Objective:To seek potential Chinese herbal medicine(CHM)for the treatment of coronavirus disease 2019(COVID-19)through the molecular docking of the medicine with SARS-CoV-23 CL hydrolytic enzyme and the angiotensin co...Objective:To seek potential Chinese herbal medicine(CHM)for the treatment of coronavirus disease 2019(COVID-19)through the molecular docking of the medicine with SARS-CoV-23 CL hydrolytic enzyme and the angiotensin converting enzymeⅡ(ACE2)as receptors,using computer virtual screening technique,so as to provide a basis for combination forecasting.Methods:The molecular docking of CHM with the SARS-Cov-23 CL hydrolase and the ACE2 converting enzyme,which were taken as the targets,was achieved by the Autodock Vina software.The CHM monomers acting on 3 CLpro and ACE2 receptors were retrieved from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform,the active ingredients were selected,and the key CHMs and compounds were speculated.Based on the perspective of network pharmacology,the chemical-target network was constructed,and the functional enrichment analysis of gene ontology and the pathway enrichment analysis of Kyoto encyclopedia of genes and genomes were carried out by DAVID to speculate about the mechanism of action of the core drug pairs.Results:There are6 small molecule compounds that have the optimal binding energy with the two target proteins.Among 238 potential anti-COVID-19 herbs screened in total,16 kinds of CHM containing the most active ingredients,and5 candidate anti-COVID-19 herbs that had been used in high frequency,as well as a core drug pair,namely,Forsythiae Fructus-Lonicerae Japonicae Flos were selected.Conclusion:The core drug pair of Forsythiae Fructus-Lonicerae Japonicae Flos containing multiple components and targets is easy to combine with 3 CLpro and ACE2,and exerts an anti-COVID-19 pneumonia effect through multi-component and multi-target,and plays the role of anti-COVID-19 pneumonia in multi-pathway.展开更多
目的研究蝙蝠来源的重症急性呼吸综合征(SARS)样冠状病毒WIV1刺突蛋白利用浣熊狗血管紧张素转换酶Ⅱ(ACE2)受体侵入细胞的能力,并探究SARS样冠状病毒WIV1潜在的跨宿主传播风险。方法构建来自浣熊狗、果子狸、中华菊头蝠和人等不同动物...目的研究蝙蝠来源的重症急性呼吸综合征(SARS)样冠状病毒WIV1刺突蛋白利用浣熊狗血管紧张素转换酶Ⅱ(ACE2)受体侵入细胞的能力,并探究SARS样冠状病毒WIV1潜在的跨宿主传播风险。方法构建来自浣熊狗、果子狸、中华菊头蝠和人等不同动物来源的ACE2表达质粒,转染至293T细胞并利用免疫印迹方法检测其在293T细胞中的表达水平;建立SARS冠状病毒(Tor2株系)及蝙蝠SARS样冠状病毒(WIV1株系)假病毒感染系统,并进行假病毒感染实验;利用假病毒感染系统及荧光素酶报告基因检测WIV1刺突蛋白对浣熊狗等不同动物来源ACE2受体利用能力;构建跨膜丝氨酸蛋白酶2(TMPRSS2)质粒,并转染至T Rex 293细胞,借助假病毒感染系统检测TMPRSS2对WIV1侵入能力的影响。结果本研究所获赠及构建的不同动物来源的ACE2质粒可经瞬时转染至细胞进行表达;与pc DNA3.1载体相比,浣熊狗、中华菊头蝠、果子狸和人的ACE2均可使蝙蝠SARS样冠状病毒WIV1侵入细胞的能力增加上万倍,上述ACE2组与载体组的荧光素酶活性差异均具有统计学意义(t=27.744、P<0.001,t=18.740、P<0.001,t=32.297、P<0.001,t=15.902、P<0.001);与TMPRSS2阴性组相比,TMPRSS2在靶细胞的表达可使WIV1假病毒的感染能力增加10倍以上,两组荧光素酶活性差异具有统计学意义(t=29.460、P<0.001)。结论蝙蝠SARS样冠状病毒WIV1的刺突蛋白除了利用人类、果子狸及中华菊头蝠的ACE2受体感染细胞,还可利用浣熊狗的ACE2受体侵入细胞,且TMPRSS2可显著促进其侵入能力,提示WIV1可能存在多种跨宿主传播的风险。展开更多
