1.KG-CNNDTI: a knowledge graph-enhanced prediction model for drug-target interactions and application in virtual screening of natural products against Alzheimer's disease.
Chengyuan YUE ; Baiyu CHEN ; Long CHEN ; Le XIONG ; Changda GONG ; Ze WANG ; Guixia LIU ; Weihua LI ; Rui WANG ; Yun TANG
Chinese Journal of Natural Medicines (English Ed.) 2025;23(11):1283-1292
Accurate prediction of drug-target interactions (DTIs) plays a pivotal role in drug discovery, facilitating optimization of lead compounds, drug repurposing and elucidation of drug side effects. However, traditional DTI prediction methods are often limited by incomplete biological data and insufficient representation of protein features. In this study, we proposed KG-CNNDTI, a novel knowledge graph-enhanced framework for DTI prediction, which integrates heterogeneous biological information to improve model generalizability and predictive performance. The proposed model utilized protein embeddings derived from a biomedical knowledge graph via the Node2Vec algorithm, which were further enriched with contextualized sequence representations obtained from ProteinBERT. For compound representation, multiple molecular fingerprint schemes alongside the Uni-Mol pre-trained model were evaluated. The fused representations served as inputs to both classical machine learning models and a convolutional neural network-based predictor. Experimental evaluations across benchmark datasets demonstrated that KG-CNNDTI achieved superior performance compared to state-of-the-art methods, particularly in terms of Precision, Recall, F1-Score and area under the precision-recall curve (AUPR). Ablation analysis highlighted the substantial contribution of knowledge graph-derived features. Moreover, KG-CNNDTI was employed for virtual screening of natural products against Alzheimer's disease, resulting in 40 candidate compounds. 5 were supported by literature evidence, among which 3 were further validated in vitro assays.
Alzheimer Disease/drug therapy*
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Biological Products/therapeutic use*
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Humans
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Neural Networks, Computer
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Machine Learning
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Drug Discovery/methods*
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Algorithms
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Drug Evaluation, Preclinical/methods*
2.Construction and identification of recombinant fowl adenovirus 4 expressing Cap protein of goose astrovirus virus genotype 2
Xingyu LI ; Yan LI ; Panpan YANG ; Junjie LIU ; Mengjia XIANG ; Yutao ZHU ; Luyao QIU ; Qilong QIAO ; Boshun ZHANG ; Dexin BU ; Chenghao HAN ; Chunmei YU ; Yanfang CONG ; Zeng WANG ; Jianli LI ; Baiyu WANG ; Jun ZHAO
Chinese Journal of Veterinary Science 2025;45(3):443-448,513
To construct a recombinant fowl adenovirus 4(FAdV-4)expressing the Cap protein of goose astrovirus genotype 2(GoAstV-2),the expression cassette of Cap gene was inserted into the natural 1 966 bp deletion region of the FAdV-4 genome in the infectious clone p15A-cm-FAdV4-HNJZ.The resulted recombinant plasmid p15A-cm-FAdV4-HNJZ-Cap/GoAstV-2 was linearized with restriction enzyme and transfected into chicken hepatoma cell line(LMH)to rescue the recombinant FAdV-4 expressing the Cap protein of GoAstV-2,rF Ad V4-Cap/GoAstV-2.After 15 passages in LMH cells,the recombinant rFAdV4-Cap/GoAstV-2 was identified by PCR using primers flanking the insertion site of the Cap gene expression cassette and using viral genome DNA extracted from rFAdV4-Cap/GoAstV-2 infected LMH cells as template.LMH cells were in-fected with 15th passage rFAdV4-Cap/GoAstV-2 and indirect immunofluorescence was performed with a polyclonal antibody against Cap protein as the primary antibody.Western blot was carried out with lysates of rFAdV4-Cap/GoAstV-2 infected LMH cells.The in vitro replication dynamic of the 15th passage of the rFAdV4-Cap/GoAstV-2 was also investigated in LMH cells.The results demonstrated that the Cap gene of GoAstV-2 was presented in the genome of the recombinant vi-rus rF AdV4-Cap/Go Ast V-2,and could be expressed stably.The prepared recombinant virus in this study will lay a foundation for developing inactivated bivalent vaccine candidate against co-in-fection of FAdV-4 and GoAstV-2 in goose.
