1.Natural product virtual-interact-phenotypic target characterization: A novel approach demonstrated with Salvia miltiorrhiza extract.
Rui XU ; Hengyuan YU ; Yichen WANG ; Boyu LI ; Yong CHEN ; Xuesong LIU ; Tengfei XU
Journal of Pharmaceutical Analysis 2025;15(2):101101-101101
Natural products (NPs) have historically been a fundamental source for drug discovery. Yet the complex nature of NPs presents substantial challenges in pinpointing bioactive constituents, and corresponding targets. In the present study, an innovative natural product virtual screening-interaction-phenotype (NP-VIP) strategy that integrates virtual screening, chemical proteomics, and metabolomics to identify and validate the bioactive targets of NPs. This approach reduces false positive results and enhances the efficiency of target identification. Salvia miltiorrhiza (SM), a herb with recognized therapeutic potential against ischemic stroke (IS), was used to illustrate the workflow. Utilizing virtual screening, chemical proteomics, and metabolomics, potential therapeutic targets for SM in the IS treatment were identified, totaling 29, 100, and 78, respectively. Further analysis via the NP-VIP strategy highlighted five high-confidence targets, including poly [ADP-ribose] polymerase 1 (PARP1), signal transducer and activator of transcription 3 (STAT3), amyloid precursor protein (APP), glutamate-ammonia ligase (GLUL), and glutamate decarboxylase 67 (GAD67). These targets were subsequently validated and found to play critical roles in the neuroprotective effects of SM. The study not only underscores the importance of SM in treating IS but also sets a precedent for NP research, proposing a comprehensive approach that could be adapted for broader pharmacological explorations.
2.Correlation analysis of genetic and environmental factors with clinical characteristics of pediatric upper urinary tract calculi
Youquan ZHAO ; Xiaochuan WANG ; Boyu YANG ; Chen NING ; Houyu ZHOU ; Huimin ZHAO ; Xiaochen WANG ; Ruiyu YUE ; Shao ZHANG ; Manjiang SUN ; Jun LI
Chinese Journal of Urology 2025;46(10):728-733
Objective:To investigate the influence of genetic and environmental factors on the clinical characteristics of upper urinary tract calculi in pediatric patients.Methods:This study was a retrospective case series. The clinical data of 179 children under the age of 14 with upper urinary tract calculi treated at Beijing Friendship Hospital,Capital Medical University,from August 2014 to February 2023 were analyzed. There were 121 males(67.60%)and 58 females(32.40%),with a median age at onset of 2.10(1.14,5.17)years. Thirty-three cases(18.44%)had a family history of urinary stone disease. Stone characteristics was defined by CT,with a median stone burden(sum of the diameters of all stones)of 1.3(1.00,1.60)cm. Fifty-four(30.17%)children had staghorn calculi. Multiple stones were present in 92 cases(51.40%),and bilateral stones in 52 cases(29.05%),with hydronephrosis was present in 119 children(66.48%). The median follow-up time was 67 months,and 36 children(20.11%)experienced stone recurrence. Dietary habits and related information were collected by electronic questionnaire,including a total of 115 children(64.25%)with an unbalanced diet,101(56.42%)with insufficient water intake,and 32 children(17.88%)with a preference for a high-protein diet. Tap water was used as the source of drinking water by 128 patients(71.51%),and 107(59.78%)took dietary supplements. Whole-exome sequencing revealed that 55 children(30.73%)carried pathogenic mutations in stone-related genes. Binary