1.ETCM v2.0: An update with comprehensive resource and rich annotations for traditional Chinese medicine.
Yanqiong ZHANG ; Xin LI ; Yulong SHI ; Tong CHEN ; Zhijian XU ; Ping WANG ; Meng YU ; Wenjia CHEN ; Bing LI ; Zhiwei JING ; Hong JIANG ; Lu FU ; Wenjing GAO ; Yanhua JIANG ; Xia DU ; Zipeng GONG ; Weiliang ZHU ; Hongjun YANG ; Haiyu XU
Acta Pharmaceutica Sinica B 2023;13(6):2559-2571
Existing traditional Chinese medicine (TCM)-related databases are still insufficient in data standardization, integrity and precision, and need to be updated urgently. Herein, an Encyclopedia of Traditional Chinese Medicine version 2.0 (ETCM v2.0, http://www.tcmip.cn/ETCM2/front/#/) was constructed as the latest curated database hosting 48,442 TCM formulas recorded by ancient Chinese medical books, 9872 Chinese patent drugs, 2079 Chinese medicinal materials and 38,298 ingredients. To facilitate the mechanistic research and new drug discovery, we improved the target identification method based on a two-dimensional ligand similarity search module, which provides the confirmed and/or potential targets of each ingredient, as well as their binding activities. Importantly, five TCM formulas/Chinese patent drugs/herbs/ingredients with the highest Jaccard similarity scores to the submitted drugs are offered in ETCM v2.0, which may be of significance to identify prescriptions/herbs/ingredients with similar clinical efficacy, to summarize the rules of prescription use, and to find alternative drugs for endangered Chinese medicinal materials. Moreover, ETCM v2.0 provides an enhanced JavaScript-based network visualization tool for creating, modifying and exploring multi-scale biological networks. ETCM v2.0 may be a major data warehouse for the quality marker identification of TCMs, the TCM-derived drug discovery and repurposing, and the pharmacological mechanism investigation of TCMs against various human diseases.
2.Mechanism of Zhizi Prescription in Protection of CCl4-induced Acute and Subacute Liver Injury in Mice
Yanlei ZHANG ; Longtao CUI ; Qiyao WANG ; Liping CHEN ; Yong ZHANG ; Jiatuo XU ; Weiliang ZHU ; Zhangbin GONG ; Kaixian CHEN
Chinese Journal of Experimental Traditional Medical Formulae 2022;28(18):30-37
ObjectiveTo investigate the protective effect of Zhizi prescription (ZZP) on carbon tetrachloride (CCl4)-induced acute and subacute liver injury and its mechanism. MethodAcute and subacute liver injury animal models were induced. C57 mice were randomly divided into a normal group, model group, obeccholic acid group, ZZP high-dose (0.5 g·kg-1) group, and ZZP low-dose (0.25 g·kg-1) group. According to the experiment design, the serum and liver tissue of mice were collected after the last administration. Hematoxylin-eosin (HE) and Sirius staining was used to observe the liver pathological changes. Serum alanine aminotransferase (ALT), aspartate aminotransferase (AST), total bilirubin (TBIL), liver homogenate hydroxyproline (Hyp), malondialdehyde (MDA), and superoxide dismutase (SOD) levels were determined by kit. The levels of tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) in the liver tissue were determined by enzyme-linked immunosorbent assay (ELISA). Real-time fluorescence quantitative polymerase chain reaction (Real-time PCR) was used to detect the mRNA expressions of collagen 1A1 (Col1a1), collagen 3A1 (Col3a1), fibronectin (FN), transforming growth factor β receptor Ⅱ (Tgfbr2) and α-smooth muscle actin (α-SMA) in the liver tissue. ResultIn terms of the acute liver injury, as compared with the normal group, the levels of ALT, AST, TBIL and MDA in the model group were significantly increased (P<0.01), while the activity of liver SOD was significantly decreased (P<0.01). Compared with model group, the ZZP high-dose and low-dose groups both significantly reduced the degree of liver cell injury, and protected the acute liver injury induced by CCl4. The ZZP high-dose group had a better effect than the ZZP low-dose group. In terms of the subacute liver injury, the levels of ALT, AST, MDA,TNF-α and IL-6 in the model group were significantly increased (P<0.01), while the activity of liver SOD was significantly decreased (P<0.01). As compared with the model group, liver Hyp content in the ZZP high-dose and low-dose groups was significantly decreased (P<0.01), and the collagen deposition in liver of both groups was significantly reduced. The ZZP high-dose group also significantly down-regulated the mRNA expressions of α-SMA, Col1a1, Col3a1, FN, and Tgfbr2 in the liver of mice (P<0.05, P<0.01). ConclusionZZP effectively protects the acute and subacute liver injury induced by CCl4, and the protective effect is proportional to its concentration. The mechanism may be related to the increase of the activity of antioxidant enzymes in the liver tissue, the decrease of the level of lipid peroxidation, and the inhibition of inflammatory response, thus reducing collagen deposition and improving early liver fibrosis.
