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.Metabolomic study of the improvement of nitazoxanide on Western-diet induced hepatic steatosis in ApoE-/- mice
Hu-tai-long ZHU ; Xiao-fan CHENG ; Xin GUO ; Le CHANG ; Yin-di ZHAO ; Shang-ze WU ; De-li DONG
Acta Pharmaceutica Sinica 2024;59(9):2529-2538
Nitazoxanide is an FDA-approved antiprotozoal drug. Our previous study found that oral administration of nitazoxanide inhibited Western diet (WD)-induced hepatic steatosis in ApoE-/- mice. However, the specific mechanism remains to be elucidated. In the present study, we performed an untargeted metabolomics approach to reveal the effect of nitazoxanide on the liver metabolic profiles in WD-fed ApoE-/- mice, and carried out the cellular experiments to elucidate the underlying mechanisms. UPLC-MS-based untargeted metabolomics analysis was used to investigate the effect of nitazoxanide on global metabolite changes in liver tissues. The differential metabolites were screened for enrichment analysis and pathway analysis. Hepatocytes were treated with tizoxanide, the metabolite of nitazoxanide, to investigate the underlying mechanism based on the findings in metabolomics study. The improvement of liver lipid metabolism disorders by nitazoxanide treatment in WD-fed ApoE-/- mice was mainly through regulating glycerophospholipid metabolism,
3.Synthesis and evaluation for anti-HCoV-OC43 activity of novel aloperine derivatives with different core structures
Run-ze MENG ; Yue GONG ; Yu-long SHI ; Kun WANG ; Zong-gen PENG ; Dan-qing SONG
Acta Pharmaceutica Sinica 2024;59(2):404-412
In this study, we designed and synthesized 12 novel aloperine derivatives with different core structures. Among them, compound
4.Analysis of the efficacy of adjustable pericardial soft annulus plasty in the treatment of functional tricuspid regurgitation secondary to rheumatic heart disease
Sicong LI ; Xiaomao LONG ; Wei JIANG ; Kequan WEI ; Ze ZHANG ; Hui CHEN ; Songtao LIU ; Xiaohui GUAN
Chinese Journal of Thoracic and Cardiovascular Surgery 2024;40(2):65-71
Objective:To compare the surgical efficacy of pericardial soft ring tricuspid valvuloplasty with DeVega and artificial valvuloplasty.Methods:227 patients undergoing tricuspid valvuloplasty due to rheumatic heart disease complicated with functional tricuspid valve insufficiency were retrospectively analyzed and divided into 3 groups according to tricuspid valvuloplasty dynamic cohort(pericardial ring group, 89 cases; the artificial flap ring group, 61 cases, and the DeVega group, 77 cases) were matched 1∶1 for propensity score(match A: pericardial ring group and artificial flap ring group; match B: pericardial ring group and DeVega group), the successful matching was included in follow-up and data collection, and cases with incomplete case data during follow-up were removed from the study cohort in pairs according to matching conditions. The results of follow-up 1 month, 6 months and 24 months after surgery were compared.Results:1 month after operation: the tricuspid valve regurgitant in all groups was significantly reduced or even disappeared compared with that before operation, and the right atrium and right ventricle were also smaller than that before operation, with statistical significance( P<0.05). 6 months after surgery: There was no statistical significance in the area of tricuspid regurgitation and right atrial/indoor diameter between all groups compared with the results one month after surgery( P>0.05), and there was no statistical significance in the recurrence rate of tricuspid regurgitation between all groups( P>0.05). 24 months after surgery: There were no significant differences in the recurrence rate of tricuspid regurgitation, area of tricuspid regurgitation and right atrial/indoor diameter between the two groups in matching A( P>0.05). There was no statistical significance in the right atrial/indoor diameter between the matched pericardial ring group and the Devega group, but the tricuspid valve regurgentation area of the Devega group at 24 months after surgery was higher than that of the Devega group at 1 month after surgery, and the difference was statistically significant( P<0.05). The regurgitation area and recurrence rate of tricuspid valve were significantly higher than those of pericardium-TVP group( P<0.05). Conclusion:Pericardial soft ring tricuspid valvuloplasty can effectively correct functional tricuspid valvuloplasty and reverse right heart remodeling, which is an effective tricuspid valvuloplasty.