Background:Macrophages are involved in the pathogenesis of idiopathic pulmonary fibrosis,partially by activating lung fibroblasts.However,how macrophages communicate with lung fibroblasts is largely unexplored.Exosome...Background:Macrophages are involved in the pathogenesis of idiopathic pulmonary fibrosis,partially by activating lung fibroblasts.However,how macrophages communicate with lung fibroblasts is largely unexplored.Exosomes can mediate intercellular communication,whereas its role in lung fibrogenesis is unclear.Here we aim to investigate whether exosomes can mediate the crosstalk between macrophages and lung fibroblasts and subsequently induce fibrosis.Methods:In vivo,bleomycin(BLM)-induced lung fibrosis model was established and macrophages infiltration was examined.The effects of GW4869,an exosomes inhibitor,on lung fibrosis were assessed.Moreover,macrophage exosomes were injected into mice to observe its pro-fibrotic effects.In vitro,exosomes derived from angiotensin Ⅱ(Ang Ⅱ)-stimulated macrophages were collected.Then,lung fibroblasts were treated with the exosomes.Twenty-four hours later,protein levels ofα-collagen I,angiotensin Ⅱ type 1 receptor(AT1R),transforming growth factor-β(TGF-β),and phospho-Smad2/3(p-Smad2/3)in lung fibroblasts were examined.The Student's t test or analysis of variance were used for statistical analysis.Results:In vivo,BLM-treated mice showed enhanced infiltration of macrophages,increased fibrotic alterations,and higher levels of Ang Ⅱ and AT1R.GW4869 attenuated BLM-induced pulmonary fibrosis.Mice with exosomes injection showed fibrotic features with higher levels of Ang Ⅱ and AT1R,which was reversed by irbesartan.In vitro,we found that macrophages secreted a great number of exosomes.The exosomes were taken by fibroblasts and resulted in higher levels of AT1R(0.22±0.02 vs.0.07±0.02,t=8.66,P=0.001),TGF-β(0.54±0.05 vs.0.09±0.06,t=10.00,P<0.001),p-Smad2/3(0.58±0.06 vs.0.07±0.03,t=12.86,P<0.001)andα-collagen I(0.27±0.02 vs.0.16±0.01,t=7.01,P=0.002),and increased Ang Ⅱ secretion(62.27±7.32 vs.9.56±1.68,t=12.16,P<0.001).Interestingly,Ang Ⅱ increased the number of macrophage exosomes,and the protein levels of Alix(1.45±0.15 vs.1.00±0.10,t=4.32,P=0.012),AT1R(4.05±0.64 vs.1.00±0.09,t=8.17,P=0.001),and glyceraldehyde-3-phosphate dehydrogenase(2.13±0.36 vs.1.00±0.10,t=5.28,P=0.006)were increased in exosomes secreted by the same number of macrophages,indicating a positive loop between Ang Ⅱ and exosomes production.Conclusions:Exosomes mediate intercellular communication between macrophages and fibroblasts plays an important role in BLM-induced pulmonary fibrosis.展开更多