3.Effect of zearalenone on proliferation and apoptosis of sika deer antler chondro-cytes
Chenhao WANG ; Xueyuan YAO ; Baiyu LI ; Qiaoling ZHANG ; Zhanpeng YUE ; Zhanqing YANG ; Bin GUO
Chinese Journal of Veterinary Science 2025;45(1):115-120,128
To investigate the effects of zearalenone(ZEA)on the proliferation and apoptosis of sika deer antler chondrocytes,the chondrocytes were isolated and cultured in vitro and treated with 50μmol/L ZEA for 24 h.Flow cytometry was used to assess cell proliferation,cell cycle,apoptosis,mitochondrial membrane potential,and intracellular levels of reactive oxygen species(ROS).The expression changes of hypertrophic cartilage cell marker genes Col X,Runx2,Alpl,and apoptosis-related genes Casp-3,Bax,Bcl-2 were measured using quantitative PCR.Additionally,glutathione reductase(GR)activity and the levels of the oxidative stress marker malondialdehyde(MDA)were determined.The results showed that after 24 h of ZEA treatment,cell proliferation was sig-nificantly inhibited,with an increase in the number of cells in the G0/G1 phase and a decrease in the S phase.The expression levels of hypertrophic chondrocyte marker genes Col X,Runx2 and Al-pl were significantly increased.Apoptosis rate was significantly increased,with elevated expression of pro-apoptotic genes Casp-3,Bax and reduced expression of the anti-apoptotic gene Bcl-2.The content of MDA in the antler chondrocytes increased,ROS levels rose,and GR activity decreased.The mitochondrial membrane potential reduced.The results suggested that ZEA could inhibit the proliferation of antler chondrocytes and promote the apoptosis by regulating cellular oxidative stress responses and the expression of apoptosis-related genes.
4.Construction and identification of recombinant fowl adenovirus 4 expressing Cap protein of goose astrovirus virus genotype 2
Xingyu LI ; Yan LI ; Panpan YANG ; Junjie LIU ; Mengjia XIANG ; Yutao ZHU ; Luyao QIU ; Qilong QIAO ; Boshun ZHANG ; Dexin BU ; Chenghao HAN ; Chunmei YU ; Yanfang CONG ; Zeng WANG ; Jianli LI ; Baiyu WANG ; Jun ZHAO
Chinese Journal of Veterinary Science 2025;45(3):443-448,513
To construct a recombinant fowl adenovirus 4(FAdV-4)expressing the Cap protein of goose astrovirus genotype 2(GoAstV-2),the expression cassette of Cap gene was inserted into the natural 1 966 bp deletion region of the FAdV-4 genome in the infectious clone p15A-cm-FAdV4-HNJZ.The resulted recombinant plasmid p15A-cm-FAdV4-HNJZ-Cap/GoAstV-2 was linearized with restriction enzyme and transfected into chicken hepatoma cell line(LMH)to rescue the recombinant FAdV-4 expressing the Cap protein of GoAstV-2,rF Ad V4-Cap/GoAstV-2.After 15 passages in LMH cells,the recombinant rFAdV4-Cap/GoAstV-2 was identified by PCR using primers flanking the insertion site of the Cap gene expression cassette and using viral genome DNA extracted from rFAdV4-Cap/GoAstV-2 infected LMH cells as template.LMH cells were in-fected with 15th passage rFAdV4-Cap/GoAstV-2 and indirect immunofluorescence was performed with a polyclonal antibody against Cap protein as the primary antibody.Western blot was carried out with lysates of rFAdV4-Cap/GoAstV-2 infected LMH cells.The in vitro replication dynamic of the 15th passage of the rFAdV4-Cap/GoAstV-2 was also investigated in LMH cells.The results demonstrated that the Cap gene of GoAstV-2 was presented in the genome of the recombinant vi-rus rF AdV4-Cap/Go Ast V-2,and could be expressed stably.The prepared recombinant virus in this study will lay a foundation for developing inactivated bivalent vaccine candidate against co-in-fection of FAdV-4 and GoAstV-2 in goose.