logistic regression was used for univariate analysis of above risk factors. Variables with P < 0.1 in univariate analysis and without multicollinearity were included in multivariate logistic regression to further screen for independent risk factors. Results:Multivariate analysis confirmed that carrying stone-related pathogenic gene mutations( OR = 3.06,95% CI 1.25?7.45, P = 0.014)and insufficient water intake( OR = 3.28,95% CI 1.14?9.47, P = 0.028)were independent risk factors for higher stone burden. A high-protein diet( OR = 2.40,95% CI 1.03?5.63, P = 0.044),carrying stone-related pathogenic gene mutations( OR = 4.57,95% CI 2.21?9.46, P<0.01),and a family history of stones( OR = 3.18,95% CI 1.28 ~ 7.91, P = 0.013)were independent risk factors for staghorn calculi. Multiple stones were closely associated with a family history of stones( OR = 2.66,95% CI 1.15-6.17, P = 0.022)and carrying stone-related pathogenic gene mutations( OR = 3.22,95% CI 1.60-6.48, P = 0.001). Moreover,carrying stone-related pathogenic gene mutations( OR = 5.19,95% CI 2.52?13.82, P < 0.01)were an independent risk factor for stone recurrence,whereas dietary supplement intake was a protective factor( OR = 0.26,95% CI 0.11?0.62, P = 0.002). Conclusions:Genetic and environmental factors play significant roles in the occurrence and development of pediatric upper urinary tract stones. A high-protein diet as well as a positive family history of stones are independent risk factors for staghorn calculi,and insufficient water intake is a critical environmental factor for stone formation,while appropriate use of dietary supplements may help reduce the risk of stone recurrence. Genetic testing indicates that approximately 30% of children carry stone-related pathogenic gene mutations,and these patients prone to severe stone and an increased risk of recurrence.
3.Natural product virtual-interact-phenotypic target characterization:A novel approach demonstrated with Salvia miltiorrhiza extract
Rui XU ; Hengyuan YU ; Yichen WANG ; Boyu LI ; Yong CHEN ; Xuesong LIU ; Tengfei XU
Journal of Pharmaceutical Analysis 2025;15(2):425-441
Natural products(NPs)have historically been a fundamental source for drug discovery.Yet the complex nature of NPs presents substantial challenges in pinpointing bioactive constituents,and corresponding targets.In the present study,an innovative natural product virtual screening-interaction-phenotype(NP-VIP)strategy that integrates virtual screening,chemical proteomics,and metabolomics to identify and validate the bioactive targets of NPs.This approach reduces false positive results and enhances the ef-ficiency of target identification.Salvia miltiorrhiza(SM),a herb with recognized therapeutic potential against ischemic stroke(IS),was used to illustrate the workflow.Utilizing virtual screening,chemical proteomics,and metabolomics,potential therapeutic targets for SM in the IS treatment were identified,totaling 29,100,and 78,respectively.Further analysis via the NP-VIP strategy highlighted five high-confidence targets,including poly[ADP-ribose]polymerase 1(PARP1),signal transducer and activator of transcription 3(STAT3),amyloid precursor protein(APP),glutamate-ammonia ligase(GLUL),and glutamate decarboxylase 67(GAD67).These targets were subsequently validated and found to play critical roles in the neuroprotective effects of SM.The study not only underscores the importance of SM in treating IS but also sets a precedent for NP research,proposing a comprehensive approach that could be adapted for broader pharmacological explorations.
