1.Proteomics and Network Pharmacology Reveal Mechanism of Xiaoer Huatan Zhike Granules in Treating Allergic Cough
Youqi DU ; Yini XU ; Jiajia LIAO ; Chaowen LONG ; Shidie TAI ; Youwen DU ; Song LI ; Shiquan GAN ; Xiangchun SHEN ; Ling TAO ; Shuying YANG ; Lingyun FU
Chinese Journal of Experimental Traditional Medical Formulae 2025;31(3):69-79
ObjectiveTo explore the pharmacological mechanism involved in the treatment of allergic cough (AC) by Xiaoer Huatan Zhike granules (XEHT) based on proteomics and network pharmacology. MethodsAfter sensitization by intraperitoneal injection of 1 mL suspension containing 2 mg ovalbumin (OVA) and 100 mg aluminum hydroxide, a guinea pig model of allergic cough was constructed by nebulization with 1% OVA. The modeled guinea pigs were randomized into the model, low-, medium- and high-dose (1, 5, 20 g·kg-1, respectively) XEHT, and sodium montelukast (1 mg·kg-1) groups (n=6), and another 6 guinea pigs were selected as the blank group. The guinea pigs in drug administration groups were administrated with the corresponding drugs by gavage, and those in the blank and model groups received the same volume of normal saline by gavage, 1 time·d-1. After 10 consecutive days of drug administration, the guinea pigs were stimulated by 1% OVA nebulization, and the coughs were observed. The pathological changes in the lung tissue were observed by hematoxylin-eosin staining. The enzyme-linked immunosorbent assay was performed to measure the levels of C-reactive protein (CRP), interleukin-6 (IL-6), tumor necrosis factor-α (TNF-α), superoxide dismutase (SOD), and malondialdehyde (MDA) in the bronchoalveolar lavage fluid (BALF) and immunoglobulin G (IgG) and immunoglobulin A (IgA) in the serum. Immunohistochemistry (IHC) was employed to observe the expression of IL-6 and TNF-α in the lung tissue. Transmission electron microscopy was employed observe the alveolar type Ⅱ epithelial cell ultrastructure. Real-time PCR was employed to determine the mRNA levels of IL-6, interleukin-1β (IL-1β), and TNF-α in the lung tissue. Label-free proteomics was used to detect the differential proteins among groups. Network pharmacology was used to predict the targets of XEHT in treating AC. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was performed to search for the same pathways from the results of proteomics and network pharmacology. ResultsCompared with the blank group, the model group showed increased coughs (P<0.01), elevated levels of CRP, TNF-α, IL-6, and MDA and lowered level of SOD in the BALF (P<0.05, P<0.01), elevated levels of IgA and IgG in the serum (P<0.05, P<0.01), congestion of the lung tissue and infiltration of inflammatory cells, increased expression of IL-6 and TNF-α (P<0.01), large areas of low electron density edema in type Ⅱ epithelial cells, obvious swelling and vacuolization of the organelles, karyopyknosis or sparse and dissolved chromatin, and up-regulated mRNA levels of IL-6, IL-1β, and TNF-α (P<0.01). Compared with the model group, the drug administration groups showed reduced coughs (P<0.01), lowered levels of CRP, TNF-α, IL-6, and MDA and elevated level of SOD in the BALF (P<0.05, P<0.01), alleviated lung tissue congestion, inflammatory cell infiltration, and type Ⅱ epithelial cell injury, and decreased expression of IL-6 and TNF-α (P<0.01). In addition, the medium-dose XEHT group and the montelukast sodium group showcased lowered serum levels of IgA and IgG (P<0.05, P<0.01). The medium- and high-dose XEHT groups and the montelukast sodium showed down-regulated mRNA levels of IL-6, IL-1β, and TNF-α and the low-dose XEHT group showed down-regulated mRNA levels of IL-6 and TNF-α (P<0.05, P<0.01). Phospholipase D, mammalian target of rapamycin (mTOR), and epidermal growth factor receptor family of receptor tyrosine kinase (ErbB) signaling pathways were the common pathways predicted by both proteomics and network pharmacology. ConclusionProteomics combined with network pharmacology reveal that XEHT can ameliorate AC by regulating the phospholipase D, mTOR, and ErbB signaling pathways.
