集相關最多的基因,心肌中的PDGFRB信號隨著年齡的增長而減少,且激活心肌細胞中PDGFRB可促進心肌細胞增殖[44];心臟缺血再灌注模型[45]和壓力負荷模型[46]中,PDGFRB可改善心臟微循環(huán)。
綜上所述,利用網絡藥理學和生物信息學揭示了扶正養(yǎng)心方治療心力衰竭合并糖尿病的潛在活性成分及作用機制。今后研究中,通過體內、體外實驗進行驗證,以期為扶正養(yǎng)心方、中醫(yī)復方的基礎研究提供思路。
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(收稿日期:2022-05-25)
(本文編輯薛妮)
基金項目 國家重點研發(fā)計劃課題項目(No.2018YFC1707410-02);首都臨床特色應用研究項目(No.Z181100001718128)
作者單位 中國中醫(yī)科學院西苑醫(yī)院(北京" 100091)
通訊作者 馬曉昌,E-mail:maxiaochang@x263.net
引用信息 王安鑄,馬曉昌.基于網絡藥理學和生物信息學探討扶正養(yǎng)心方治療心力衰竭合并糖尿病的機制[J].中西醫(yī)結合心腦血管病雜志,2023,21(16):2897-2908.