4.Correlation analysis of genetic and environmental factors with clinical characteristics of pediatric upper urinary tract calculi
Youquan ZHAO ; Xiaochuan WANG ; Boyu YANG ; Chen NING ; Houyu ZHOU ; Huimin ZHAO ; Xiaochen WANG ; Ruiyu YUE ; Shao ZHANG ; Manjiang SUN ; Jun LI
Chinese Journal of Urology 2025;46(10):728-733
Objective:To investigate the influence of genetic and environmental factors on the clinical characteristics of upper urinary tract calculi in pediatric patients.Methods:This study was a retrospective case series. The clinical data of 179 children under the age of 14 with upper urinary tract calculi treated at Beijing Friendship Hospital,Capital Medical University,from August 2014 to February 2023 were analyzed. There were 121 males(67.60%)and 58 females(32.40%),with a median age at onset of 2.10(1.14,5.17)years. Thirty-three cases(18.44%)had a family history of urinary stone disease. Stone characteristics was defined by CT,with a median stone burden(sum of the diameters of all stones)of 1.3(1.00,1.60)cm. Fifty-four(30.17%)children had staghorn calculi. Multiple stones were present in 92 cases(51.40%),and bilateral stones in 52 cases(29.05%),with hydronephrosis was present in 119 children(66.48%). The median follow-up time was 67 months,and 36 children(20.11%)experienced stone recurrence. Dietary habits and related information were collected by electronic questionnaire,including a total of 115 children(64.25%)with an unbalanced diet,101(56.42%)with insufficient water intake,and 32 children(17.88%)with a preference for a high-protein diet. Tap water was used as the source of drinking water by 128 patients(71.51%),and 107(59.78%)took dietary supplements. Whole-exome sequencing revealed that 55 children(30.73%)carried pathogenic mutations in stone-related genes. Binary logistic regression was used for univariate analysis of above risk factors. Variables with P < 0.1 in univariate analysis and without multicollinearity were included in multivariate logistic regression to further screen for independent risk factors. Results:Multivariate analysis confirmed that carrying stone-related pathogenic gene mutations( OR = 3.06,95% CI 1.25?7.45, P = 0.014)and insufficient water intake( OR = 3.28,95% CI 1.14?9.47, P = 0.028)were independent risk factors for higher stone burden. A high-protein diet( OR = 2.40,95% CI 1.03?5.63, P = 0.044),carrying stone-related pathogenic gene mutations( OR = 4.57,95% CI 2.21?9.46, P<0.01),and a family history of stones( OR = 3.18,95% CI 1.28 ~ 7.91, P = 0.013)were independent risk factors for staghorn calculi. Multiple stones were closely associated with a family history of stones( OR = 2.66,95% CI 1.15-6.17, P = 0.022)and carrying stone-related pathogenic gene mutations( OR = 3.22,95% CI 1.60-6.48, P = 0.001). Moreover,carrying stone-related pathogenic gene mutations( OR = 5.19,95% CI 2.52?13.82, P < 0.01)were an independent risk factor for stone recurrence,whereas dietary supplement intake was a protective factor( OR = 0.26,95% CI 0.11?0.62, P = 0.002). Conclusions:Genetic and environmental factors play significant roles in the occurrence and development of pediatric upper urinary tract stones. A high-protein diet as well as a positive family history of stones are independent risk factors for staghorn calculi,and insufficient water intake is a critical environmental factor for stone formation,while appropriate use of dietary supplements may help reduce the risk of stone recurrence. Genetic testing indicates that approximately 30% of children carry stone-related pathogenic gene mutations,and these patients prone to severe stone and an increased risk of recurrence.
5.Genetic analysis of a child with Primary hypertrophic osteoarthropathy
Chen WANG ; Xueping QIU ; Yating CHENG ; Boyu LI ; Yuanzhen ZHANG ; Jianhong MA ; Fang ZHENG
Chinese Journal of Medical Genetics 2024;41(9):1100-1104
Objective:To explore the genetic etiology of a child with primary hypertrophic osteoarthropathy(PHO).Methods:A child who was admitted to Zhongnan Hospital of Wuhan University on July 27, 2021 was selected as the study subject. Genomic DNA was extracted from peripheral blood samples of the child and his parents and subjected to whole exome sequencing. Suspected splicing variant was verified by Sanger sequencing of family members. In vitro function was validated through a minigene assay, whilst the suspected exonic deletion was validated by long-fragment PCR. This study was approved by the Children′s Hospital Affiliated to Zhengzhou University (Ethics No. 2023-K-011). Results:Whole exome sequencing revealed that the child has harbored compound heterozygous variants of HPGD gene, including a heterozygous deletion (Exon 3 del) derived from his father and a splicing variant (c.421+ 1G>T) derived from his mother. Long-fragment PCR verified that the child and his father had both harbored a 7 565 bp heterozygous deletion (c.218-1304_324+ 6156del), whilst the minigene assay proved that the splicing variant has resulted in skipping of exon 4. Conclusion:The heterozygous c. 218-1304_324+ 6156del deletion and the c. 421+ 1G>T splicing variant of the HPGD gene probably underlay the pathogenesis in this child. Above finding has enriched the mutational spectrum of the HPGD gene and provided a basis for genetic counseling and prenatal diagnosis for this family.
