3.Application of support vector machine in screening neurotoxic compounds from traditional Chinese medicine.
Jing-Fang ZHANG ; Lu-Di JIANG ; Yan-Ling ZHANG
China Journal of Chinese Materia Medica 2014;39(17):3330-3334
In this study, based on web database, 324 neurotoxic compounds and 234 non-neurotoxic compounds were selected as a data set for neurotoxicity discriminative model. 6 122 molecular descriptors, including charge distribution, physicochemical and geometrical descriptors,were calculated to characterize the molecular structure of neurotoxic compounds. The combination of Cfs Subset Evaluation and Best First-D1-N5 searching was used to select molecular descriptors. A discrimination model with high accuracy was built based on the support vector machine (SVM) approach. Meanwhile, the model accuracy, sensitivity and specificity were all above 80%. Besides, 30 traditional Chinese medicine compositions with neurotoxicity were set as external validation to further verify the model accuracy,with anaccuracy of 73.333%. Using the model, 13 potential neurotoxic compounds were screened from Sophorae subprostrate Radix,4 of them were verified by literatures. The results demonstrated that the discrimination model can be applied to screen neurotoxic compounds from Chinese medicinal materials.
Computer Simulation
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Drug Evaluation, Preclinical
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methods
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Medicine, Chinese Traditional
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methods
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Models, Theoretical
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Neurotoxins
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analysis
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chemistry
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Reproducibility of Results
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Support Vector Machine
4.Application of support vector machine approach in studying nephron toxicity of Chinese medicinal materials.
Jing-fang ZHANG ; Lu-di JIANG ; Yan-ling ZHANG
China Journal of Chinese Materia Medica 2015;40(6):1134-1138
On the basis of web databases, 111 compounds with nephrotoxicity and 90 compounds without nephrotoxicity were collected as data set of nephrotoxicity discrimination model, 39 compounds with tubular necrosis and 39 compounds without tubular necrosis were collected as data set of tubular necrosis discrimination model. The 6 122 molecular descriptors, including physicochemical, charge distribution and geometrical descriptors were calculated to characterize the molecular structure of the above-mentioned compounds. CfsSubsetEval valuation method and BestFirst-D1-N5 searching method were used to select molecular descriptors. Two models with high accuracy were built based on the support vector machine (SVM) approach, respectively. Accuracy, sensitivity, specificity and matthew's correlation coefficient of the two models were all above 70%. By using 22 nephrotoxicity compounds of Chinese medicine, the nephrotoxicity discrimination model was further verified with an accuracy of 72.73%. Using the tubular necrosis discrimination model, 10 potential compounds which can cause tubular necrosis were screened from the positive results of nephrotoxicity discrimination model, 6 of them have been verified by literatures. The results demonstrated that the discrimination models can be applied to screen nephrotoxic compounds from Chinese medicinal materials, and they also offer a new research idea for the further studies on the mechanism of nephrotoxicity.
Drugs, Chinese Herbal
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toxicity
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Nephrons
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drug effects
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Support Vector Machine
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Toxicity Tests
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instrumentation
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methods
5.Discovery of potential nicotinic acid receptor agonists from Chinese herbal medicines based on molecular simulation.
Lu-Di JIANG ; Yu-Su HE ; Yan-Ling ZHANG
China Journal of Chinese Materia Medica 2014;39(23):4653-4657
Nicotinic acid could increase high density lipoprotein and reduce serum total cholesterol, low density lipoprotein cholesterol and triglycerides in human bodies, thus is frequently applied in treating low high-density lipoprotein cholesterol and hypertriglyceridemia in clinic. However, according to the findings, nicotinic acid could also cause adverse effects, such as skin flush, beside its curative effects. In this study, bioisosterism, fragment-based search and Lipinski's Rule of Five were used to preliminarily screen out potential TCM ingredients that may have similar pharmacological effects with nicotinic acid from Traditional Chinese medicine database (TCMD). Afterwards, homology modeling and flexible docking were used to further screen out potential nicotinic acid receptor agonists. As a result, eleven candidate compounds were derived from eight commonly used traditional Chinese medicines. Specifically, all of the candidate compounds' interaction with nicotinic acid receptor was similar to nicotinic acid, and their docking scores were all higher than that of nicotinic acid, but their druggability remained to be further studied. Some of the eight source traditional Chinese medicines were used to lower lipid according to literature studies, implying that they may show effect through above means. In summary, this study provides basis and reference for extracting new nicotinic acid receptor agonists from traditional Chinese medicines and improving the medication status of hyperlipidemia.