目的:基于网络药理学及分子对接技术探讨香连片对新型冠状病毒肺炎(Corona Virus Disease 2019, COVID-19)的作用机制。方法:通过中药系统药理学数据库与分析平台(Traditional Chinese Medicine Systems Pharmacology Database and Anal...目的:基于网络药理学及分子对接技术探讨香连片对新型冠状病毒肺炎(Corona Virus Disease 2019, COVID-19)的作用机制。方法:通过中药系统药理学数据库与分析平台(Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform, TCMSP)、PubChem数据库、生物信息学分析工具(a bioinformatics analysis tool for molecular mechanism of traditional Chinese medicine, BATMAN-TCM)及SwissTarget Prediction平台查询香连片活性成分及其对应的靶点基因;根据大于2倍中位数的节点度值(degree)为条件,筛选香连片关键活性成分,并运用Cytoscape 3.6.1软件绘制关键活性成分-对应靶点网络;通过GeneCards及PHARMGKB疾病数据库,以"coronavirus pneumonia"、"COVID-19"及"SARS-CoV-2"为关键词进行检索疾病靶点基因。运用Cytoscape 3.6.1软件进行交集,得到共同靶点并构建成分-靶点-疾病网络图;通过STRING网站对共同靶点构建蛋白相互作用(Protein Protein interaction, PPI)网络,通过DAVID数据库对共同靶点进行基因本位(gene ontology, GO)和京都基因与基因组百科全书(Kyoto encyclopedia of genes and genomes, KEGG)分析;利用CB-Dock网站对筛选出的活性成分及抗病毒化药和SARS-CoV-2 3CL水解酶及血管紧张素转化酶Ⅱ (angiotensin converting enzyme Ⅱ, ACE2)进行分子对接。结果:香连片共得到41个活性成分,其中16个关键活性成分,并与疾病靶点相交得到24个共同靶点;GO功能富集得到分子功能(molecular function, MF)、细胞组分(cellular component, CC)及其所参与的生物过程(biological process, BP)分别为125条、16条及24条;KEGG富集得到94条通路,其通路多与免疫反应和炎症反应有关,主要有PI3K-Akt、Ras、HIF-1、MAPK、NF-kB以及TNF等信号通路;分子对接得出黄柏酮、氧化小檗碱、吴茱萸碱、吴茱萸次碱及豆甾醇等多种成分与SARS-CoV-2 3CL水解酶及ACE2的对接亲和力均强于2种临床化学药物(阿比多尔及利巴韦林)。结论:香连片多是通过作用于MAPK家族、IL1B、NFKB1、CASP3、CCL5、TNF等靶点因子来调节PI3K-Akt、MAPK、NF-kB及TNF等炎症免疫通路,以多成分、多靶点、多途径参与COVID-19的多种生理过程,从而对COVID-19有一定治疗作用;在中药成分上,黄柏酮、氧化小檗碱、吴茱萸碱、吴茱萸次碱、豆甾醇、吴茱萸酰胺类成分等可以很好作用于COVID-19治疗中涉及到的2种关键酶(SARS-CoV-2 3CL水解酶及ACE2),故这几种中药单体成分有作为治疗COVID-19的新药潜能。展开更多
目的:通过网络药理学和分子对接技术挖掘《新型冠状病毒肺炎诊疗方案(试行第七版)》中具有清热功效的中药治疗COVID-19的共有活性成分及作用机制。方法:通过TCMSP数据库及BATMAN-TCM数据库检索清热药的化学成分和作用靶点;通过UniProt...目的:通过网络药理学和分子对接技术挖掘《新型冠状病毒肺炎诊疗方案(试行第七版)》中具有清热功效的中药治疗COVID-19的共有活性成分及作用机制。方法:通过TCMSP数据库及BATMAN-TCM数据库检索清热药的化学成分和作用靶点;通过UniProt数据库检索靶点对应基因,运用Cytoscape Version 3.7.2软件绘制药物-化合物-靶点网络;利用STRING数据库绘制靶点间作用关系网络;通过DAVID数据库进行GO功能富集分析及KEGG通路富集分析;利用Autodock软件对筛选出的活性成分及抗病毒化药和SARS-CoV-23CL水解酶及ACE2进行分子对接。结果:药物-化合物-靶点网络共有401个节点(15个药物节点,120个化合物节点,266个靶点节点);GO条目1422个(P<0.05);KEGG通路富集筛选共得到61条通路(P<0.05);分子对接结果显示脱水淫羊藿素、木犀草素、槲皮素等关键化合物具有与抗病毒化药相近或更好的亲和力。结论:清热药通过与ACE2结合调控多条通路、与病毒特定部位的结合阻断病毒入侵及抑制炎症因子风暴等方面达到治疗COVID-19的作用。展开更多
基金Supported by the Fundamental Research Funds for the Central Central University,Scientific Research Project on Prevention and Treatment Emergency in Novel Coronavirus(No.20720200034)。