6.The application value of artificial intelligence in evaluating brain atrophy in patients with spinocerebellar ataxia type 3
Sidan CHEN ; Jiaojiao WU ; Boyu CAO ; Kuanghui XU ; Yugang LI ; Zhouyao HU ; Rui HUA ; Feng SHI ; Xiaochuan WANG ; Le QI
Journal of Practical Radiology 2024;40(7):1037-1042
Objective To evaluate the degree of brain atrophy in spinocerebellar ataxia type 3(SCA3)patients based on artificial intelligence(AI)technology,and to explore the correlation between the degree of brain atrophy and the severity of the disease.Methods The clinical and imaging data of 23 SCA3 patients(SCA3 group)and 24 healthy controls(HC)(HC group)were collected.The International Cooperative Ataxia Rating Scale(ICARS)was used to evaluate the severity of ataxia in patients with SCA3.AI technology was used to process the 3D-T1 WI MR image data of the SCA3 and HC groups to segment and measure the volume and volume percentage of brain,followed by correlation analyses between brain structural alterations and the severity of ataxia in SCA3 patients.Results There were no significant differences in gender and age between the two groups(P>0.05).The SCA3 group had a significant reduction in the volume and volume percentage of various brain regions,such as the frontal,temporal,parietal,occipital,limbic,right cerebral white mat-ter,subcortical gray matter,cerebellum and brainstem,compared to the HC group(multiple hypothesis testing adjusted P<0.01).In the SCA3 group,the ICARS showed positive correlation with patient age(r=0.571,P=0.004)and negative correlation with the vol-ume of the left cerebellar white matter,vermis,medulla oblongata,and the volume percentages of bilateral cerebellar white matter,vermis,pons,medulla oblongata(P<0.05).Conclusion The significant atrophy of the supratentorial and subtentorial regions of the brain in SCA3 patients.The globus pallidus exhibits the most substantial atrophy,suggesting its potential as an imaging diagnostic marker of SC A3.
7.Efficacy comparison of percutaneous nephrolithotomy with Holmium laser for upper urinary calculi in Uyghur and Han pediatric patients
Jun LI ; Ruiyu YUE ; Xiaochuan WANG ; Islam KAHRIMAN· ; Batur JESUR· ; Youquan ZHAO ; Boyu YANG ; Chen NING
Chinese Journal of Urology 2024;45(7):532-538
Objective:To compare the effectiveness, safety and postoperative recurrence of percutaneous nephrolithotomy (PCNL) with Holmium laser for upper urinary calculi in Uyghur and Han pediatric patients.Methods:The data of 123 Uyghur and 71 Han pediatric patients with upper urinary calculi admitted to First People's Hospital of Kashgar, Xinjiang and Beijing Friendship Hospital, Capital Medical University respectively, from August 2018 to August 2023, were retrospectively reviewed. The gender [males 73 (59.3%) vs.46 (64.8%) ], laterality (single/bilateral: 94/29 vs. 59/12), hydronephrosis [115 (93.5%) vs. 63 (88.7%)] and anatomical abnormalities [2(1.6%) vs. 5(7.0%)] of Uyghur and Han children were not statistically significant ( P>0.05). Uyghur children were older than Han children [5 (3, 7) vs. 3 (2, 6) years old], with a higher proportion of emaciated children [27 (21.9%) vs. 6 (8.5%) cases], a larger maximum stone diameter [(2.30±0.78) vs. (1.96±1.50) cm] and a lower proportion of multiple stones [46 (37.4%) vs. 52 (73.2%) cases] (all P<0.05). All the patients were treated with Holmium laser PCNL. The channels of the procedures in this study include F12-18 small channels and visual puncture channels. The operation datas, stone-free rate (SFR), complication rate (CR) and stone recurrence rate of the two groups