Drug Evaluation, Preclinical
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Drugs, Chinese Herbal
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chemistry
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Humans
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Models, Molecular
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Molecular Structure
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Nicotinic Acids
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chemistry
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Nicotinic Agonists
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chemistry
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Protein Binding
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Receptors, G-Protein-Coupled
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agonists
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chemistry
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Receptors, Nicotinic
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chemistry
6.The Revision and Significance of 2013 Declaration of Helsinki
Di WANG ; Jing YANG ; Zhonglin CHEN ; Yan DING ; Yifeng JIANG
Chinese Medical Ethics 2015;(4):618-621
The new revision of Declaration of Helsinki in 2013 has adjusted the structure, added or deleted some provisions on the content and modification, and modificated on the details of some words.Revision of the new version has improved the architecture, perfected the content of the declaration, strengthened the protection of the subjects, increased demand for researchers, and cleared the duty of country, research institutions and bidders.The enlighten-ment to our country are:constantly revised involving human clinical trials of the relevant laws and regulations , to pro-tect rights and interests of the subjects;National obligations for protection of the subjects, clinical trials explore the establishment of national compensation system;Ethics committee responsibilities and clearly positioning, exploring to establish an independent ethical review body.
7.Biological Effects of Wnt in Wnt/β-catenin Signaling Pathway on Kidney Cancer Cell
Fandong MENG ; Yan LI ; Di WU ; Tao JIANG ; Yang WANG ; Chengguang SUI ; Youhong JIANG
Journal of China Medical University 2016;45(4):289-292,297
Objective To investigate the biological effects of Wnt gene in kidney cancer Caki?2 cells. Methods The Wnt gene was silenced in kidney cancer Caki?2 cells by lentivirus vector. The cell proliferate ability of cells in each group were assayed by CCK?8 kit at different time points. The apoptosis of Caki?2 cells was observed after silencing Wnt gene by transmission electron microscope. The invasion ability of each group cells was tested using Transwell chambers. The genes expression changes of Wnt/β?catenin signaling pathway and apoptosis related gene were determined by realtime PCR. Results Compared with the other two groups,the cell proliferate ability of the cells after silencing Wntgene was suppressed,and the difference was statistically significant(P<0.05). Apoptosis increased significantly in shRNA+Caki?2+Wnt group cells with silencing of Wntgene, and apoptotic body appeared in these cells. In invasive experiment,the number of emigrated cells in shRNA+Caki?2+Wnt group were significantly lower than other groups(P<0.05). The expression of Wnt mRNA,β?catenin mRNA and Bcl?2 mRNA in shRNA+Caki?2+Wnt group cells was lower than other groups(P<0.05). Conclusion Silencing of Wnt gene of kidney cancer Caki?2 cells can affect the proliferation rate of the cells, promote the cell apoptosis,and inhibit the invasion ability,which provide certain theoretical basis for the research and development of new drugs and new therapeutic targets.
8.Influence of different treatment time on the relapse and prognosis of patients with newly diagnosed epilepsy
Qing DI ; Yukui YAN ; Nian YU ; Ying JIANG ; Yong HU ; Yanfang ZHANG
Chinese Journal of Neurology 2011;44(1):10-14
Objective To explore the influence of different treatment time on the relapse and prognosis of patients with newly diagnosed epilepsy. Methods To prospectively studied the clinical characteristics of 155 patients with newly diagnosed epilepsy. Patients were separated into immediate ( n =84, seizures ≤3 times) or deferred (n =71, seizures > 3 times) treatment groups according to number of seizures before treatment with appropriate antiepileptic drugs (AEDs). The patients were followed up for at least one year (median, 29 months). Kaplan-Meier survival statistics was used to analyze time to first seizure or time to treatment failure (inadequate seizure control and (or) intolerable side-effects ). The proportions of patients with treatment failure and seizure free during follow up were also compared. Results There was no significant difference in time to first seizure or time to treatment failure between immediate ( 1484 days and 2992 days) and deferred treatment ( 1104 days and 1964 days; Log-Rank test x2 =0. 571 and 0. 018 respectively, P = 0. 450 and 0. 893 ). Subgroup analyses according to etiology ( primary and cryptogenic/symptomatic epilepsy) and age (children ≤ 16 years; adult > 16 years) did not reveal any difference between immediate and deferred treatment. During follow up, there were 20 treatment failure patients ( 23. 8% ) in immediate treatment group and 16 ( 22.5% ) in deferred treatment group ( no statistical difference, x2 =0. 035 ,P =0. 852). There were 40 seizure free patients (47. 6% ) in immediate treatment group and 30 (42. 3% ) in deferred treatment group ( no statistical difference, x2 = 0. 447, P =0. 504 ). Conclusions For newly diagnosed epilepsy patients with a few seizures ( seizures ≤ 3 ), immediate AEDs treatment does not affect the relapse and prognosis.
9.Preparation of CD40L-PLL-CpG ODN conjugated complex and its targeting B lymphocytes
Jianwei JIANG ; Meizhen ZHENG ; Huilan ZENG ; Yaoying ZENG ; Jingfang DI ; Yuxia YAN ; Meiyu WU
Chinese Journal of Pathophysiology 1989;0(05):-
98%), the peak level of uptake occurred earlier, intracellular fluorescence intensity maintained much more stable. Expressions of CD19+, CD22+, CD20+ increased significantly. A_~570 values of MNCs proliferation and IgG levels in supernatant were all higher. CONCLUSION: CD40 ligand-PLL carrier system may delivery CpG ODN targeting to B lymphocytes, enhancing its immunological efficiency.