1.Structural and Spatial Analysis of The Recognition Relationship Between Influenza A Virus Neuraminidase Antigenic Epitopes and Antibodies
Zheng ZHU ; Zheng-Shan CHEN ; Guan-Ying ZHANG ; Ting FANG ; Pu FAN ; Lei BI ; Yue CUI ; Ze-Ya LI ; Chun-Yi SU ; Xiang-Yang CHI ; Chang-Ming YU
Progress in Biochemistry and Biophysics 2025;52(4):957-969
ObjectiveThis study leverages structural data from antigen-antibody complexes of the influenza A virus neuraminidase (NA) protein to investigate the spatial recognition relationship between the antigenic epitopes and antibody paratopes. MethodsStructural data on NA protein antigen-antibody complexes were comprehensively collected from the SAbDab database, and processed to obtain the amino acid sequences and spatial distribution information on antigenic epitopes and corresponding antibody paratopes. Statistical analysis was conducted on the antibody sequences, frequency of use of genes, amino acid preferences, and the lengths of complementarity determining regions (CDR). Epitope hotspots for antibody binding were analyzed, and the spatial structural similarity of antibody paratopes was calculated and subjected to clustering, which allowed for a comprehensively exploration of the spatial recognition relationship between antigenic epitopes and antibodies. The specificity of antibodies targeting different antigenic epitope clusters was further validated through bio-layer interferometry (BLI) experiments. ResultsThe collected data revealed that the antigen-antibody complex structure data of influenza A virus NA protein in SAbDab database were mainly from H3N2, H7N9 and H1N1 subtypes. The hotspot regions of antigen epitopes were primarily located around the catalytic active site. The antibodies used for structural analysis were primarily derived from human and murine sources. Among murine antibodies, the most frequently used V-J gene combination was IGHV1-12*01/IGHJ2*01, while for human antibodies, the most common combination was IGHV1-69*01/IGHJ6*01. There were significant differences in the lengths and usage preferences of heavy chain CDR amino acids between antibodies that bind within the catalytic active site and those that bind to regions outside the catalytic active site. The results revealed that structurally similar antibodies could recognize the same epitopes, indicating a specific spatial recognition between antibody and antigen epitopes. Structural overlap in the binding regions was observed for antibodies with similar paratope structures, and the competitive binding of these antibodies to the epitope was confirmed through BLI experiments. ConclusionThe antigen epitopes of NA protein mainly ditributed around the catalytic active site and its surrounding loops. Spatial complementarity and electrostatic interactions play crucial roles in the recognition and binding of antibodies to antigenic epitopes in the catalytic region. There existed a spatial recognition relationship between antigens and antibodies that was independent of the uniqueness of antibody sequences, which means that antibodies with different sequences could potentially form similar local spatial structures and recognize the same epitopes.
2.Effect and Safety of Fuzheng Huazhuo Decoction against Prolonged SARS-CoV-2 Clearance: A Retrospective Cohort Study.
Wen ZHANG ; Hong-Ze WU ; Xiang-Ru XU ; Yu-Ting PU ; Cai-Yu CHEN ; Rou DENG ; Min CAO ; Ding SUN ; Hui YI ; Shuang ZHOU ; Bang-Jiang FANG
Chinese journal of integrative medicine 2025;31(5):387-393
OBJECTIVE:
To evaluate the effect and safety of Chinese medicine (CM) Fuzheng Huazhuo Decoction (FHD) in treating patients with coronavirus disease 2019 (COVID-19) who persistently tested positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
METHODS:
This retrospective cohort study was conducted at Shanghai New International Expo Center shelter hospital in China between April 1 and May 30, 2022. Patients diagnosed as COVID-19 with persistently positive SARS-CoV-2 reverse transcription-polymerase chain reaction (RT-PCR) test results for ⩾8 days after diagnosis were enrolled. Patients in the control group received conventional Western medicine (WM) treatment, while those in the FHD group received conventional WM plus FHD for at least 3 days. The primary outcome was viral clearance time. Secondary outcomes included negative conversion rate within 14 days, length of hospital stay, cycle threshold (Ct) values of the open reading frame 1ab (ORF1ab) and nucleocapsid protein (N) genes, and incidence of new-onset symptoms during hospitalization. Adverse events (AEs) that occurred during the study period were recorded.
