1.Unveiling the metabolic fate of drugs through metabolic reaction-based molecular networking.
Haodong ZHU ; Xupeng TONG ; Qi WANG ; Aijing LI ; Zubao WU ; Qiqi WANG ; Pei LIN ; Xinsheng YAO ; Liufang HU ; Liangliang HE ; Zhihong YAO
Acta Pharmaceutica Sinica B 2025;15(6):3210-3225
Effective annotation of in vivo drug metabolites using liquid chromatography-mass spectrometry (LC-MS) remains a formidable challenge. Herein, a metabolic reaction-based molecular networking (MRMN) strategy is introduced, which enables the "one-pot" discovery of prototype drugs and their metabolites. MRMN constructs networks by matching metabolic reactions and evaluating MS2 spectral similarity, incorporating innovations and improvements in feature degradation of MS2 spectra, exclusion of endogenous interference, and recognition of redundant nodes. A minimum 75% correlation between structural similarity and MS2 similarity of neighboring metabolites was ensured, mitigating false negatives due to spectral feature degradation. At least 79% of nodes, 49% of edges, and 97% of subnetworks were reduced by an exclusion strategy of endogenous ions compared to the Global Natural Products Social Molecular Networking (GNPS) platform. Furthermore, an approach of redundant ions identification was refined, achieving a 10%-40% recognition rate across different samples. The effectiveness of MRMN was validated through a single compound, plant extract, and mixtures of multiple plant extracts. Notably, MRMN is freely accessible online at https://yaolab.network, broadening its applications.
2.Inhibition of WAC alleviates the chondrocyte proinflammatory secretory phenotype and cartilage degradation via H2BK120ub1 and H3K27me3 coregulation.
Peitao XU ; Guiwen YE ; Xiaojun XU ; Zhidong LIU ; Wenhui YU ; Guan ZHENG ; Zepeng SU ; Jiajie LIN ; Yunshu CHE ; Yipeng ZENG ; Zhikun LI ; Pei FENG ; Qian CAO ; Zhongyu XIE ; Yanfeng WU ; Huiyong SHEN ; Jinteng LI
Acta Pharmaceutica Sinica B 2025;15(8):4064-4077
Several types of arthritis share the common feature that the generation of inflammatory mediators leads to joint cartilage degradation. However, the shared mechanism is largely unknown. H2BK120ub1 was reportedly involved in various inflammatory diseases but its role in the shared mechanism in inflammatory joint conditions remains elusive. The present study demonstrated that levels of cartilage degradation, H2BK120ub1, and its regulator WW domain-containing adapter protein with coiled-coil (WAC) were increased in cartilage in human rheumatoid arthritis (RA) and osteoarthritis (OA) patients as well as in experimental RA and OA mice. By regulating H2BK120ub1 and H3K27me3, WAC regulated the secretion of inflammatory and cartilage-degrading factors. WAC influenced the level of H3K27me3 by regulating nuclear entry of the H3K27 demethylase KDM6B, and acted as a key factor of the crosstalk between H2BK120ub1 and H3K27me3. The cartilage-specific knockout of WAC demonstrated the ability to alleviate cartilage degradation in collagen-induced arthritis (CIA) and collagenase-induced osteoarthritis (CIOA) mice. Through molecular docking and dynamic simulation, doxercalciferol was found to inhibit WAC and the development of cartilage degradation in the CIA and CIOA models. Our study demonstrated that WAC is a key factor of cartilage degradation in arthritis, and targeting WAC by doxercalciferol could be a viable therapeutic strategy for treating cartilage destruction in several types of arthritis.
3.Evolution-guided design of mini-protein for high-contrast in vivo imaging.
Nongyu HUANG ; Yang CAO ; Guangjun XIONG ; Suwen CHEN ; Juan CHENG ; Yifan ZHOU ; Chengxin ZHANG ; Xiaoqiong WEI ; Wenling WU ; Yawen HU ; Pei ZHOU ; Guolin LI ; Fulei ZHAO ; Fanlian ZENG ; Xiaoyan WANG ; Jiadong YU ; Chengcheng YUE ; Xinai CUI ; Kaijun CUI ; Huawei CAI ; Yuquan WEI ; Yang ZHANG ; Jiong LI
Acta Pharmaceutica Sinica B 2025;15(10):5327-5345
Traditional development of small protein scaffolds has relied on display technologies and mutation-based engineering, which limit sequence and functional diversity, thereby constraining their therapeutic and application potential. Protein design tools have significantly advanced the creation of novel protein sequences, structures, and functions. However, further improvements in design strategies are still needed to more efficiently optimize the functional performance of protein-based drugs and enhance their druggability. Here, we extended an evolution-based design protocol to create a novel minibinder, BindHer, against the human epidermal growth factor receptor 2 (HER2). It not only exhibits super stability and binding selectivity but also demonstrates remarkable properties in tissue specificity. Radiolabeling experiments with 99mTc, 68Ga, and 18F revealed that BindHer efficiently targets tumors in HER2-positive breast cancer mouse models, with minimal nonspecific liver absorption, outperforming scaffolds designed through traditional engineering. These findings highlight a new rational approach to automated protein design, offering significant potential for large-scale applications in therapeutic mini-protein development.