5.Effects of microplastics exposure on learning and memory in mice and its mechanism
Xin-Ze JIANG ; Qiang LIU ; Xu SUN ; Jiang-Shan HOU ; Rui MA ; Mei CHENG ; Yu-Long WU
Acta Anatomica Sinica 2024;55(5):541-546
Objective To investigate the effect of microplastic(MPs)exposure on learning and memory in mice,and its mechanism by observing the protein expression of brain-derived neurotrophic factor(BDNF)/tyrosine receptor kinase B(TrkB)/N-methyl-D-aspartate receptor subtype 2B(NR2B)signaling pathway and neurogenesis.Methods Forty male C57BL/6 mice were randomly divided into control group(Ctrl)and microplastics exposure group(MPs).Mice in MPs group were treated with 0.3 mg/(kg·d)microplastics,administered by gavage at a volume of 200 μl for 30 consecutive days.Morris water maze test was used to evaluate the spatial learning and memory ability of mice.Western blotting was used to detect the protein levels of BDNF,TrkB and NR2B in hippocampus of mice.Immunofluorescent staining was used to observe the number of doublecortin(DCX)and neuronal nuclei antigen(NeuN)positive cells in the hippocampus of mice to evaluate hippocampal neurogenesis.Results Compared with the control group,the ability of learning and memory decreased significantly in MPs group mice(P<0.01).The expression levels of BDNF,TrkB and NR2B in the hippocampus of MPs group mice were significantly lower than those of control group(P<0.05).The number of DCX and NeuN positive cells in the hippocampus of MPs group was significantly lower than that of control group(P<0.01).Conclusion MPs exposure induces learning and memory impairment which may be related to inhibiting BDNF/TrkB/NR2B signaling pathway and reducing hippocampal neurogenesis.
6.Prefabricated curvature internal fixation with Kirschner needle for forearm fracture in children
Yong-Qing SONG ; Ru-Long SONG ; Yi-Quan OU ; Ze-Gang CHEN
China Journal of Orthopaedics and Traumatology 2024;37(3):311-315
Objective To explore clinical effect of precast curvature internal fixation with Kirschner needle in treating forearm fracture in children.Methods From October 2019 to December 2022,32 children with forearm fractures were treated with precast curvature internal fixation with Kirkler's needles,including 25 males and 7 females,aged from 3 to 15 years old with an average of(8.0±0.5)years old,18 patients on the left side and 14 on the right side,24 patients with double fractures of radial and ulna,3 patients with Monteggia fractures,and 4 patients with Galeazzi fractures,and 1 patient with radial neck frac-ture of crooked cap.Operation time,intraoperative blood loss,C-arm fluoroscopy,fracture healing time and complications were recorded,and disabilities of arm,shoulder and hand(DASH)scale and Grace-Eversman forearm double fracture evaluation system were used to evaluate clinical efficacy of precast curvature internal fixation with Kirschner's needle for forearm fracture in children.Resluts All 32 patients were followed up for 2 to 12 months with an average of(7.16±2.51)months.Intraoperative blood loss was(20.68±5.50)ml,C-arm fluoroscopy was(5.80±2.50),and operation time was(24.34±5.10)min,fracture healing time was(8.82±1.62)weeks.Two patients occurred complications,including postoperative rupture of extensor pollicis longus tendon in 1 patient and obvious displacement of fracture caused by rotation of prefabricated curvature Kirschler needle on bone marrow cavity in 1 patient.DASH scores ranged from 0 to 16 scores with an average of(8.32±1.50)scores.According to Grace-Eversman double fracture evaluation system,28 patients got excellent result,2 good and 2 fair.Conclusion The treatment of forearm fracture with Kirschner's needle prefabricated curvature internal fixation has advantages of less trauma,less bleeding,good reduction,stable fixation,fast fracture healing and good functional recovery.
7.Research progress of cement-augmented pedicle screw instrumentation technique
Yong-Cun WEI ; Yan-Chun XIE ; An-Wu XUAN ; Hong-Wen GU ; Bin ZHENG ; Yi LIAN ; Ze-Ning WANG ; Hai-Long YU
Journal of Regional Anatomy and Operative Surgery 2024;33(5):455-459
Osteoporosis is an important cause of internal fixation loosening after spinal surgery.Cement-augmented pedicle screw instru-mentation(CAPSI)technique is the most widely used technique in clinical practice to improve the stability of pedicle screw,mainly applied in osteoporosis and revision surgery,which included conventional solid pedicles crews and fenestrated/cannulated pedicle screws technique.CAPSI technique may cause cement leakage and pulmonary embolism,and there is no consensus on its indications or technical points.Therefore,this article reviews the research progress of CAPSI,in order to provide relevant reference for clinical practice.