文摘Objective:To seek potential Chinese herbal medicine(CHM)for the treatment of coronavirus disease 2019(COVID-19)through the molecular docking of the medicine with SARS-CoV-23 CL hydrolytic enzyme and the angiotensin converting enzymeⅡ(ACE2)as receptors,using computer virtual screening technique,so as to provide a basis for combination forecasting.Methods:The molecular docking of CHM with the SARS-Cov-23 CL hydrolase and the ACE2 converting enzyme,which were taken as the targets,was achieved by the Autodock Vina software.The CHM monomers acting on 3 CLpro and ACE2 receptors were retrieved from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform,the active ingredients were selected,and the key CHMs and compounds were speculated.Based on the perspective of network pharmacology,the chemical-target network was constructed,and the functional enrichment analysis of gene ontology and the pathway enrichment analysis of Kyoto encyclopedia of genes and genomes were carried out by DAVID to speculate about the mechanism of action of the core drug pairs.Results:There are6 small molecule compounds that have the optimal binding energy with the two target proteins.Among 238 potential anti-COVID-19 herbs screened in total,16 kinds of CHM containing the most active ingredients,and5 candidate anti-COVID-19 herbs that had been used in high frequency,as well as a core drug pair,namely,Forsythiae Fructus-Lonicerae Japonicae Flos were selected.Conclusion:The core drug pair of Forsythiae Fructus-Lonicerae Japonicae Flos containing multiple components and targets is easy to combine with 3 CLpro and ACE2,and exerts an anti-COVID-19 pneumonia effect through multi-component and multi-target,and plays the role of anti-COVID-19 pneumonia in multi-pathway.
文摘目的研究蝙蝠来源的重症急性呼吸综合征(SARS)样冠状病毒WIV1刺突蛋白利用浣熊狗血管紧张素转换酶Ⅱ(ACE2)受体侵入细胞的能力,并探究SARS样冠状病毒WIV1潜在的跨宿主传播风险。方法构建来自浣熊狗、果子狸、中华菊头蝠和人等不同动物来源的ACE2表达质粒,转染至293T细胞并利用免疫印迹方法检测其在293T细胞中的表达水平;建立SARS冠状病毒(Tor2株系)及蝙蝠SARS样冠状病毒(WIV1株系)假病毒感染系统,并进行假病毒感染实验;利用假病毒感染系统及荧光素酶报告基因检测WIV1刺突蛋白对浣熊狗等不同动物来源ACE2受体利用能力;构建跨膜丝氨酸蛋白酶2(TMPRSS2)质粒,并转染至T Rex 293细胞,借助假病毒感染系统检测TMPRSS2对WIV1侵入能力的影响。结果本研究所获赠及构建的不同动物来源的ACE2质粒可经瞬时转染至细胞进行表达;与pc DNA3.1载体相比,浣熊狗、中华菊头蝠、果子狸和人的ACE2均可使蝙蝠SARS样冠状病毒WIV1侵入细胞的能力增加上万倍,上述ACE2组与载体组的荧光素酶活性差异均具有统计学意义(t=27.744、P<0.001,t=18.740、P<0.001,t=32.297、P<0.001,t=15.902、P<0.001);与TMPRSS2阴性组相比,TMPRSS2在靶细胞的表达可使WIV1假病毒的感染能力增加10倍以上,两组荧光素酶活性差异具有统计学意义(t=29.460、P<0.001)。结论蝙蝠SARS样冠状病毒WIV1的刺突蛋白除了利用人类、果子狸及中华菊头蝠的ACE2受体感染细胞,还可利用浣熊狗的ACE2受体侵入细胞,且TMPRSS2可显著促进其侵入能力,提示WIV1可能存在多种跨宿主传播的风险。
基金supported by the Science and Technology Project in Guangzhou(No.201904010482)the National Natural Science Foundation of China(Nos.81570064,81870068,and 82070063).
