Acquired immunodeficiency syndrome (AIDS) is a fatal disease which highly threatens the health of human being. Human immunodeficiency virus (HIV) is the pathogeny for this disease. Investigating HIV-1 protease cleavag...Acquired immunodeficiency syndrome (AIDS) is a fatal disease which highly threatens the health of human being. Human immunodeficiency virus (HIV) is the pathogeny for this disease. Investigating HIV-1 protease cleavage sites can help researchers find or develop protease inhibitors which can restrain the replication of HIV-1, thus resisting AIDS. Feature selection is a new approach for solving the HIV-1 protease cleavage site prediction task and it’s a key point in our research. Comparing with the previous work, there are several advantages in our work. First, a filter method is used to eliminate the redundant features. Second, besides traditional orthogonal encoding (OE), two kinds of newly proposed features extracted by conducting principal component analysis (PCA) and non-linear Fisher transformation (NLF) on AAindex database are used. The two new features are proven to perform better than OE. Third, the data set used here is largely expanded to 1922 samples. Also to improve prediction performance, we conduct parameter optimization for SVM, thus the classifier can obtain better prediction capability. We also fuse the three kinds of features to make sure comprehensive feature representation and improve prediction performance. To effectively evaluate the prediction performance of our method, five parameters, which are much more than previous work, are used to conduct complete comparison. The experimental results of our method show that our method gain better performance than the state of art method. This means that the feature selection combined with feature fusion and classifier parameter optimization can effectively improve HIV-1 cleavage site prediction. Moreover, our work can provide useful help for HIV-1 protease inhibitor developing in the future.展开更多
Quantitative structure–activity relationship study using artificial neural network (ANN) methodology were conducted to predict the inhibition constants of 127 symmetrical and unsymmetrical cyclic urea and cyclic cyan...Quantitative structure–activity relationship study using artificial neural network (ANN) methodology were conducted to predict the inhibition constants of 127 symmetrical and unsymmetrical cyclic urea and cyclic cyanoguanidine derivatives containing different substituent groups such as: benzyl, isopropyl, 4-hydroxybenzyl, ketone, oxime, pyrazole, imidazole, triazole and having anti-HIV-1 protease activities. The results obtained by artificial neural network give advanced regression models with good prediction ability. The two optimal artificial neural network models obtained have coefficients of determination of 0.746 and 0.756. The lowest prediction’s root mean square error obtained is 0.607. Artificial neural networks provide improved models for heterogeneous data sets without splitting them into families. Both the external and cross-validation methods are used to validate the performances of the resulting models. Randomization test is employed to check the suitability of the models.展开更多
Site-directed spin-labeling with continuous wave electron paramagnetic resonance spectroscopy was used to monitor autoproteolysis of HIV-1 protease, an enzyme essential for viral maturation. Two protein constructs wer...Site-directed spin-labeling with continuous wave electron paramagnetic resonance spectroscopy was used to monitor autoproteolysis of HIV-1 protease, an enzyme essential for viral maturation. Two protein constructs were examined, namely subtype F and the circulating recombinant form CRF01_A/E. As the protease undergoes self-cleavage, protein unfolds and small peptide fragments containing the spin label are generated, which collectively give rise to a sharp spectral component that is easily discernable in the high-field resonance line in the EPR spectrum. By monitoring the intensity of this spectral