3.Advances in the treatment of intervertebral disc degeneration by stem cell exosomes
Weiliang SU ; Xiaolin WU ; Zhu GUO ; Nana SHEN ; Chang LIU ; Shuai YANG ; Yan WANG ; Guoqing ZHANG ; Wujun CHEN ; Hongfei XIANG ; Bohua CHEN
Chinese Journal of Orthopaedics 2021;41(4):253-261
Exosomes are vesicles with a double globular membrane of lipids that can be secreted by a variety of cells, including stem cells. Exosomes have unique biological characteristics and irreplaceable powerful functions which play an important role in intercellular communication. The various cytokines, signal proteins, lipids and regulatory nucleic acids contained in stem cell exosomes can play a protective role against the injury of kidney, liver, heart, blood vessels and nerves. Stem cell exosomes delay the process of intervertebral disc degeneration by inhibiting the apoptosis of nucleus pulposus cells and increasing the synthesis of extracellular matrix, etc. The mechanism of its role is mainly through miRNA and related signaling pathways. Exosomes contain complex components. Although the mechanism of action of exosomes in intervertebral discs has been preliminarily explored, the components contained in exosomes are complex and the specific situation has not been fully understood, which still needs further study. In this review, the characteristics and functions of stem cell exosomes, extraction, identification and storage methods, the impacttovarious other tissues, as well as the effects on intervertebral discs and their mechanisms were elaborated in order to provide a basis for the study of intervertebral disc degenerative diseases.
4.ASER:Animal Sex Reversal Database
Li YANGYANG ; Chen ZONGGUI ; Liu HAIRONG ; Li QIMING ; Lin XING ; Ji SHUHUI ; Li RUI ; Li SHAOPENG ; Fan WEILIANG ; Zhao HAIPING ; Zhu ZUOYAN ; Hu WEI ; Zhou YU ; Luo DAJI
Genomics, Proteomics & Bioinformatics 2021;19(6):873-881
Sex reversal, representing extraordinary sexual plasticity during the life cycle, not only triggers reproduction in animals but also affects reproductive and endocrine system-related diseases and cancers in humans. Sex reversal has been broadly reported in animals; however, an integrated resource hub of sex reversal information is still lacking. Here, we constructed a comprehensive database named ASER (Animal Sex Reversal) by integrating sex reversal-related data of 18 species from teleostei to mammalia. We systematically collected 40,018 published papers and mined the sex reversal-associated genes (SRGs), including their regulatory networks, from 1611 core papers. We annotated homologous genes and computed conservation scores for whole genomes across the 18 species. Furthermore, we collected available RNA-seq datasets and investigated the expression dynamics of SRGs during sex reversal or sex determination processes. In addition, we manually annotated 550 in situ hybridization (ISH), fluorescence in situ hybridization (FISH), and im-munohistochemistry (IHC) images of SRGs from the literature and described their spatial expression in the gonads. Collectively, ASER provides a unique and integrated resource for researchers to query and reuse organized data to explore the mechanisms and applications of SRGs in animal breeding and human health. The ASER database is publicly available at http://aser.ihb.ac.cn/.
5.D3Targets-2019-nCoV: a webserver for predicting drug targets and for multi-target and multi-site based virtual screening against COVID-19.
Yulong SHI ; Xinben ZHANG ; Kaijie MU ; Cheng PENG ; Zhengdan ZHU ; Xiaoyu WANG ; Yanqing YANG ; Zhijian XU ; Weiliang ZHU
Acta Pharmaceutica Sinica B 2020;10(7):1239-1248
A highly effective medicine is urgently required to cure coronavirus disease 2019 (COVID-19). For the purpose, we developed a molecular docking based webserver, namely D3Targets-2019-nCoV, with two functions, one is for predicting drug targets for drugs or active compounds observed from clinic or / studies, the other is for identifying lead compounds against potential drug targets docking. This server has its unique features, (1) the potential target proteins and their different conformations involving in the whole process from virus infection to replication and release were included as many as possible; (2) all the potential ligand-binding sites with volume larger than 200 Å on a protein structure were identified for docking; (3) correlation information among some conformations or binding sites was annotated; (4) it is easy to be updated, and is accessible freely to public (https://www.d3pharma.com/D3Targets-2019-nCoV/index.php). Currently, the webserver contains 42 proteins [20 severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) encoded proteins and 22 human proteins involved in virus infection, replication and release] with 69 different conformations/structures and 557 potential ligand-binding pockets in total. With 6 examples, we demonstrated that the webserver should be useful to medicinal chemists, pharmacologists and clinicians for efficiently discovering or developing effective drugs against the SARS-CoV-2 to cure COVID-19.