were compared. Meanwhile, multiple logistic regression analysis was used to explore the factors influencing these indicators. Results:The operation time for Uyghur children was significantly longer than that of Han children [75.0 (58.0, 93.0) vs. 30.0 (20.0, 48.8) min]. Additionally, a greater proportion of Uyghur children underwent PCNL with F12-18 small channels than Han children [119 (96.7%) vs. 49(69.0%) cases]. The SFR [89.4%(110/123)vs.88.7%(63/71)], and postoperative CR [31.7%(39/123)vs. 26.8%(19/71)] in Uyghur and Han patients were not significantly different (all P>0.05). The recurrence rate in Uyghur children was higher than that observed in Han children [28.1%(25/89) vs. 15.6%(10/64), P=0.033]. The multivariate logistic regression analysis results indicated that the maximum stone diameter was an independent risk factor for SFR in both groups ( OR=0.401, 95% CI 0.191-0.842, P=0.016). Similarly, maximum stone diameter ( OR=1.896, 95% CI 1.088-3.304, P=0.024) and multiple stones ( OR=3.225, 95% CI 1.409-7.384, P=0.024) were identified as independent risk factors for CR. Ethnicity was not independent risk factor for SFR( OR=0.679, 95% CI 0.215-2.140), CR( OR=1.047, 95% CI 0.495-2.215) and stone recurrence rate( OR=0.820, 95% CI 0.285-2.356, all P>0.05). Conclusions:In comparison to Han pediatric patients during the same period, Holmium laser PCNL had similar SFR and CR for treating Uyghur children with upper urinary calculi, who were older, more emaciated and had larger average stone diameters. The higher postoperative recurrence rate of Uyghur children is likely to be associated with higher stone burden. The multivariate logistic regression analysis results showed that ethnicity was not an influential factor in SFR, complication rates, and stone recurrence rates. The findings need to be further validated in larger prospective cohort studies.
8.The relationship between intestinal microecological imbalance and heart failure based on the theory of"spleen as the guardian"
Changxing LIU ; Xinyi GUO ; Boyu WANG ; Na SHI ; Qiuhan CHEN ; Yabin ZHOU ; He WANG
Chinese Journal of Arteriosclerosis 2024;32(3):263-270
Heart failure is a fatal stage of end-stage cardiovascular disease,which brings a huge medical burden to the society because of its high mortality and re-hospitalisation rates.Intestinal microecology is the largest and most com-plex microecosystem of human body.It is inhabited by tens of thousands of microorganisms in human gastrointestinal tract.In recent years,with the deepening of the study of intestinal flora,more and more studies have found that the im-balance of intestinal microecology can cause changes of metabolites in heart failure patients,which is one of the key triggers for the development of heart failure,therefore,using the intestinal microbial homeostasis as a new entry point for the treat-ment of heart failure will be a hotspot in medical research.However,the theory of Chinese medicine,"the spleen is the guardian",covers the physiological functions of the spleen,such as the spleen's main function of transporting,spleen's main function of ascending and clearing,and its main function of hiding camping,etc.,and the functions of intestinal flora and the"spleen is the guardian"are similar to a certain extent.Therefore,this paper starts from a holistic viewpoint and takes the theory of"spleen as the guardian"in Chinese medicine as an entry point to elaborate on the pathogenesis of intes-tinal microecological imbalance and heart failure,so as to provide a reference for Chinese medicine treatment or drug re-search.