RESULTS:
A total of 1,765 eligible patients were enrolled in this study (546 in the FHD group and 1,219 in the control group). Compared with the control group, patients receiving FHD treatment showed shorter viral clearance time for nucleic acids [hazard ratio (HR): 1.500, 95% confidence interval (CI): 1.353-1.664, P<0.001] and hospital stays (HR: 1.371, 95% CI: 1.238-1.519, P<0.001), and a higher negative conversion rate within 14 days (96.2% vs. 82.6%, P<0.001). The incidence of new-onset symptoms was 59.5% in the FHD group, similar to 57.8% in the control group (P>0.05). The Ct values of ORF1ab and N genes increased more rapidly over time in the FHD group than those in the control group post-randomization (ORF1ab gene: β =0.436±0.053, P<0.001; N gene: β =0.415 ±0.053, P<0.001). The incidence of AEs in the FHD group was lower than that in the control group (24.2% vs. 35.4%, P<0.001). No serious AEs were observed.
CONCLUSION
FHD was effective and safe for patients with persistently positive SARS-CoV-2 PCR tests. (Registration No. ChiCTR2200063956).
Humans
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Drugs, Chinese Herbal/adverse effects*
;
Retrospective Studies
;
Male
;
Female
;
Middle Aged
;
COVID-19 Drug Treatment
;
SARS-CoV-2/drug effects*
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COVID-19/virology*
;
Adult
;
Aged
;
Treatment Outcome
3.Longitudinal Associations between Vitamin D Status and Systemic Inflammation Markers among Early Adolescents.
Ting TANG ; Xin Hui WANG ; Xue WEN ; Min LI ; Meng Yuan YUAN ; Yong Han LI ; Xiao Qin ZHONG ; Fang Biao TAO ; Pu Yu SU ; Xi Hua YU ; Geng Fu WANG
Biomedical and Environmental Sciences 2025;38(1):94-99
4.Research on species identification of commercial medicinal and food homology scented herbal tea
Jing SUN ; Zi-yi HUANG ; Si-qi LI ; Yu-fang LI ; Yan HU ; Shi-wen GUO ; Ge HU ; Chuan-pu SHEN ; Fu-rong YANG ; Yu-lin LIN ; Tian-yi XIN ; Xiang-dong PU
Acta Pharmaceutica Sinica 2024;59(9):2612-2624
The adulteration and counterfeiting of herbal ingredients in medicinal and food homology (MFH) have a serious impact on the quality of herbal materials, thereby endangering human health. Compared to pharmaceutical drugs, health products derived from traditional Chinese medicine (TCM) are more easily accessible and closely integrated into consumers' daily life. However, the authentication of the authenticity of TCM ingredients in MFH has not received sufficient attention. The lack of clear standards emphasizes the necessity of conducting systematic research in this area. This study utilized DNA barcoding technology, combining ITS2,
5.Pharmacological Effects of Icariin on Male Reproductive System:A Review and Literature Visualization
Jingyi ZHANG ; Junjun LI ; Chunyan FANG ; Shiyun PU ; Feng ZHANG ; Aili YANG ; Xujun YU
Herald of Medicine 2024;43(1):96-105
Icariin,which belongs to the class of flavonoids,is the main active ingredient of the traditional tonic Chinese herb Epimedii Folium.Modern studies have shown that icariin has a wide range of effects on the male reproductive system.It has various pharmacological activities such as regulating cell proliferation and apoptosis,antioxidants,promoting testosterone secretion,improving erectile function,inhibiting prostate cancer cell migration,invasion,and regulating cell cycle.It has research value and application prospects in the field of urology and assisted reproduction.Therefore,Icariin's pharmacological effects and molecular mechanisms on the male reproductive system are reviewed in this paper combined with literature visualization analysis.It is expected to provide a theoretical basis for the therapeutic value development and application of icariin in male reproductive health.