6.Discussion on installation scheme of 3.0T high field magnetic resonance equipment in hospital
Weiliang TIAN ; Kaixi XU ; Boguang ZHU
China Medical Equipment 2017;14(4):149-151
Objective: With the clinical application and popularization of magnetic resonance equipment, the installed amount of 3.0T high field magnetic resonance in the hospital was gradually increasing. This paper summarized the various technical factors involved in the installation of 3.0T high field MRI, and provided scientific and valuable reference for the installation and management of high field magnetic resonance equipment. Methods: During the installed process of GE discovery 3.0T magnetic resonance, to explore the correlative relationship among series of preparation work about installation of magnetic resonance, such as the selection of machine room, civil construction, shield construction and related electrical facilities and so on, and complete the connecting work among them. Results: Finally, the hospital has successfully completed machine room preparation for the 3.0T magnetic resonance, and has provided site guarantee for obtaining high-quality magnetic resonance images. Conclusion: In view of the special, importance and higher requirement for machine room of the magnetic resonance equipment, the seriously research and analysis should be applied and a coordinated mechanism of various type work should be established before the equipment is installed. During the construction process of machine room, enough consideration for detail in every aspect can provide guarantee for completing high-quality construction during the scheduled period, and achieve a satisfying effect.
7.Dosimetry analysis of radioactive seed implantation supported by coplanar template for lung cancer patients with mediastinal lymph node metastases 4R
Jinshuang LYU ; Guangjun ZHENG ; Shengjie ZHANG ; Jingkui YANG ; Weiliang YAN ; Shuyuan SHI ; Zhen FENG ; Xiaolei ZHU ; Shude CHAI ; Junjie WANG
Chinese Journal of Radiological Medicine and Protection 2017;37(7):533-538
Objective To compare the planned radiation dose and the actual dose received after 125I radioactive seeds implantation supported by coplanar template (CPT) in lung cancer patients with mediastinal node metastases 4R,and to evaluate the clinical efficacy.Methods Totally 32 patients with lung cancer with mediastinal lymph node metastases 4R who had been diagnosed via cellular pathology studies were selected from January 2008 to December 2014.The mediastinal lymph node metastases were treated by CPT-assisted 125I radioactive seed implantation.Digital imaging and communications in medicine (DICOM) data were acquired by chest CT scan before implantation,brachytherapy radiation treatment planning system (BTPS) was introduced to carry out the plan,and the prescribed dose(PD) was 120 Gy.CPT was used to control the precision of needle penetration and implantation of radioactive seeds.Computer tomography (CT) was used to ensure the correct position of needles and radioactive seeds.Dose evaluation was performed immediately after implantation and was compared with planned dose using paired t-test.The 6-months postoperative chest CT was conducted to evaluate treatment efficacy according to response evaluation criteria in solid tumors(RECIST Version 1.1).Results All patients went through implantation procedure successfully.Dose evaluation after implantation was as followed.The average dose received (231.9 ±29.6)Gy,the dose received by 90% of the target(D90) (150.8 ± 16.6) Gy,the dose received by 100% of the target(D100) (100.4 ± 12.6)Gy,the volume of 100%PD covering the target(V100)(94.1 ± 2.6) %,the volume of 200% PD covering the target(V200) (33.0 ± 5.7) %,the conformal index (CI) 0.75 ±0.06,the external index(EI) (22.7 ± 5.8)%,the average dose received by the superior vena cava (19.3 ± 7.2)Gy,and the average dose received by aorta (12.1 ± 5.1)Gy.Efficacy was followed for 6 months after implantation and the effective rate was 84.37%.There was no serious complications (such as radioactive lung injury,major vascular injury,bleeding,and et al.) occurred in follow-up period.Conclusions CPT assisted CT guided 125I radioactive seed imnplantation in treating mediastinal node metastases 4R can achieve preoperative BTPS,minimize major vascular or organ injury.It is an accurate,effective and safe treatment approach and may be of great value to standardize the procedure of radioactive seed implantation in mediastinal metastases.