component over time, the autoproteolytic stability of each construct was characterized under various conditions. Data were collected for samples stored at 4 °C, 25 °C, and 37 °C, and on a subtype F HIV-1 protease sample stored at 25 °C and containing the FDA-approved protease inhibitor Tipranavir. As expected, the rate of autoproteolysis decreased as the storage temperature was lowered. Minimal autoproteolysis was seen for the sample that contained Tipranavir, providing direction for future spectroscopic studies of active protease samples. When compared to standard methods of monitoring protein degradation such as gel electrophoresis or chromatographic analyses, spin-labeling with CW EPR offers a facile, real-time, non-consuming way to monitor autoproteolysis or protein degradation. Additionally, mass spectrometry studies revealed that the N-termini of both constructs are sensitive to degradation and that the sites of specific autoproteolysis vary.展开更多
Objective:To explore the effect of the protease inhibitor from Agaricus bisporus(J.E.Lange)Imbach(AbPI)on glucose uptake and oxidative stress in 3 T3-L1 adipocytes.Methods:Adipocytes were differentiated and stained wi...Objective:To explore the effect of the protease inhibitor from Agaricus bisporus(J.E.Lange)Imbach(AbPI)on glucose uptake and oxidative stress in 3 T3-L1 adipocytes.Methods:Adipocytes were differentiated and stained with OilRed-O staining to confirm adipogenesis.The toxic/protective effect of AbPI on the adipocytes was determined by MTT assay,intracellular reactive oxygen species generation through flow cytometry,and morphologically through confocal microscopy using propidium iodide,4,6-diamino-2-phenylindol dihydrochloride,and 2’,7’-dichlorofluorescein diacetate dyes.The uptake of fluorescent glucose analog,2-[N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino]-2-deoxy-d-glucose by adipocytes was also studied through confocal microscopy.Results:MTT assay showed that the cell survival rate was(28.00±3.00)%,(92.33±2.60)%,and(71.34±2.10)%in the presence of 2 mM H2O2,AbPI alone,and AbPI and H2O2 both,respectively,in comparison to the control.Oil-Red-O staining indicated that Ab PI enhanced adipogenesis.AbPI stimulated the glucose uptake by adipocytes similar to the drug rosiglitazone,and showed insulinsensitizing effect in the presence of insulin,but failed to stimulate the uptake in the absence of insulin.Intracellular reactive oxygen species generation was reduced in differentiating adipocytes upon Ab PI treatment.Confocal microscopy showed that the damaged cell population rose to 3.50%,117.84%,and 261.50%in the presence of Ab PI alone,AbPI with H2O2,and H2O2 alone,respectively.Conclusions:The protease inhibitor enhances glucose uptake by adipocytes and exhibits a cytoprotective effect on them.展开更多
以蛹虫草子实体为材料,经水提醇沉后获得沉淀样品 P 和上清样品 L,初步抗 HIV-1蛋白酶检测显示活性成份集中在样品 L 中.进一步利用大孔吸附树脂和高压液相对 L 进行分离纯化,并对纯化样品的体外抗HIV-1蛋白酶活性和抗 HIV-1逆转录酶活...以蛹虫草子实体为材料,经水提醇沉后获得沉淀样品 P 和上清样品 L,初步抗 HIV-1蛋白酶检测显示活性成份集中在样品 L 中.进一步利用大孔吸附树脂和高压液相对 L 进行分离纯化,并对纯化样品的体外抗HIV-1蛋白酶活性和抗 HIV-1逆转录酶活性进行了测定.结果显示,L 经大孔吸附树脂和高压液相分离纯化后得到三种物质均具有抗 HIV-1蛋白酶活性 f1,f2和 f3,其中 f1对 HIV-1蛋白酶抑制作用最强,比 L 提高了约29%;三种物质对 HIV-1逆转录酶均有一定的抑制作用.展开更多
目的:运用计算机虚拟筛选技术从传统中药数据库(TCMSP)中快速搜索HIV-1蛋白酶(Protease,PR)的中药小分子抑制剂。方法:采用Scripps研究所的Auto Dock Vina软件,对蛋白质晶体结构数据库PDB中PR与小分子抑制剂沙奎那韦(Saquinavir)形成的...目的:运用计算机虚拟筛选技术从传统中药数据库(TCMSP)中快速搜索HIV-1蛋白酶(Protease,PR)的中药小分子抑制剂。方法:采用Scripps研究所的Auto Dock Vina软件,对蛋白质晶体结构数据库PDB中PR与小分子抑制剂沙奎那韦(Saquinavir)形成的复合物(PDB代码:1HXB)三维结构活性部位进行分析,基于传统中药配体库进行分子对接初次筛选。综合运用传统中药系统药理学数据库及分析平台TCMSP及Accelrys公司开发的Discovery Studio 2.5分子模拟软件包内TOPKAT模块计算药代动力学参数和毒性预测对分子对接结果进行2次筛选。结果:以原配体(沙奎那韦)为阳性对照,筛选出传统中药库TCMSP中2个类药性良好的化学成分与PR亲和力高于上市的抗艾滋病药物沙奎那韦的天然小分子化合物,并且确定了它们的中草药来源。结论:该研究结果可促进从传统中药库中提取、设计以及实验合成新的抗艾滋病药物。展开更多