文摘Background:Macrophages are involved in the pathogenesis of idiopathic pulmonary fibrosis,partially by activating lung fibroblasts.However,how macrophages communicate with lung fibroblasts is largely unexplored.Exosomes can mediate intercellular communication,whereas its role in lung fibrogenesis is unclear.Here we aim to investigate whether exosomes can mediate the crosstalk between macrophages and lung fibroblasts and subsequently induce fibrosis.Methods:In vivo,bleomycin(BLM)-induced lung fibrosis model was established and macrophages infiltration was examined.The effects of GW4869,an exosomes inhibitor,on lung fibrosis were assessed.Moreover,macrophage exosomes were injected into mice to observe its pro-fibrotic effects.In vitro,exosomes derived from angiotensin Ⅱ(Ang Ⅱ)-stimulated macrophages were collected.Then,lung fibroblasts were treated with the exosomes.Twenty-four hours later,protein levels ofα-collagen I,angiotensin Ⅱ type 1 receptor(AT1R),transforming growth factor-β(TGF-β),and phospho-Smad2/3(p-Smad2/3)in lung fibroblasts were examined.The Student's t test or analysis of variance were used for statistical analysis.Results:In vivo,BLM-treated mice showed enhanced infiltration of macrophages,increased fibrotic alterations,and higher levels of Ang Ⅱ and AT1R.GW4869 attenuated BLM-induced pulmonary fibrosis.Mice with exosomes injection showed fibrotic features with higher levels of Ang Ⅱ and AT1R,which was reversed by irbesartan.In vitro,we found that macrophages secreted a great number of exosomes.The exosomes were taken by fibroblasts and resulted in higher levels of AT1R(0.22±0.02 vs.0.07±0.02,t=8.66,P=0.001),TGF-β(0.54±0.05 vs.0.09±0.06,t=10.00,P<0.001),p-Smad2/3(0.58±0.06 vs.0.07±0.03,t=12.86,P<0.001)andα-collagen I(0.27±0.02 vs.0.16±0.01,t=7.01,P=0.002),and increased Ang Ⅱ secretion(62.27±7.32 vs.9.56±1.68,t=12.16,P<0.001).Interestingly,Ang Ⅱ increased the number of macrophage exosomes,and the protein levels of Alix(1.45±0.15 vs.1.00±0.10,t=4.32,P=0.012),AT1R(4.05±0.64 vs.1.00±0.09,t=8.17,P=0.001),and glyceraldehyde-3-phosphate dehydrogenase(2.13±0.36 vs.1.00±0.10,t=5.28,P=0.006)were increased in exosomes secreted by the same number of macrophages,indicating a positive loop between Ang Ⅱ and exosomes production.Conclusions:Exosomes mediate intercellular communication between macrophages and fibroblasts plays an important role in BLM-induced pulmonary fibrosis.