8.Two new sulfated sesquiterpenoids from Petasites tricholobus.
Yong ZHANG ; Yuanyuan GAO ; Qi JIA ; Fujiang GUO ; Bo LI ; Zhijian XU ; Yiming LI ; Weiliang ZHU ; Kaixian CHEN
Acta Pharmaceutica Sinica 2014;49(10):1433-7
Two new sulfated sesquiterpenoids, megastigman-7-ene-3, 5, 6, 9-tetrol-3-O-β-D-6'-sulfonated-glucopyranoside (1) and 3-O-β-D-6'-sulfonated-glucopyranosyl-6-(3-oxo-2-butenylidenyl)-1, 1, 5-trimethylcyclohexan-5-ol (2), along with one known sesquitepenoid compound icariside B1 (3) were isolated from the whole herb of Petasites tricholobus Franch. Their structures were identified by their chemical and spectroscopic characters. All obtained compounds were tested for their cytotoxicity against four cancer cell lines.
9.Relationship between genotypes HBV C and B with specific cytotoxic T lymphocyte surface PD-1 expression in patients with chronic hepatitis B
Yulin ZHOU ; Xuecai WANG ; Yongfei TAN ; Yanping ZHAO ; Weiliang DING ; Yinfang ZHU
Chinese Journal of Experimental and Clinical Virology 2014;28(4):258-261
Objective To explore relationship between genotypes HBV C and B with HBV specific cytotoxic T lymphocyte (CTL) surface programmed death receptor-1 (PD-1) and its significance in patients with chronic hepatitis B (CHB).Methods A total of 71 CHB patients were studied,human leukocyte antigen(HLA)-A2 positive,HBV DNA > 103 copies/ml,of which 34 cases(47.89%)had genotype C and 36 cases (50.70%) had genotype B.Peripheral blood HBV specific CTL surface PD-1 expression level,HBV specific CTL level,HBV DNA level,ALT and TBil levels of patients infected with genotype C and B were compared.Results HBV specific CTL surface PD-1 expression level of CHB patients infected with genotype C (37.30 ± 3.05%) was higher than that of patients infected with genotype B (26.19 ± 3.06%),t =15.47,P < 0.001,HBV specific CTL level (0.25 ± 0.03%) was lower than that of patients infected with genotype B (0.45 ±0.13%),t =21.54,P <0.001,HBV DNA level (6.75 ±0.77 log10 copies/ml) was higher than that of patients infected with genotype B (4.96 ± 1.12 log10 copies/ml),t =7.93,P < 0.001,ALT level (487.39 ± 87.36IU/L) was higher than that of patients infected with genotype B (235.25 ± 90.911U/L),t =12.32,P < 0.001,TBil level (49.73 ± 6.45) was higher than that of patients infected with genotype B (28.48 ± 5.89%),t =9.01,P < 0.001.Conclusion Peripheral blood HBV specific CTL surface PD-1 expression level of CHB patients infected with genotype C was higher than that of patients infected with genotype B,resulting in lower HBV specific CTL level and higher HBV DNA level of patients infected with genotype C than patients infected with genotype B,so damage to liver functions was more serious than patients infected with genotype B.
10.Phenolic constituents from Lysimachia patungensis.
Peng ZENG ; Yong ZHANG ; Chen PAN ; Qi JIA ; Fujiang GUO ; Weiliang ZHU ; Yiming LI ; Kaixian CHEN
Acta Pharmaceutica Sinica 2013;48(3):377-82
To study the chemical constituents of Lysimachia patungensis Hand.-Mazz., silica gel column chromatography, reverse phase ODS column chromatography, MCI and Sephadex LH-20, were used to separate the 95% EtOH extract of the whole plant of Lysimachia patungensis Hand.-Mazz.. The structures of the isolated compounds have been established on the basis of chemical and NMR spectroscopic evidence as well as ESI-MS in some cases. Twelve phenolic compounds were obtained and identified as quercetin-3, 3'-di- O-alpha-L-rhamnoside (1), myricetrin (2), quercitrin (3), rutin (4), 2-hydroxynaringenin-4'-O-glucopyranoside (5), naringenin 7-O-glucopyranoside (6), liquiritin apioside (7), licochalcone B (8), tetrahydroxymethoxy chalcone (9), methyl-p-coumarate (10), 2, 4, 6-trihydroxy acetophenone-2-O-glucopyranoside (11) and vaccihein A (12). Among them, compound 1 is a new compound, and compounds 5, 11 and 12 are isolated from the genus Lysimachia L. for the first time, and the others are isolated from the plant for the first time.


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