文摘Acquired immunodeficiency syndrome (AIDS) is a fatal disease which highly threatens the health of human being. Human immunodeficiency virus (HIV) is the pathogeny for this disease. Investigating HIV-1 protease cleavage sites can help researchers find or develop protease inhibitors which can restrain the replication of HIV-1, thus resisting AIDS. Feature selection is a new approach for solving the HIV-1 protease cleavage site prediction task and it’s a key point in our research. Comparing with the previous work, there are several advantages in our work. First, a filter method is used to eliminate the redundant features. Second, besides traditional orthogonal encoding (OE), two kinds of newly proposed features extracted by conducting principal component analysis (PCA) and non-linear Fisher transformation (NLF) on AAindex database are used. The two new features are proven to perform better than OE. Third, the data set used here is largely expanded to 1922 samples. Also to improve prediction performance, we conduct parameter optimization for SVM, thus the classifier can obtain better prediction capability. We also fuse the three kinds of features to make sure comprehensive feature representation and improve prediction performance. To effectively evaluate the prediction performance of our method, five parameters, which are much more than previous work, are used to conduct complete comparison. The experimental results of our method show that our method gain better performance than the state of art method. This means that the feature selection combined with feature fusion and classifier parameter optimization can effectively improve HIV-1 cleavage site prediction. Moreover, our work can provide useful help for HIV-1 protease inhibitor developing in the future.
文摘Quantitative structure–activity relationship study using artificial neural network (ANN) methodology were conducted to predict the inhibition constants of 127 symmetrical and unsymmetrical cyclic urea and cyclic cyanoguanidine derivatives containing different substituent groups such as: benzyl, isopropyl, 4-hydroxybenzyl, ketone, oxime, pyrazole, imidazole, triazole and having anti-HIV-1 protease activities. The results obtained by artificial neural network give advanced regression models with good prediction ability. The two optimal artificial neural network models obtained have coefficients of determination of 0.746 and 0.756. The lowest prediction’s root mean square error obtained is 0.607. Artificial neural networks provide improved models for heterogeneous data sets without splitting them into families. Both the external and cross-validation methods are used to validate the performances of the resulting models. Randomization test is employed to check the suitability of the models.
文摘Site-directed spin-labeling with continuous wave electron paramagnetic resonance spectroscopy was used to monitor autoproteolysis of HIV-1 protease, an enzyme essential for viral maturation. Two protein constructs were examined, namely subtype F and the circulating recombinant form CRF01_A/E. As the protease undergoes self-cleavage, protein unfolds and small peptide fragments containing the spin label are generated, which collectively give rise to a sharp spectral component that is easily discernable in the high-field resonance line in the EPR spectrum. By monitoring the intensity of this spectral component over time, the autoproteolytic stability of each construct was characterized under various conditions. Data were collected for samples stored at 4 °C, 25 °C, and 37 °C, and on a subtype F HIV-1 protease sample stored at 25 °C and containing the FDA-approved protease inhibitor Tipranavir. As expected, the rate of autoproteolysis decreased as the storage temperature was lowered. Minimal autoproteolysis was seen for the sample that contained Tipranavir, providing direction for future spectroscopic studies of active protease samples. When compared to standard methods of monitoring protein degradation such as gel electrophoresis or chromatographic analyses, spin-labeling with CW EPR offers a facile, real-time, non-consuming way to monitor autoproteolysis or protein degradation. Additionally, mass spectrometry studies revealed that the N-termini of both constructs are sensitive to degradation and that the sites of specific autoproteolysis vary.