6.Clinical value of immature granulocyte percentage in pre-dicting severity of acute appendicitis in children
Xin-Li ZHANG ; Kai-Jiang LI ; Pu-Yu ZHAO ; Liang ZHAO ; Bing LIANG ; Dong-Fang LU ; Yu-Cheng SHI
Chinese Journal of Current Advances in General Surgery 2024;27(7):533-537
Objective:To investigate the clinical value immature granulocyte percentage(IG%)and other inflammatory indicators in the severity of acute appendicitis.Methods:A total of 201 pediatric patients undergoing appendicitis surgery admitted to Zhoukou Central Hospital from June 2022 to August 2023 were included.Patients with pathologically confirmed actue appendici-tis were divided two subgroups:actue simple appendicitis(ASA)group and actue complicated ap-pendicitis(ACA)group,The variables that included IG%,white blood cell(WBC)count,absolute neutrophil count(ANC),absolute lymphocyte count(ALC),neutrophil to lymphocyte ratio(NLR),pro-calcitonin(PCT),C-reactive protein(CRP),platelet to lymphocyte(PLR)and other indexes were ana-lyzed between ASA and ACA group.The logistic regression model for diagnosis of ACA was es-tablished,and the diagostic value of this model and other inflammtory indicators for ACA was evaluated by receiver operating characteristic(ROC)curve analysis.Results:The levels of IG%,WBC,ANC,ALC,NLR,PCT and PLR were higher and the level of ALC was lower in ACA group than those in ASA group(all P<0.05).Logistic regression analysis showed that IG%,NLR and CRP were three diagnostic determinants of ACA(all P<0.05).The AUC of the established logistic model and IG%,NLR,CRP were 0.868,0.821,0.691 and 0.790(all P<0.001).The logistic model was vali-dated by independent cohorts,and the AUC was 0.872,the sensitivity was 90.0%and the speci-ficity was 75.6%.Conlusions:The IG%value can early indicator for pediatric ACA,and the es-tablished logistic regression model based on biomarkers including IG%,NLR and CRP has clinical value in diagnosing ACA in children.
7.Simultaneous transcatheter aortic valve replacement and mitral balloon dilatation in patients with severe aortic stenosis and mitral stenosis: two case reports.
Hao Jian DONG ; Rui WANG ; Xia WANG ; Jian LIU ; Bu Zha Xi PU ; Jie LI ; Yu Jing MO ; Ming FU ; Guang LI ; Jian Fang LUO
Chinese Journal of Cardiology 2023;51(10):1082-1086
8.Simultaneous transcatheter aortic valve replacement and mitral balloon dilatation in patients with severe aortic stenosis and mitral stenosis: two case reports.
Hao Jian DONG ; Rui WANG ; Xia WANG ; Jian LIU ; Bu Zha Xi PU ; Jie LI ; Yu Jing MO ; Ming FU ; Guang LI ; Jian Fang LUO
Chinese Journal of Cardiology 2023;51(10):1082-1086
9.Mechanism of Jiming Powder in ameliorating heart failure with preserved ejection fraction based on metabolomics.
Xiao-Qi WEI ; Xin-Yi FAN ; Hai-Yin PU ; Shuai LI ; Jia-Yang TANG ; Kuo GAO ; Fang-He LI ; Xue YU ; Shu-Zhen GUO
China Journal of Chinese Materia Medica 2023;48(17):4747-4760
In this study, untargeted metabolomics was conducted using the liquid chromatography-tandem mass spectrometry(LC-MS/MS) technique to analyze the potential biomarkers in the plasma of mice with heart failure with preserved ejection fraction(HFpEF) induced by a high-fat diet(HFD) and nitric oxide synthase inhibitor(Nω-nitro-L-arginine methyl ester hydrochloride, L-NAME) and explore the pharmacological effects and mechanism of Jiming Powder in improving HFpEF. Male C57BL/6N mice aged eight weeks were randomly assigned to a control group, a model group, an empagliflozin(10 mg·kg~(-1)·d~(-1)) group, and high-and low-dose Jiming Powder(14.3 and 7.15 g·kg~(-1)·d~(-1)) groups. Mice in the control group were fed on a low-fat diet, and mice in the model group and groups with drug intervention were fed on a high-fat diet. All mice had free access to water, with water in the model group and Jiming Powder groups being supplemented with L-NAME(0.5 g·L~(-1)). Drugs were administered on the first day of modeling, and 15 weeks later, blood pressure and cardiac function of the mice in each group were measured. Heart tissues were collected for hematoxylin-eosin(HE) staining to observe pathological changes and Masson's staining to observe myocardial collagen deposition. Untargeted metabolomics analysis was performed on the plasma collected from mice in each group, and metabolic pathway analysis was conducted using MetaboAnalyst 5.0. The results showed that the blood pressure was significantly lower and the myocardial concentric hypertrophy and left ventricular diastolic dysfunction were significantly improved in both the high-dose and low-dose Jiming Powder groups as compared with those in the model group. HE and Masson staining showed that both high-dose and low-dose Jiming Powder significantly alleviated myocardial fibrosis. In the metabolomics experiment, 23 potential biomarkers were identified and eight strongly correlated metabolic pathways were enriched, including linoleic acid metabolism, histidine metabolism, alpha-linolenic acid metabolism, glycerophospholipid metabolism, purine metabolism, porphyrin and chlorophyll metabolism, arachidonic acid metabolism, and pyrimidine metabolism. The study confirmed the pharmacological effects of Jiming Powder in lowering blood pressure and ameliorating HFpEF and revealed the mechanism of Jiming Powder using the metabolomics technique, providing experimental evidence for the clinical application of Jiming Powder in treating HFpEF and a new perspective for advancing and developing TCM therapy for HFpEF.