文摘目的通过网络药理学及分子对接技术预测金振口服液(Jinzhen Oral Liquid,JOL)干预新型冠状病毒肺炎(COVID-19)的作用机制。方法通过文献挖掘以及DisGeNET、OMIM、KEGG、UniProt数据库联用检索与COVID-19相关的蛋白靶点。借助Traditional Chinese Medicine Network(TCMN)信息平台检索JOL中的化合物,运用Cytoscape3.2.1构建药材-化合物-靶点网络来预测JOL治疗COVID-19的活性成分及作用靶点。在RCSBPDB数据库中检索获取新型冠状病毒(SARS-CoV-2)3CL水解酶(3CLpro)和血管紧张素转化酶Ⅱ(ACE2)的晶体结构,借助AutoDock Vina软件将活性化合物与2个蛋白进行分子对接。结果药材-化合物-靶点网络包含异甘草酸内酯、贝母辛、番泻苷B等75个化合物分别来自甘草、大黄和平贝母3味药材,哺乳动物雷帕霉素靶蛋白(m TOR)、Janus激酶3(JAK3)、丝裂原活化蛋白激酶激酶1(MEK1)等28个靶点。网络特征分析阐明了JOL治疗COVID-19的9个关键化合物(异甘草酸内酯、甘草内酯、去氢鄂贝定碱、desoxo-glabrolid-acetate、贝母辛、贝母素乙、乌苏里啶酮、西贝素和euchrenone A5)以及10个潜在作用靶(m TOR、JAK3、ACE2、TNFA、AKT2、PIK3CA、MEK1、BRD2、ACE、ANPEP)。分子对接显示,JOL中部分活性化合物对3CLpro和ACE2蛋白具有一定的亲和力。结论JOL可能是通过调节溴结构域包含蛋白2(Brd2)、氨肽酶N(CD13)和ACE2的表达以及干预PI3K/Akt、Jak-STAT、TNF和MAPK信号通路来遏制COVID-19细胞因子风暴的发生和发展,并与3CLpro结合抑制病毒复制,从而有可能对COVID-19有防治作用。
文摘目的:基于网络药理学及分子对接技术探讨香连片对新型冠状病毒肺炎(Corona Virus Disease 2019, COVID-19)的作用机制。方法:通过中药系统药理学数据库与分析平台(Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform, TCMSP)、PubChem数据库、生物信息学分析工具(a bioinformatics analysis tool for molecular mechanism of traditional Chinese medicine, BATMAN-TCM)及SwissTarget Prediction平台查询香连片活性成分及其对应的靶点基因;根据大于2倍中位数的节点度值(degree)为条件,筛选香连片关键活性成分,并运用Cytoscape 3.6.1软件绘制关键活性成分-对应靶点网络;通过GeneCards及PHARMGKB疾病数据库,以"coronavirus pneumonia"、"COVID-19"及"SARS-CoV-2"为关键词进行检索疾病靶点基因。运用Cytoscape 3.6.1软件进行交集,得到共同靶点并构建成分-靶点-疾病网络图;通过STRING网站对共同靶点构建蛋白相互作用(Protein Protein interaction, PPI)网络,通过DAVID数据库对共同靶点进行基因本位(gene ontology, GO)和京都基因与基因组百科全书(Kyoto encyclopedia of genes and genomes, KEGG)分析;利用CB-Dock网站对筛选出的活性成分及抗病毒化药和SARS-CoV-2 3CL水解酶及血管紧张素转化酶Ⅱ (angiotensin converting enzyme Ⅱ, ACE2)进行分子对接。结果:香连片共得到41个活性成分,其中16个关键活性成分,并与疾病靶点相交得到24个共同靶点;GO功能富集得到分子功能(molecular function, MF)、细胞组分(cellular component, CC)及其所参与的生物过程(biological process, BP)分别为125条、16条及24条;KEGG富集得到94条通路,其通路多与免疫反应和炎症反应有关,主要有PI3K-Akt、Ras、HIF-1、MAPK、NF-kB以及TNF等信号通路;分子对接得出黄柏酮、氧化小檗碱、吴茱萸碱、吴茱萸次碱及豆甾醇等多种成分与SARS-CoV-2 3CL水解酶及ACE2的对接亲和力均强于2种临床化学药物(阿比多尔及利巴韦林)。结论:香连片多是通过作用于MAPK家族、IL1B、NFKB1、CASP3、CCL5、TNF等靶点因子来调节PI3K-Akt、MAPK、NF-kB及TNF等炎症免疫通路,以多成分、多靶点、多途径参与COVID-19的多种生理过程,从而对COVID-19有一定治疗作用;在中药成分上,黄柏酮、氧化小檗碱、吴茱萸碱、吴茱萸次碱、豆甾醇、吴茱萸酰胺类成分等可以很好作用于COVID-19治疗中涉及到的2种关键酶(SARS-CoV-2 3CL水解酶及ACE2),故这几种中药单体成分有作为治疗COVID-19的新药潜能。
文摘目的:通过网络药理学和分子对接技术挖掘《新型冠状病毒肺炎诊疗方案(试行第七版)》中具有清热功效的中药治疗COVID-19的共有活性成分及作用机制。方法:通过TCMSP数据库及BATMAN-TCM数据库检索清热药的化学成分和作用靶点;通过UniProt数据库检索靶点对应基因,运用Cytoscape Version 3.7.2软件绘制药物-化合物-靶点网络;利用STRING数据库绘制靶点间作用关系网络;通过DAVID数据库进行GO功能富集分析及KEGG通路富集分析;利用Autodock软件对筛选出的活性成分及抗病毒化药和SARS-CoV-23CL水解酶及ACE2进行分子对接。结果:药物-化合物-靶点网络共有401个节点(15个药物节点,120个化合物节点,266个靶点节点);GO条目1422个(P<0.05);KEGG通路富集筛选共得到61条通路(P<0.05);分子对接结果显示脱水淫羊藿素、木犀草素、槲皮素等关键化合物具有与抗病毒化药相近或更好的亲和力。结论:清热药通过与ACE2结合调控多条通路、与病毒特定部位的结合阻断病毒入侵及抑制炎症因子风暴等方面达到治疗COVID-19的作用。