5.Associations of Genetic Risk and Physical Activity with Incident Chronic Obstructive Pulmonary Disease: A Large Prospective Cohort Study.
Jin YANG ; Xiao Lin WANG ; Wen Fang ZHONG ; Jian GAO ; Huan CHEN ; Pei Liang CHEN ; Qing Mei HUANG ; Yi Xin ZHANG ; Fang Fei YOU ; Chuan LI ; Wei Qi SONG ; Dong SHEN ; Jiao Jiao REN ; Dan LIU ; Zhi Hao LI ; Chen MAO
Biomedical and Environmental Sciences 2025;38(10):1194-1204
OBJECTIVE:
To investigate the relationship between physical activity and genetic risk and their combined effects on the risk of developing chronic obstructive pulmonary disease.
METHODS:
This prospective cohort study included 318,085 biobank participants from the UK. Physical activity was assessed using the short form of the International Physical Activity Questionnaire. The participants were stratified into low-, intermediate-, and high-genetic-risk groups based on their polygenic risk scores. Multivariate Cox regression models and multiplicative interaction analyses were used.
RESULTS:
During a median follow-up period of 13 years, 9,209 participants were diagnosed with chronic obstructive pulmonary disease. For low genetic risk, compared to low physical activity, the hazard ratios ( HRs) for moderate and high physical activity were 0.853 (95% confidence interval [ CI]: 0.748-0.972) and 0.831 (95% CI: 0.727-0.950), respectively. For intermediate genetic risk, the HRs were 0.829 (95% CI: 0.758-0.905) and 0.835 (95% CI: 0.764-0.914), respectively. For participants with high genetic risk, the HRs were 0.809 (95% CI: 0.746-0.877) and 0.818 (95% CI: 0.754-0.888), respectively. A significant interaction was observed between genetic risk and physical activity.
CONCLUSION
Moderate or high levels of physical activity were associated with a lower risk of developing chronic obstructive pulmonary disease across all genetic risk groups, highlighting the need to tailor activity interventions for genetically susceptible individuals.
Humans
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Pulmonary Disease, Chronic Obstructive/epidemiology*
;
Exercise
;
Male
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Female
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Middle Aged
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Prospective Studies
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Aged
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Genetic Predisposition to Disease
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Risk Factors
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United Kingdom/epidemiology*
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Incidence
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Adult
6.Effect of slurry proportion on the microstructure and properties of dental lithium disilicate ceramics manufactured through 3D printing.
Baoxin LIN ; Xiaoxuan CHEN ; Ruyi LI ; Qianbing WAN ; Xibo PEI
West China Journal of Stomatology 2025;43(2):175-182
OBJECTIVES:
This study aims to use 3D prin-ting technology based on the principle of stereo lithography apparatus (SLA) to shape dental lithium disilicate ceramics and study the effects of different slurry proportions on the microstructure and properties of heat-treated samples.
METHODS:
The experimental group comprised lithium disilicate ceramics manufactured through SLA 3D printing, and the control group comprised lithium disilicate ceramics (IPS e.max CAD) fabricated through commercial milling. An array of different particle sizes of lithium disilicate ceramic powder materials (nano and micron) was selected for mixing with photocurable acrylate resin. The proportion of experimental raw materials was adjusted to prepare five groups of ceramic slurries for 3D printing (Groups S1-S5) on the basis of rheological properties, stability, and other factors. Printing, debonding, and sintering were conducted on the experimental group with the optimal ratio, followed by measurements of microstructure, crystallographic information, shrinkage, and mechanical properties.