文摘Objective:To explore the effect of the protease inhibitor from Agaricus bisporus(J.E.Lange)Imbach(AbPI)on glucose uptake and oxidative stress in 3 T3-L1 adipocytes.Methods:Adipocytes were differentiated and stained with OilRed-O staining to confirm adipogenesis.The toxic/protective effect of AbPI on the adipocytes was determined by MTT assay,intracellular reactive oxygen species generation through flow cytometry,and morphologically through confocal microscopy using propidium iodide,4,6-diamino-2-phenylindol dihydrochloride,and 2’,7’-dichlorofluorescein diacetate dyes.The uptake of fluorescent glucose analog,2-[N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino]-2-deoxy-d-glucose by adipocytes was also studied through confocal microscopy.Results:MTT assay showed that the cell survival rate was(28.00±3.00)%,(92.33±2.60)%,and(71.34±2.10)%in the presence of 2 mM H2O2,AbPI alone,and AbPI and H2O2 both,respectively,in comparison to the control.Oil-Red-O staining indicated that Ab PI enhanced adipogenesis.AbPI stimulated the glucose uptake by adipocytes similar to the drug rosiglitazone,and showed insulinsensitizing effect in the presence of insulin,but failed to stimulate the uptake in the absence of insulin.Intracellular reactive oxygen species generation was reduced in differentiating adipocytes upon Ab PI treatment.Confocal microscopy showed that the damaged cell population rose to 3.50%,117.84%,and 261.50%in the presence of Ab PI alone,AbPI with H2O2,and H2O2 alone,respectively.Conclusions:The protease inhibitor enhances glucose uptake by adipocytes and exhibits a cytoprotective effect on them.
文摘以蛹虫草子实体为材料,经水提醇沉后获得沉淀样品 P 和上清样品 L,初步抗 HIV-1蛋白酶检测显示活性成份集中在样品 L 中.进一步利用大孔吸附树脂和高压液相对 L 进行分离纯化,并对纯化样品的体外抗HIV-1蛋白酶活性和抗 HIV-1逆转录酶活性进行了测定.结果显示,L 经大孔吸附树脂和高压液相分离纯化后得到三种物质均具有抗 HIV-1蛋白酶活性 f1,f2和 f3,其中 f1对 HIV-1蛋白酶抑制作用最强,比 L 提高了约29%;三种物质对 HIV-1逆转录酶均有一定的抑制作用.
文摘目的:运用计算机虚拟筛选技术从传统中药数据库(TCMSP)中快速搜索HIV-1蛋白酶(Protease,PR)的中药小分子抑制剂。方法:采用Scripps研究所的Auto Dock Vina软件,对蛋白质晶体结构数据库PDB中PR与小分子抑制剂沙奎那韦(Saquinavir)形成的复合物(PDB代码:1HXB)三维结构活性部位进行分析,基于传统中药配体库进行分子对接初次筛选。综合运用传统中药系统药理学数据库及分析平台TCMSP及Accelrys公司开发的Discovery Studio 2.5分子模拟软件包内TOPKAT模块计算药代动力学参数和毒性预测对分子对接结果进行2次筛选。结果:以原配体(沙奎那韦)为阳性对照,筛选出传统中药库TCMSP中2个类药性良好的化学成分与PR亲和力高于上市的抗艾滋病药物沙奎那韦的天然小分子化合物,并且确定了它们的中草药来源。结论:该研究结果可促进从传统中药库中提取、设计以及实验合成新的抗艾滋病药物。