5.Effect of zearalenone on proliferation and apoptosis of sika deer antler chondro-cytes
Chenhao WANG ; Xueyuan YAO ; Baiyu LI ; Qiaoling ZHANG ; Zhanpeng YUE ; Zhanqing YANG ; Bin GUO
Chinese Journal of Veterinary Science 2025;45(1):115-120,128
To investigate the effects of zearalenone(ZEA)on the proliferation and apoptosis of sika deer antler chondrocytes,the chondrocytes were isolated and cultured in vitro and treated with 50μmol/L ZEA for 24 h.Flow cytometry was used to assess cell proliferation,cell cycle,apoptosis,mitochondrial membrane potential,and intracellular levels of reactive oxygen species(ROS).The expression changes of hypertrophic cartilage cell marker genes Col X,Runx2,Alpl,and apoptosis-related genes Casp-3,Bax,Bcl-2 were measured using quantitative PCR.Additionally,glutathione reductase(GR)activity and the levels of the oxidative stress marker malondialdehyde(MDA)were determined.The results showed that after 24 h of ZEA treatment,cell proliferation was sig-nificantly inhibited,with an increase in the number of cells in the G0/G1 phase and a decrease in the S phase.The expression levels of hypertrophic chondrocyte marker genes Col X,Runx2 and Al-pl were significantly increased.Apoptosis rate was significantly increased,with elevated expression of pro-apoptotic genes Casp-3,Bax and reduced expression of the anti-apoptotic gene Bcl-2.The content of MDA in the antler chondrocytes increased,ROS levels rose,and GR activity decreased.The mitochondrial membrane potential reduced.The results suggested that ZEA could inhibit the proliferation of antler chondrocytes and promote the apoptosis by regulating cellular oxidative stress responses and the expression of apoptosis-related genes.
6.Comparison of mid-to-long term outcomes between mitral valve repair and biological valve replacement in patients over 60 with rheumatic mitral valve disease based on a propensity score matching study
Wenbo ZHANG ; Jie HAN ; Tiange LUO ; Baiyu TIAN ; Fei MENG ; Wenjian JIANG ; Yuqing JIAO ; Xiaoming LI ; Jintao FU ; Yichen ZHAO ; Fei LI ; Xu MENG ; Jiangang WANG
Chinese Journal of Surgery 2024;62(11):1016-1023
Objective:To compare and discuss the mid-to-long-term outcomes of mitral valve repair (MVP) versus biological mitral valve replacement (bMVR) in patients aged 60 years and above with rheumatic mitral valve disease.Methods:This is a retrospective cohort study. A total of 765 patients aged 60 years and older, diagnosed with rheumatic mitral valve disease and who underwent MVP or bMVR at Beijing Anzhen Hospital from January 2010 to January 2023, were retrospectively included. Among them, 186 were male and 579 were female, with an age of (66.1±4.5) years (range: 60 to 82 years). Patients were divided into two groups based on the surgical method: the mitral valve repair group (MVP group, n=256) and the bioprosthetic mitral valve replacement group (bMVR group, n=509). A 1∶1 propensity score matching was performed using a caliper value of 0.2 based on preoperative data. Paired sample t-tests, χ2 tests, or Fisher′s exact tests were used for intergroup comparisons. Kaplan-Meier method was employed to plot survival curves and valve-related reoperation rate curves for both groups before and after matching, and Log-rank tests were used to compare the mid-to long-term survival rates and valve-related reoperation rates between the two groups. Results:A total of 765 patients who completed follow-up were ultimately included, with a follow-up period ( M(IQR)) of 5.1(5.0) years (range: 1.0 to 12.9 years). After matching, each group consisted of 256 patients. The incidence of early postoperative atrial fibrillation (39.1% vs. 49.2%, χ2=4.95, P=0.026) and early mortality rates (2.0% vs. 6.2%, χ2=4.97, P=0.026) were lower in the MVP group. Unadjusted Kaplan-Meier analysis showed significantly higher 5-year and 10-year survival rates for the MVP group (92.54% vs. 83.02%, 86.22% vs. 70.19%, Log-rank: P=0.001). After adjustment with propensity scores, the Kaplan-Meier analysis still indicated higher 5-year and 10-year survival rates in the MVP group compared to the bMVR group (92.54% vs. 85.89%, 86.22% vs. 74.83%, Log-rank: P=0.024). There were no significant differences in the rates of valve-related reoperation between the two groups before and after matching (5-year and 10-year reoperation rates pre-matching: 1.75% vs. 0.57%, 5.39% vs. 7.54%, Log-rank: P=0.207; post-matching: 1.75% vs. 0, 5.39% vs. 9.27%, Log-rank: P=0.157). Conclusion:For patients aged 60 years and above with rheumatic mitral valve disease, mitral valve repair offers better mid-to-long-term survival compared to biological valve replacement.