RESULTS:
Five groups of lithium disilicate ceramic slurries were prepared, of which two groups with high solid content (75%) (Groups S2 and S3) were selected for 3D printing. X-ray diffraction and scanning electron microscopy results showed that lithium disilicate was the main crystalline phase in Groups S2 and S3, and its microstructure was slender, uniform, and compact. The average grain sizes of Groups S2 and S3 were (559.79±84.58) nm and (388.26±61.49) nm, respectively (P<0.05). Energy spectroscopy revealed that the samples in the two groups contained a high proportion of Si and O elements. After heat treatment, the shrinkage rate of the two groups of ceramic samples was 18.00%-20.71%. Test results revealed no statistical difference in all mechanical properties between Groups S2 and S3 (P>0.05). The flexural strengths of Groups S2 and S3 were (231.79±21.71) MPa and (214.86±46.64) MPa, respectively, which were lower than that of the IPS e.max CAD group (P<0.05). The elasticity modulus of Groups S2 and S3 were (87.40±12.99) GPa and (92.87±19.76) GPa, respectively, which did not significantly differ from that of the IPS e.max CAD group (P>0.05). The Vickers hardness values of Groups S2 and S3 were (6.53±0.19) GPa and (6.25±0.12) GPa, respectively, which were higher than that of the IPS e.max CAD group (P<0.05). The fracture toughness values of Groups S2 and S3 were (1.57±0.28) MPa·m0.5 and (1.38±0.17) MPa·m0.5, respectively, which did not significantly differ from that of the IPS e.max CAD group (P>0.05).
CONCLUSIONS
The combination of lithium disilicate ceramic powders with different particle sizes can yield a slurry with high solid content (75%) and suitable viscosity and stability. The dental lithium disilicate ceramic material is successfully prepared by using 3D printing technology. The 3D-printed samples show a small shrinkage rate after heat treatment. Their microstructure conforms to the crystal phase of lithium disilicate ceramics, and their mechanical properties are close to those of milled lithium disilicate ceramics.
Printing, Three-Dimensional
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Dental Porcelain/chemistry*
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Ceramics/chemistry*
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Materials Testing
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Particle Size
7.Research progress on the diagnosis of ectodermal dysplasia and early oral prosthodontic treatment.
West China Journal of Stomatology 2025;43(4):478-485
Ectodermal dysplasia is a group of hereditary diseases characterized by developmental defects of ectodermal structures. Its oral manifestations mainly center on congenital missing teeth, abnormal tooth morphology, and maxillofacial bone developmental disorders, which seriously affect the masticatory function, maxillofacial development, and mental health of affected children. In this article, the multidimensional diagnostic strategy system for children with ectodermal dysplasia and the related progress of early oral prosthodontic treatment methods were systematically reviewed to provide references for clinicians in the diagnosis and treatment of children with ectodermal dysplasia.
Child
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Humans
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Anodontia
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Ectodermal Dysplasia/diagnosis*
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Prosthodontics
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Tooth Abnormalities/therapy*
8.Chemical Constituents and Pharmacological Effect of Epimedium sagittatum: A Review
Lixin PEI ; Lin CHEN ; Nuo LI ; Mengyao ZHAO ; Haoyuan YANG ; Xiaoyu YANG ; Baoyu JI
Chinese Journal of Experimental Traditional Medical Formulae 2025;31(21):282-290
Epimedium sagittatum is a perennial herb of Berberidaceae. Its leaves have a long history of medicinal use in China. This plant is widely used as a Chinese traditional medicine,with the main functions of tonifying kidney Yang,strengthening bones and muscles,and dispelling wind and dampness. It can be used for treating kidney Yang deficiency,impotence,spermatorrhea,flaccidity of bones and muscles,rheumatic arthralgia,numbness,and spasms. The chemical constituents of this plant include flavonoids,polysaccharides,lignans,and alkaloids. Flavonoids are the main active ingredients. These compounds show a wide range of biological activities,including cartilage repair,anti-aging,anti-fatigue,cough-relieving,blood glucose-lowering,and anti-tumor effects. Modern pharmacological research has shown that E. sagittatum has definite pharmacological effects on the reproductive system,respiratory system,nervous system,cardiovascular system,skeletal system,etc. It has remarkable effects of helping pregnancy,resisting osteoporosis,controlling diabetes,improving immunity,and inhibiting tumor. Under the background of advocating one health and Chinese medicine,E. sagittatum is widely used in health care products,serving as the main raw material of various products. It has great market potential and is a Chinese medicinal herb with great clinical application and research value. This paper reviews the main chemical constituents and pharmacological effects of E. sagittatum based on domestic and foreign reports, providing a theoretical basis for further study on E. sagittatum and its safe clinical application.