2.Prediction of Protein Thermodynamic Stability Based on Artificial Intelligence
Lin-Jie TAO ; Fan-Ding XU ; Yu GUO ; Jian-Gang LONG ; Zhuo-Yang LU
Progress in Biochemistry and Biophysics 2025;52(8):1972-1985
In recent years, the application of artificial intelligence (AI) in the field of biology has witnessed remarkable advancements. Among these, the most notable achievements have emerged in the domain of protein structure prediction and design, with AlphaFold and related innovations earning the 2024 Nobel Prize in Chemistry. These breakthroughs have transformed our ability to understand protein folding and molecular interactions, marking a pivotal milestone in computational biology. Looking ahead, it is foreseeable that the accurate prediction of various physicochemical properties of proteins—beyond static structure—will become the next critical frontier in this rapidly evolving field. One of the most important protein properties is thermodynamic stability, which refers to a protein’s ability to maintain its native conformation under physiological or stress conditions. Accurate prediction of protein stability, especially upon single-point mutations, plays a vital role in numerous scientific and industrial domains. These include understanding the molecular basis of disease, rational drug design, development of therapeutic proteins, design of more robust industrial enzymes, and engineering of biosensors. Consequently, the ability to reliably forecast the stability changes caused by mutations has broad and transformative implications across biomedical and biotechnological applications. Historically, protein stability was assessed via experimental methods such as differential scanning calorimetry (DSC) and circular dichroism (CD), which, while precise, are time-consuming and resource-intensive. This prompted the development of computational approaches, including empirical energy functions and physics-based simulations. However, these traditional models often fall short in capturing the complex, high-dimensional nature of protein conformational landscapes and mutational effects. Recent advances in machine learning (ML) have significantly improved predictive performance in this area. Early ML models used handcrafted features derived from sequence and structure, whereas modern deep learning models leverage massive datasets and learn representations directly from data. Deep neural networks (DNNs), graph neural networks (GNNs), and attention-based architectures such as transformers have shown particular promise. GNNs, in particular, excel at modeling spatial and topological relationships in molecular structures, making them well-suited for protein modeling tasks. Furthermore, attention mechanisms enable models to dynamically weigh the contribution of specific residues or regions, capturing long-range interactions and allosteric effects. Nevertheless, several key challenges remain. These include the imbalance and scarcity of high-quality experimental datasets, particularly for rare or functionally significant mutations, which can lead to biased or overfitted models. Additionally, the inherently dynamic nature of proteins—their conformational flexibility and context-dependent behavior—is difficult to encode in static structural representations. Current models often rely on a single structure or average conformation, which may overlook important aspects of stability modulation. Efforts are ongoing to incorporate multi-conformational ensembles, molecular dynamics simulations, and physics-informed learning frameworks into predictive models. This paper presents a comprehensive review of the evolution of protein thermodynamic stability prediction techniques, with emphasis on the recent progress enabled by machine learning. It highlights representative datasets, modeling strategies, evaluation benchmarks, and the integration of structural and biochemical features. The aim is to provide researchers with a structured and up-to-date reference, guiding the development of more robust, generalizable, and interpretable models for predicting protein stability changes upon mutation. As the field moves forward, the synergy between data-driven AI methods and domain-specific biological knowledge will be key to unlocking deeper understanding and broader applications of protein engineering.