8.Clinical Results of Implantation of Subcutaneous Implantable Cardioverter Defibrillator After Transvenous Lead Extraction
Cuizhen YUAN ; Feng ZE ; Ding LI ; Jiangbo DUAN ; Cuncao WU ; Jinshan HE ; Xu ZHOU ; Long WANG ; Xuebin LI
Chinese Circulation Journal 2024;39(8):781-784
Objectives:To evaluate the safety and efficacy of implantation of subcutaneous implantable cardioverter defibrillator(S-ICD)after transvenous lead extraction(TLE)in ICD patients without pacing indications. Methods:All patients who underwent TLE at Peking University People's Hospital from June 2018 to October 2023 were consecutively included.TLE indication,S-ICD implantation indication,defibrillation threshold(DFT)test,complications and postoperative follow-up were collected and analyzed. Results:A total of 11 patients with TV-ICD underwent S-ICD implantation after TLE,eight patients were males and median age were 56(44,65)years.The indications for TLE were infection and lead dysfunction.Nine patients were implanted with S-ICD for secondary prevention,and the most common cause of implantation was ion channelopathies(5 cases).The operative time for S-ICD was 51(48,58)minutes and no perioperative complications were noted.Eight patients underwent DFT testing,and 100%were successful.During a median follow up of 30(9,39)months,a total of six appropriate treatments occurred in two patients,and no complications occurred,including inappropriate treatment,ineffective treatment,infection,lead malfunction and death. Conclusions:Our study provides evidence for S-ICD implantation as a replacement after TV-ICD removal.The S-ICD implantation after TLE is safe and effective.
9.Impact of bladder-neck angle on urination:An application study based on fluid-structure interaction
Xu-Dong JIA ; Xiao-Wan GUO ; Wan-Ze ZHANG ; Li-Juan LU ; Ya-Xuan WANG ; Kai-Long LIU ; Dong-Bin WANG ; Yue-Peng LIU ; Jin-Chun QI
National Journal of Andrology 2024;30(9):789-797
Objective:To assess the deformation of the bladder-neck opening and the impact of the bladder-neck angle(BNA)on urination in male patients by fluid-structure interaction(FSI)analysis.Methods:We established geometric models of the blad-der,prostate and urethra were established,incorporating both normal and enlarged BNAs,and assessed the effects of BNA alteration on urinary flow by FSI simulation of the flow rate and pressure of the urine within the bladder,bladder neck and urethra,and that of pros-tate displacement as well.We retrospectively analyzed the clinical data on 145 male patients from the Second Hospital of Hebei Medical University between June 2020 and June 2023,39 with acute urine retention(the AUR group)and 106 without(the non-AUR group),and evaluate the impact of BNA on urination based on the urinary flow rate and prostate volume.Results:Comparative simulation a-nalysis showed significant differences in the total urethral pressure and flow rate between the normal and enlarged BNA models(P<0.05).The maximum prostate displacement was found at the bladder neck,with moderate displacement and unchanged urethral diame-ter in the normal BNA model,but significant displacement and a reduced urethral opening diameter in the enlarged BNA model.FSI analysis confirmed an evident impact of enlarged BNA on urination,more significant in the AUR than in the non-AUR patients(P<0.05).The BNAs in the patients with the maximum urinary flow rate(Qmax)of<10,10-15 or>15 ml/s were 83.7°±2.5°,67.5°±1.8° and 65.1°±4.8° respectively,with statistically significant difference between the former one and the latter two groups(P<0.05).The BNAs in the patients with normal prostate volume or BPH of grade Ⅰ,Ⅱ,Ⅲ or Ⅳ were 65.0°±3.7°,67.2°±3.1°,71.5°±2.0°,82.8°±3.5° and 105.8°±6.0°,respectively(P<0.05),with statistically significant difference between BPH grades Ⅲ and Ⅳ(P<0.05)as well as between these two and the other three groups(P<0.05),but not among the normal prostate volume,BPH grade Ⅰ and BPH grade Ⅱ groups(P>0.05).Spearman correlation analysis indicated that BNA was strongly correlated with total prostate volume(TPV),transition zone volume(TZV),intravesical prostatic protrusion(IPP),prostatic urethral angle(PUA),IPSS,and Qmax(P<0.05).Conclusion:Changes in BNA affect urination and are closely associated with the se-verity of prostate hyperplasia.The BNA may be an important anatomical factor for assessing the severity of lower urinary tract symptoms in BPH patients.
10. Study on alternative method for vasopressin impurity test of oxytocin injection from biological extraction
Long-Jing GUO ; Ze-An YANG ; Yan-Lin WU ; Tong CAI ; Hua GAO ; Yuan ZHANG
Chinese Pharmacological Bulletin 2023;39(4):794-799
Aim To explore the alternative study on rat blood pressure method and HPLC method for vasopressin impurity test of oxytocin injection from biological extraction. Methods The HPLC method for the vasopressin impurity test in vitro was established and validated. The bio-extrac tion oxytocin injection samples and simulated samples were examined for vasopressin impurity by HPLC and rat blood pressure methods respectively. Results Vasopressin and adjacent impurity peaks were successfully separated by the established method. In the range of 210~13 330 IU•L -1the concentration of vasopressin had a good linear relationship with its peak area with r=0.999 9. The results of HPLC method were consistent with the biological examination method-rat blood pressure method in the current standard. Conclusions The method is proved to be specific, sensitive, and accurate, which can be used as a test method for vasopressin impurity to replace the rat blood pressure method in the current standard.

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