9.Amikacin therapy and management of premature infants infected with carbapenem-resistant Klebsiella pneumoniae
Wenjuan HU ; Qiaoling YANG ; Xuebin WANG ; Boyu TAN ; Yihuan CHEN ; Huajun SUN
Chinese Journal of Clinical Pharmacology and Therapeutics 2024;29(12):1401-1408
AIM:To understand the efficacy and safety of amikacin(AMK)for the treatment of car-bapenem-resistant Klebsiella pneumoniae pneu-moniae(CRKP)in preterm infants and to establish a management process for the use of amikacin in preterm infants.METHODS:CRKP-infected preterm infants treated with amikacin between January 2019 and December 2021 were retrospectively ana-lyzed,and parametric data paired t-tests were used to assess the efficacy and safety of amikacin for the included infectious and safety indicators,and to es-tablish a management process for amikacin use in preterm infants.RESULTS:Eight cases of CRKP in-fection were included,with the main diagnosis of pneumonia and sepsis.eight preterm infants were screened for the AMK ototoxicity gene mitochon-drial gene MT-RNR1(MT-RNR1 1494C>T and MT-RNR11555A>G)before amikacin treatment,and none of them were found to have the gene variant.after receiving amikacin sulphate injection treat-ment for 7 days,the indicators of infectivity were improved,and was statistically significant(P<0.01).No clinical ototoxicity or nephrotoxicity was ob-served in the children before or after treatment.CONCLUSION:Aminoglycosides are still the main antibiotics used for the empirical treatment of sus-pected infections in preterm infants,especially drug-resistant bacterial infections.Despite the risk of ototoxicity and nephrotoxicity,we provide man-agement procedures and recommendations for neonatal treatment with amikacin to reduce the risk of ototoxicity and nephrotoxicity in AMK.
10.Study on the Mechanism of Exosomal miRNA Regulation by Si-Miao-San in Intervening Knee Osteoarthritis
Boyu WU ; Lei YANG ; Xinyu QI ; Gonghui JIAN ; Pei CHEN ; Guoliang LU ; Hui XIONG
World Science and Technology-Modernization of Traditional Chinese Medicine 2024;26(12):3160-3170
Objective Based on exosomal miRNA and their downstream pathways,we investigated the mechanisms related to the alleviation of cartilage damage in the knee damp-heat type osteoarthritis(KOA)model in rats by Si-Miao-San.Methods Damp-heat type KOA rat model was successfully established and divided into normal control group,model group,positive drug group,and low,medium and high dose groups of Si-Miao-San.The general conditions of the rats were observed daily;behavioural,imaging and histopathological methods were used to assess the effects of Si-Miao-San on pain,swelling,cartilage degeneration,subchondral bone damage and osteophyte formation in rats with damp-heat type KOA.The miRNA high-throughput sequencing technology was used to screen the differentially expressed miRNA after Si-Miao-San intervention in model rats;Western blot was used to test the expression of PI3K/Akt/mTOR pathway(downstream pathway of differentially expressed miRNA)and autophagy-related proteins in the cartilage tissues of rats in each group.Results Compared with the model group,Si-Miao-San could effectively improve the symptoms of damp-heat,mechanical pain threshold and knee joint swelling in rats with damp-heat type KOA model,and at the same time,it could reduce the cartilage damage of the knee joints of the model rats,inhibit the destruction of the subchondral bone and the formation of osteophyte,and the overall efficacy was better in the high-dose group.A total of seven differentially expressed exosomal miRNA were screened after Si-Miao-San intervention in model rats,among which the PI3K/Akt/mTOR pathway might be its key downstream pathway.Si-Miao-San significantly down-regulated the phosphorylation levels of PI3K,AKT,mTOR,and the expression level of P62 protein,and up-regulated the expression level of Beclin-1 protein.Conclusion Si-Miao-San can exert anti-KOA effects by affecting the differential expression of serum exosomal miRNA while inhibiting the PI3K/Akt/mTOR pathway and enhancing chondrocyte autophagy.

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