3.Investigation of an outbreak of group A human G9P [8] rotavirus infectious diarrhea among adults in Chongqing
Yang WANG ; Yuan KONG ; Ning CHEN ; Lundi YANG ; Jiang LONG ; Qin LI ; Xiaoyang XU ; Wei ZHENG ; Hong WEI ; Jie LU ; Quanjie XIAO ; Yingying BA ; Wenxi WU ; Qian XU ; Ju YAN
Shanghai Journal of Preventive Medicine 2025;37(8):663-668
ObjectiveTo investigate and analyze an outbreak of rotavirus infectious diarrhea in a prison in Chongqing Municipality, to provide a basis for adult rotavirus surveillance and prevention, and to explore the public health problems in special settings. MethodsA retrospective survey was conducted to collect and analyze data on individual cases with diarrheal disease on-site. The clinical characteristics, as well as the temporal, spatial and geographical distribution patterns of the epidemic were described. Multi-pathogen detection tests were conducted both on diarrhea cases and environmental samples, with viral genotyping performed on positive samples. A case-control analysis was performed to identify the causes of the outbreak, and an SEIR model was adopted to predict the outbreak trend and evaluate the effectiveness of interventions. ResultsA total of 65 cases were found among the inmates, with an attack rate of 2.03%. The predominant clinical manifestations included diarrhea (89.23%), watery stool (73.85%), and dehydration (18.46%). The epidemic curve indicated a “human-to-human” transmission pattern, with an average incubation period of 5‒6 days. The attack rates among chefs in the main canteen (80.00%, 8/10) and caterers (28.33%, 17/60) were significantly higher than those of other inmates (P<0.05). Multi-pathogen polymerase chain reaction (PCR) testing detected positive for group A rotavirus, with the viral genotyping identified as G9P [8] strain. Factors such as unprotected "bare-handed" food distribution among cases with diarrhea (OR=9.512, 95%CI: 4.261‒21.234) and close contact with diarrhea cases (OR=3.656, 95%CI: 1.719‒7.778) were the possible cause of the outbreak. The SEIR model (r0=5, α=0.3, β1=0.08, β2=0.04) was constructed using prison inmates as susceptible population, aiming at fitting the initial transmission trend of the outbreak, and the epidemic rate declined rapidly after intervention measures were implemented (rt≈0). ConclusionThis rare rotavirus infection diarrhea outbreak among adults in confined settings suggests that the construction of public health prevention and control systems in prison may be overlooked. Cross infection during meal processing and distribution in the canteens of such settings is likely to be the cause of the outbreak. Given the potential neglect of public heath system construction in special settings, it is imperative to enhance the surveillance and monitoring of rotavirus and other intestinal multi-pathogens among adults, as well as the construction of public health prevention and control systems in these special settings.
4.A Case Report of Pachydermoperiostosis by Multidisciplinary Diagnosis and Treatment
Jie ZHANG ; Yan ZHANG ; Li HUO ; Ke LYU ; Tao WANG ; Ze'nan XIA ; Xiao LONG ; Kexin XU ; Nan WU ; Bo YANG ; Weibo XIA ; Rongrong HU ; Limeng CHEN ; Ji LI ; Xia HONG ; Yan ZHANG ; Yagang ZUO
JOURNAL OF RARE DISEASES 2025;4(1):75-82
A 20-year-old male patient presented to the Department of Dermatology of Peking Union Medical College Hospital with complaints of an 8-year history of facial scarring, swelling of the lower limbs, and a 4-year history of scalp thickening. Physical examination showed thickening furrowing wrinkling of the skin on the face and behind the ears, ciliary body hirsutism, blepharoptosis, and cutis verticis gyrate. Both lower limbs were swollen, especially the knees and ankles. The skin of the palms and soles of the feet was keratinized and thickened. Laboratory examination using bone and joint X-ray showed periostosis of the proximal middle phalanges and metacarpals of both hands, distal ulna and radius, tibia and fibula, distal femurs, and metatarsals.Genetic testing revealed two variants in
5.Effects of different levels of ophthalmic surgical stimulation on blood glucose changes in patients with type 2 diabetes mellitus
Yanqun XU ; Xiubin TAO ; Zichen SENG ; Pengfei ZHANG ; Lele LONG ; Qingting YANG
Journal of Shenyang Medical College 2024;26(2):136-140
Objective:To investigate the effects of different levels of ophthalmic surgical stimulation on blood glucose in patients with type 2 diabetes mellitus(T2DM).Methods:From Mar to Oct 2021,236 patients with T2DM who underwent ophthalmic surgery in our hospital were enrolled,including 71 cases of secondary surgery,89 cases of tertiary surgery,and 76 cases of quaternary surgery.According to the operation time,the 236 patients were divided into groups A(<60 min),B(60-120 min)and C(>120 min).The preoperative and postoperative blood glucose levels were compared in patients with different levels of surgery,and in groups A,B and C.Results:The postoperative blood glucose level was lower than that before surgery in secondary and tertiary surgery,and it was higher than that before surgery in quaternary surgery(P<0.05).The fluctuation value of blood glucose in secondary and tertiary surgery was higher than that in quaternary surgery(P<0.05).In groups A,B and C,the postoperative blood glucose level was lower than that before surgery in secondary and tertiary surgery(P<0.05).In group A,there was no significant difference in the blood glucose before and after surgery in quaternary surgery(P>0.05),and in groups B and C,the postoperative blood glucose was higher than that before surgery in quaternary surgery(P<0.05).In group A,there was no difference in the fluctuation value of blood glucose at different levels of surgery(P>0.05).In group B,the fluctuation value of blood glucose in patients with secondary and tertiary surgery was higher than that in quaternary surgery(P<0.05).In group C,the fluctuation value of blood glucose in patients with tertiary and quaternary surgery was higher than that in patients with secondary surgery(P<0.05).Conclusions:For ophthalmic surgery patients with T2DM,the postoperative blood glucose values of patients undergoing secondary and tertiary surgery generally show a downward trend,while the postoperative blood glucose value of patients undergoing quaternary surgery generally shows an upward trend.It is suggested that clinical workers should actively manage the perioperative blood glucose of patients with high-level surgery.