7.Comparison of mid-to-long term outcomes between mitral valve repair and biological valve replacement in patients over 60 with rheumatic mitral valve disease based on a propensity score matching study
Wenbo ZHANG ; Jie HAN ; Tiange LUO ; Baiyu TIAN ; Fei MENG ; Wenjian JIANG ; Yuqing JIAO ; Xiaoming LI ; Jintao FU ; Yichen ZHAO ; Fei LI ; Xu MENG ; Jiangang WANG
Chinese Journal of Surgery 2024;62(11):1016-1023
Objective:To compare and discuss the mid-to-long-term outcomes of mitral valve repair (MVP) versus biological mitral valve replacement (bMVR) in patients aged 60 years and above with rheumatic mitral valve disease.Methods:This is a retrospective cohort study. A total of 765 patients aged 60 years and older, diagnosed with rheumatic mitral valve disease and who underwent MVP or bMVR at Beijing Anzhen Hospital from January 2010 to January 2023, were retrospectively included. Among them, 186 were male and 579 were female, with an age of (66.1±4.5) years (range: 60 to 82 years). Patients were divided into two groups based on the surgical method: the mitral valve repair group (MVP group, n=256) and the bioprosthetic mitral valve replacement group (bMVR group, n=509). A 1∶1 propensity score matching was performed using a caliper value of 0.2 based on preoperative data. Paired sample t-tests, χ2 tests, or Fisher′s exact tests were used for intergroup comparisons. Kaplan-Meier method was employed to plot survival curves and valve-related reoperation rate curves for both groups before and after matching, and Log-rank tests were used to compare the mid-to long-term survival rates and valve-related reoperation rates between the two groups. Results:A total of 765 patients who completed follow-up were ultimately included, with a follow-up period ( M(IQR)) of 5.1(5.0) years (range: 1.0 to 12.9 years). After matching, each group consisted of 256 patients. The incidence of early postoperative atrial fibrillation (39.1% vs. 49.2%, χ2=4.95, P=0.026) and early mortality rates (2.0% vs. 6.2%, χ2=4.97, P=0.026) were lower in the MVP group. Unadjusted Kaplan-Meier analysis showed significantly higher 5-year and 10-year survival rates for the MVP group (92.54% vs. 83.02%, 86.22% vs. 70.19%, Log-rank: P=0.001). After adjustment with propensity scores, the Kaplan-Meier analysis still indicated higher 5-year and 10-year survival rates in the MVP group compared to the bMVR group (92.54% vs. 85.89%, 86.22% vs. 74.83%, Log-rank: P=0.024). There were no significant differences in the rates of valve-related reoperation between the two groups before and after matching (5-year and 10-year reoperation rates pre-matching: 1.75% vs. 0.57%, 5.39% vs. 7.54%, Log-rank: P=0.207; post-matching: 1.75% vs. 0, 5.39% vs. 9.27%, Log-rank: P=0.157). Conclusion:For patients aged 60 years and above with rheumatic mitral valve disease, mitral valve repair offers better mid-to-long-term survival compared to biological valve replacement.
8.Reflections on improving drug success rates with AIDD and CADD
Baiyu CHEN ; Lunan LYU ; Xiaodi XU ; Ying ZHANG ; Wei LI ; Wei FU
Journal of China Pharmaceutical University 2024;55(3):284-294
The rapid advancements in artificial intelligence(AI)and computational sciences,particularly through the introduction of artificial intelligence drug design(AIDD)and computer-aided drug design(CADD)technologies,have revolutionized pathways in drug development.These include techniques such as natural language processing,image recognition,deep learning,and machine learning.By employing advanced algorithms and data processing techniques,these technologies have significantly enhanced the efficiency and success rate of R&D processes.In drug discovery,AI technologies have accelerated the identification of drug targets,screening of candidate drugs,pharmacological assessments,and quality control,effectively reducing R&D risks and costs.This article delves into the application of AIDD and CADD in drug development,analyzing their roles in enhancing the success rates and efficiencies of drug design,exploring their future trends,and addressing the potential challenges.