9.Study on the differences in dual-energy CT findings and clinical and laboratory indicators of frequent versus infrequent gout flares in the feet and ankles
Meihan CHEN ; Pei NIE ; Xiaoli LI ; Tong YU ; Fengjiao LI ; Changgui LI ; Ying CHEN ; Lin HAN ; Wenjian XU
Journal of Practical Radiology 2025;41(7):1177-1181,1233
Objective To explore the differences in the radiological features,clinical,and laboratory indicators of frequent versus infrequent gout flares in the feet and ankles using dual-energy computed tomography(DECT).Methods A retrospective selection was made on 385 gout patients,who were divided into the frequent flare group(≥2 gout attacks per year,219 cases)and the infre-quent flare group(<2 gout attacks per year,166 cases).Clinical data,laboratory indicators,and DECT imaging findings were col-lected for statistical analysis.Binary logistic regression was used to analyze the independent risk factors for frequent gout flares and receiver operating characteristic(ROC)curve was plotted.Results Statistically significant differences were found between the fre-quent flare group and the infrequent flare group in terms of disease duration,body mass index(BMI),blood pressure,triglyceride(TG),serum uric acid(SUA),monosodium urate(MSU)crystal deposition,total volume of MSU crystals,maximum diameter of individ-ual tophi,number of affected joints,bone erosion,maximum depth of bone erosion,soft tissue swelling,bone proliferation and sclero-sis,and joint space narrowing(P<0.05).SUA levels,MSU crystal deposition,total volume of MSU crystals,and maximum depth of bone erosion were identified as independent risk factors for frequent gout(P<0.05).Both the combination of four factors model and the maximum depth of bone erosion model had better diagnostic efficacy.Conclusion Gout patients with high SUA levels,MSU crystal deposition,larger total volume of MSU crystals,and greater maximum depth of bone erosion are more likely to experience frequent gout attacks.Patients with bone erosion depth>3.200 mm are more likely identified early as having frequent gout.
10.Effects of Yiqi Juanbi Formula on chondrocyte pyroptosis in collagen-induced arthritic rats via NF-κB/NLRP3/Caspase-1 signaling pathway
Xin-yu CUI ; Hao-lin LI ; Wei-qing LI ; Hui-qin KANG ; Wei-gang CHENG ; Pei-xin HE ; Cai-hong YANG ; Ping CHEN ; Hai-dong WANG
Chinese Traditional Patent Medicine 2025;47(9):2880-2887
AIM To investigate the effects of Yiqi Juanbi Formula on chondrocyte pyroptosis in rat models of collagen-induced arthritis(CIA).METHODS Fifty rats were subcutaneously injected at the tail base with an emulsion containing equal volumes of bovine type Ⅱ collagen and incomplete Freund's adjuvant(IFA)to establish the CIA models.These rats were then randomly assigned to the model group,the methotrexate group(0.35 mg/kg),and the low-dose,medium-dose,and high-dose Yiqi Juanbi Formula groups(9.4,18.7,37.4 g/kg),in contrast to the ten intact rats serving in the normal control group.Following four weeks of intragastric administration,the rats had their general conditions observed;their joint swelling and arthritis indices measured;their ankle joint pathology assessed by HE staining;their serum levels of IL-1β,IL-18 and TNF-ɑ detected by ELISA;their mRNA expressions of NLRP3,Caspase-1,GSDMD,IL-1β,IL-18 and TNF-ɑ in ankle cartilage quantified by RT-qPCR;their protein expressions of NF-κB,NLRP3 and Caspase-1 in ankle cartilage analyzed by Western blot;and their NLRP3 and GSDMD positive expressions in ankle cartilage examined by immunohistochemistry.RESULTS Compared to the control group,the model group showed significantly increased joint swelling and arthritis indices(P<0.01);elevated serum levels of IL-1 β,IL-18 and TNF-ɑ(P<0.01);pathological changes including cartilage surface defects,reduced cell count,altered cellular morphology,irregular cell arrangement,and significant inflammatory cell infiltration in synovial tissue;upregulated mRNA expressions of NF-κB,NLRP3,Caspase-1,GSDMD,IL-1β,IL-18 and TNF-ɑ(P<0.01)and increased protein expressions of NF-κB,NLRP3 and Caspase-1(P<0.01)in ankle cartilage;enhanced positive expressions of NLRP3 and GSDMD in ankle cartilage(P<0.01).Compared to the model group,the groups intervened with methotrexate or medium-or high-dose Yiqi Juanbi Formula exhibited reduced joint swelling and arthritis indices(P<0.01);alleviated pathological damage in ankle joints;decreased serum levels of IL-1β,IL-18 and TNF-ɑ(P<0.01);downregulated mRNA expressions of NF-κB,NLRP3,Caspase-1,GSDMD,IL-1β,IL-18 and TNF-ɑ(P<0.05,P<0.01),and reduced protein expressions of NF-κB,NLRP3 and Caspase-1(P<0.05,P<0.01)in ankle cartilage;and diminished positive expressions of NLRP3 and GSDMD in ankle cartilage(P<0.01).CONCLUSION Yiqi Juanbi Formula alleviates inflammation in CIA rats,potentially by inhibiting the activation of the NF-κB/NLRP3/Caspase-1 signaling pathway,thereby suppressing chondrocyte pyroptosis.

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