6.Efficacy and safety of camrelizumab monoclonal antibody combined with molecular-targeted therapy in elderly patients with advanced hepatocellular carcinoma
Long CHENG ; Yue ZHANG ; Yushen LIU ; Zhaoqing DU ; Zhaoyang GUO ; Yangwei FAN ; Ting LI ; Xu GAO ; Enrui XIE ; Zixuan XING ; Wenhua WU ; Yinying WU ; Mingbo YANG ; Jie LI ; Yu ZHANG ; Wen KANG ; Wenjun WANG ; Fanpu JI ; Jiang GUO ; Ning GAO
Journal of Clinical Hepatology 2024;40(10):2034-2041
Objective To investigate the efficacy and safety of camrelizumab monoclonal antibody combined with molecular-targeted therapy in elderly patients with unresectable or advanced hepatocellular carcinoma(HCC).Methods A retrospective analysis was performed for the patients with unresectable/advanced HCC who attended six hospitals from January 1,2019 to March 31,2021,and all patients received camrelizumab monoclonal antibody treatment,among whom 84.8%also received targeted therapy.According to the age of the patients,they were divided into elderly group(≥65 years)and non-elderly group(<65 years).The two groups were assessed in terms of overall survival(OS),progression-free survival(PFS),objective response rate(ORR),disease control rate(DCR),and immune-related adverse events(irAE).The chi-square test or the Fisher's exact test was used for comparison of categorical data between groups;the independent samples t-test was used for comparison of normally distributed continuous data,and the Mann-Whitney U test was used for comparison of non-normally distributed continuous data between two groups.The Kaplan-Meier method was used for survival analysis,and the log-rank test was used for comparison of survival curves.Univariate and multivariate Cox proportional hazards regression analyses were used to determine the independent influencing factors for PFS and DCR at 6 months.Results A total of 99 HCC patients were enrolled,with 27 in the elderly group and 72 in the non-elderly group.The elderly group had an OS rate of 67.8%,an ORR of 44.4%,and a DCR of 74.1%at 12 months and a median PFS of 6.4(95%confidence interval[CI]:3.0-12.4)months,with no significant differences compared with the non-elderly group(all P>0.05).The median OS was unavailable for the elderly group,while the non-elderly group had an OS of 18.9(95%CI:13.0-24.8)months;there was no significant difference between the two groups(P=0.485).The univariate and multivariate Cox regression analyses showed that major vascular invasion(MVI)was an independent risk factor for PFS(hazard ratio[HR]=2.603,95%CI:1.136-5.964,P=0.024)and DCR(HR=3.963,95%CI:1.671-9.397,P=0.002)at 6 months,while age,sex,etiology of HBV infection,presence of extrahepatic metastasis,Child-Pugh class B,and alpha-fetoprotein>400 ng/mL were not associated with PFS or DCR at 6 months.For the elderly group,the incidence rates of any irAE and grade 3/4 irAE were 51.9%and 25.9%,respectively,with no significant differences compared with the non-elderly group(P>0.05),and skin disease was the most common irAE in both groups(39.4%).Conclusion Camrelizumab monoclonal antibody combined with molecular-targeted therapy has similar efficacy and safety in patients with unresectable/advanced HCC aged≥65 years and those aged<65 years.MVI is associated with suboptimal response to immunotherapy and poor prognosis.