9.Analyzing the social health status of older adults in urban communities and its associated factors
Jiawei LI ; Xiaoqing MENG ; Chao GAO ; Baiyu ZHOU ; Shangxin LIU ; Jiahui YAN ; Qiyu PAN ; Yan CEN ; Juqiang CHEN ; Pulin YU
Chinese Journal of Geriatrics 2024;43(10):1321-1325
Objective:To examines the social health status and influencing factors affecting the elderly population in urban communities of Beijing, based on the "the Standard for Healthy Chinese Older Adults(2022)" .Methods:Using the stratified sampling method, a total of 159 elderly individuals aged 60 and above from the Lanyuan community in the Malianwa street jurisdiction of Haidian district, Beijing, were selected as research subjects.The average age of the participants was(70.7±7.9)years, comprising 74 males and 85 females.Household face-to-face interviews were conducted, utilizing self-compiled questionnaires to perform a comprehensive assessment and analysis of the social health status of the elderly.Results:In the study involving community-based elderly participants, 32.1%(51 cases)were classified as healthy.The analysis revealed statistically significant differences in the social health status among various age groups of the elderly( χ2=11.802, P=0.019), with a notable downward trend in social health status as age increases( χ2=9.626, P=0.002).Furthermore, the results of multivariate Logistic regression analysis indicated that educational level( OR=2.119, 95% CI: 1.044-4.031, P=0.038)and chronic disease status( OR=5.007, 95% CI: 1.083-23.140, P=0.039)are significant influencing factors on the social health status of older adults. Conclusions:The social health status of the elderly in urban communities in Beijing is generally low and deteriorates progressively with age.Both educational attainment and chronic disease prevalence significantly influence the social health of this demographic.For elderly individuals with lower educational levels and poor chronic disease management, it is essential to conduct social health assessments and implement targeted intervention strategies to enhance their overall social health.
10.An investigation on multidimensional health status and its influencing factors among the elderly in a community of Beijing
Shangxin LIU ; Jiahui YAN ; Jing SHI ; Chao GAO ; Baiyu ZHOU ; Jiawei LI ; Xiao TAN ; Yongquan LIU ; Jing QI ; Pulin YU
Chinese Journal of Geriatrics 2024;43(12):1623-1629
Objective:To evaluate the health status of elderly individuals by examining physical, psychological, and social health, as well as analyzing the risk factors that affect these dimensions of health among community-dwelling residents.Methods:Utilizing whole group sampling, a total of 404 elderly individuals from the Meiyuan community, located under the jurisdiction of Malianwa Street in Haidian District, Beijing, were selected for this study.The status of physical health, mental health, social health and overall health in the elderly were evaluated by a self-made questionnaire.The influencing factors of health status in all dimensions were analyzed by Chi-square test and multiple logistic regression.Results:The overall health rate among elderly community-dwelling residents in the study was 21.3%(86 cases), while the rates for physical health, mental health, and social health were 66.8%(270 cases), 86.6%(350 cases), and 24.3%(98 cases), respectively.Marital status( OR=2.872, 95% CI: 1.462-5.641), residential status( OR=4.819, 95% CI: 1.294-17.952), cognitive function( OR=3.833, 95% CI: 1.899-7.734), health literacy( OR=0.455, 95% CI: 0.226-0.916), social participation( OR=1.642, 95% CI: 1.192-2.263), social adaptation( OR=1.716, 95% CI: 1.125-2.618), and social network( OR=1.727, 95% CI: 1.147-2.598)were identified as influencing factors for physical health in the elderly(all P<0.05).Factors affecting mental health included instrumental activities of daily living( OR=3.248, 95% CI: 1.997-5.282)and health risk factors( OR=2.475, 95% CI: 1.315-4.656)(all P<0.05).For social health, the influencing factors were residence status( OR=3.158, 95% CI: 1.280-7.794), sleep status( OR=1.801, 95% CI: 1.101-2.947), instrumental activities of daily living( OR=2.966, 95% CI: 1.374-6.405), and life satisfaction( OR=2.362, 95% CI: 1.140-4.893)(all P<0.05).Additionally, education( OR=0.588, 95% CI: 0.360-0.962)and home care services( OR=2.272, 95% CI: 1.278-4.039)were found to affect the overall health of the elderly(all P<0.05). Conclusions:In this study, the overall health rate among community-dwelling elderly residents is reported to be 21.3%.Health status in this population gradually deteriorates with advancing age.Numerous factors influence the multidimensional health of the elderly, with education level and caregiving status identified as significant determinants of their overall health.

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