Male
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Mice
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Animals
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Heart Failure/metabolism*
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Powders
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Stroke Volume/physiology*
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Chromatography, Liquid
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NG-Nitroarginine Methyl Ester/therapeutic use*
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Mice, Inbred C57BL
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Tandem Mass Spectrometry
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Metabolomics
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Biomarkers
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Water
10.Effect and mechanism of Jiming Powder on myocardial fibrosis in mice with myocardial infarction.
Xin-Yi FAN ; Xiao-Qi WEI ; Yun-Yang ZHANG ; Hai-Yin PU ; Fang-He LI ; Kuo GAO ; Xue YU ; Shu-Zhen GUO
China Journal of Chinese Materia Medica 2023;48(21):5838-5850
Jiming Powder is a traditional ancient prescription with good therapeutic effect in the treatment of heart failure, but its mechanism lacks further exploration. In this study, a mouse model of coronary artery ligation was used to evaluate the effect and mechanism of Jiming Powder on myocardial fibrosis in mice with myocardial infarction. The study constructed a mouse model of heart failure after myocardial infarction using the method of left anterior descending coronary artery ligation. The efficacy of Jiming Powder was evaluated from multiple angles, including ultrasound imaging, hematoxylin-eosin(HE) staining, Masson staining, Sirius Red staining, and serum myocardial enzyme spectrum detection. Western blot analysis was performed to detect key proteins involved in ventricular remodeling, including transforming growth factor-β1(TGF-β1), α-smooth muscle actin(α-SMA), wingless-type MMTV integration site family member 3a(Wnt3a), β-catenin, matrix metallopeptidase 2(MMP2), matrix metallopeptidase 3(MMP3), TIMP metallopeptidase inhibitor 1(TIMP1), and TIMP metallopeptidase inhibitor 2(TIMP2). The results showed that compared with the model group, the high and low-dose Jiming Powder significantly reduced the left ventricular internal diameter in systole(LVID;s) and diastole(LVID;d), increased the left ventricular ejection fraction(LVEF) and left ventricular fractional shortening(LVFS), effectively improved cardiac function in mice after myocardial infarction, and effectively reduced the levels of myocardial injury markers such as creatine kinase(CK), creatine kinase isoenzyme(CK-MB), and lactic dehydrogenase(LDH), thus protecting ischemic myocardium. HE staining showed that Jiming Powder could attenuate myocardial inflammatory cell infiltration after myocardial infarction. Masson and Sirius Red staining demonstrated that Jiming Powder effectively inhibited myocardial fibrosis, reduced the collagen Ⅰ/Ⅲ ratio in myocardial tissues, and improved collagen remodeling after myocardial infarction. Western blot results showed that Jiming Powder reduced the expression of TGF-β1, α-SMA, Wnt3a, and β-catenin, decreased the levels of MMP2, MMP3, and TIMP2, and increased the level of TIMP1, suggesting its role in inhibiting cardiac fibroblast transformation, reducing extracellular matrix metabolism in myocardial cells, and lowering collagen Ⅰ and α-SMA content, thus exerting an anti-myocardial fibrosis effect after myocardial infarction. This study revealed the role of Jiming Powder in improving ventricular remodeling and treating myocardial infarction, laying the foundation for further research on the pharmacological effect of Jiming Powder.
Mice
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Animals
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Transforming Growth Factor beta1/metabolism*
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Matrix Metalloproteinase 2/metabolism*
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beta Catenin/metabolism*
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Matrix Metalloproteinase 3/therapeutic use*
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Powders
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Ventricular Remodeling
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Stroke Volume
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Ventricular Function, Left
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Myocardial Infarction/drug therapy*
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Myocardium/pathology*
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Heart Failure/metabolism*
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Collagen/metabolism*
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Creatine Kinase
;
Fibrosis

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