7.Based on supramolecular chemistry to explore the scientific connotation of predecocting gypsum in Maxingshigan decoction preliminarily
Yao-zhi ZHANG ; Shu-chang YAO ; Lu-ping YANG ; Yi-hang ZHAO ; An-qi XU ; Xue-mei HUANG ; Peng-long WANG
Acta Pharmaceutica Sinica 2024;59(6):1828-1840
It has gradually become a consensus in the industry that the traditional Chinese medicine gypsum should be decocted first, but the understanding of decocting method is not completely unified in the works of doctors since ancient times, and there are occasional disputes about whether it is necessary to decocting first. In this study, the phase determination, physical and chemical characterization, qualitative and quantitative analysis of inorganic and organic components of the decoctions of herbal pairs and the whole prescription Maxingshigan decoction with gypsum as the center, and the pre-decoctions and co-decoctions of them were carried out to explore the scientific connotation of the pre-decoctions of gypsum. Results show that decoction phases were different between the co-decoctions and pre-decoctions of licorice-gypsum (Gancao-Shigao, GC-SG), ephedra-gypsum (Mahuang-Shigao, MH-SG) and almond-gypsum (Xingren-Shigao, XR-SG). The results of the micromorphology, particle size and zeta potential of herbal pairs and prescription (Quanfang, QF) showed that the supramolecular particles in pre-decoctions were smaller, more uniform and more stable than the co-decoctions. The results of organic components analysis showed that different cooking methods did not change the organic composition and content. ICP-OES results showed that the content of inorganic components in pre-decoctions was higher than in co-decoctions for the same boiling time of gypsum. The IR results showed that the pre-decoctions had stronger chemical functional group effect than the co-decoctions. To sum up, compared with the co-decoction, the pre-decoction of gypsum has different phase state and chemical composition interaction, and the difference of inorganic composition is an important material basis affecting the change of phase state compared with the co-decoction. It indicates that the material basis of traditional Chinese medicine decoction is indeed different whether gypsum is decocted first or not, which can provide a basis for the clinical application of decocted gypsum.
8.Analysis of the biosynthesis pathways of phenols in the leaves of Tetrastigma hemsleyanum regulated by supplemental blue light based on transcriptome sequencing
Hui-long XU ; Nan YANG ; Yu-yan HONG ; Meng-ting PAN ; Yu-chun GUO ; Shi-ming FAN ; Wen XU
Acta Pharmaceutica Sinica 2024;59(10):2864-2870
Analyze the changes in phenolic components and gene expression profiles of
9.A brief discussion on the development and challenges of smoking cessation services led by pharmacist abroad
Ruirui WEN ; Long XU ; Wenjing ZHU ; Jianwei YANG
Journal of Pharmaceutical Practice and Service 2024;42(12):537-541
Objective To investigate the role of pharmacists in smoking cessation abroad and foster the dissemination and initiation of smoking cessation services led by pharmacist. Methods A search and compiles information on the value of pharmacists in offering smoking cessation services were carried out through the PubMed and Scopus electronic databases and the evolution of supportive policies were analyzed. The feasibility and barriers to pharmacists providing these services were examined. Results The involvement of pharmacists in smoking cessation positively impacted public health and the economy. Endowing pharmacists with the authority to prescribe smoking cessation medications, providing training in this service, and bolstering their potential through interprofessional collaboration can effectively address the barriers to their role in smoking cessation. Conclusion It is advisable to consider integrating smoking cessation services led by pharmacist into healthcare and public health policy guidelines ,which could enhance the efficacy and sustainability of smoking cessation initiatives.
10.Application of Mitochondrial Targeting Strategy of Nano-delivery System in Tumor Diagnosis and Treatment
Jun QU ; Shuang YAN ; Long-Tian-Yang LEI ; Fei-Jun OUYANG ; Hai-Tao ZHANG ; Xu-Ping QIN
Progress in Biochemistry and Biophysics 2024;51(1):70-81
Tumor is one of the major diseases that endanger people’s health. At present, the treatments used for tumor include surgery, chemotherapy, radiotherapy and so on. Nonetheless, the traditional treatments have some disadvantages, such as insufficient treatment effect, liable to cause multidrug resistance, toxicity and side effect. Further research and exploration of tumor treatment schemes are still necessary. As the energy converter of cells, mitochondria are currently considered to be one of the most important targets for the design of new drugs for tumor, cardiovascular and neurological diseases. Nano-drug delivery carriers have the characteristics of being easily modified with active targeting groups, and it can achieve accurate targeted drug delivery to cells and organelles. This paper reviews the application of mitochondrial targeted nanoparticles in tumor diagnosis and treatment from the aspects of inhibiting tumor cell proliferation, promoting tumor cell apoptosis, inhibiting tumor recurrence and metastasis, and inducing cell autophagy.

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