1.Exploring artificial intelligence approaches for predicting synergistic effects of active compounds in traditional Chinese medicine based on molecular compatibility theory.
Yiwen WANG ; Tong WU ; Xingyu LI ; Qilan XU ; Heshui YU ; Shixin CEN ; Yi WANG ; Zheng LI
Chinese Journal of Natural Medicines (English Ed.) 2025;23(11):1409-1424
Due to its synergistic effects and reduced side effects, combination therapy has become an important strategy for treating complex diseases. In traditional Chinese medicine (TCM), the "monarch, minister, assistant, envoy" compatibilities theory provides a systematic framework for drug compatibility and has guided the formation of a large number of classic formulas. However, due to the complex compositions and diverse mechanisms of action of TCM, it is difficult to comprehensively reveal its potential synergistic patterns using traditional methods. Synergistic prediction based on molecular compatibility theory provides new ideas for identifying combinations of active compounds in TCM. Compared to resource-intensive traditional experimental methods, artificial intelligence possesses the ability to mine synergistic patterns from multi-omics and structural data, providing an efficient means for modeling and optimizing TCM combinations. This paper systematically reviews the application progress of AI in the synergistic prediction of TCM active compounds and explores the challenges and prospects of its application in modeling combination relationships, thereby contributing to the modernization of TCM theory and methodological innovation.
Artificial Intelligence
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Medicine, Chinese Traditional/methods*
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Drugs, Chinese Herbal/pharmacology*
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Humans
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Drug Synergism
2.Study on the mechanism of Xiongshi Shiwei Wendan decoction pro-moting RCT and treat AS based on network pharmacology,molecular docking and in vitro experiment
Xingyu MA ; Xuejiao XIE ; Chunqiao LI ; Zheng ZHANG
Chinese Journal of Clinical Pharmacology and Therapeutics 2025;30(8):1026-1036
AIM:Xiongshi Shiwei Wendan decoc-tion(SWD)comes from Xiong Jibai,a master of tra-ditional Chinese medicine,and has been widely used in the treatment of AS.ABCA1 is an important pathway for macrophages to export cholesterol and plays a protective role in the occurrence and development of AS.The purpose of this study was to study the effects of SWD on ABCA1 expression and cholesterol efflux through network pharmacol-ogy,molecular docking and in vitro experiments,and explore the pathway mechanism of promoting reverse cholesterol transport(RCT).METHODS:The active components of SWD drugs were screened by TCMSP and HERB databases,RCT targets were pre-dicted,the component-target network map was constructed,the PPI network was constructed and the GO and KEGG pathways were enriched and ana-lyzed by STRING database,and the key active com-ponents of SWD were selected for molecular dock-ing with ABCA1 protein and miR-33 by AutoDockVi-na.In vitro,RAW264.7 was used to establish foam cell model,oil red O staining,NBD-cholesterol staining and lentivirus overexpression cell miRNA-33 were used to study the effect of SWD on lipid accumulation and cholesterol outflow rate of RAW264.7 cells.Western blotting was used to de-tect the expression of ABCA1.RESULTS:According to network pharmacology,336 active components of SWD,267 targets of RCT and 46 targets of inter-section of RCT and SWD were obtained,which in-volved multiple signal pathways such as lipid and atherosclerosis.Molecular docking showed that the main active components had stable conforma-tion with ABCA1 and miR-33.In vitro experiment,it was found that the lipid content was significantly decreased(P<0.01),the cholesterol outflow rate was significantly increased(P<0.01)and the expres-sion of ABCA1 protein was up-regulated in SWD group(P<0.01),but the expression of ABCA1 in miR-33 overexpression group was significantly de-creased(P<0.01).CONCLUSION:SWD has the char-acteristics of multi-components and multi-targets,which can promote RCT and treat AS through miR-NA-33-ABCA1 pathway.
3.Rapid enrichment and SERS differentiation of various bacteria in skin interstitial fluid by 4-MPBA-AuNPs-functionalized hydrogel microneedles
Ying YANG ; Xingyu WANG ; Yexin HU ; Zhongyao LIU ; Xiao MA ; Feng FENG ; Feng ZHENG ; Xinlin GUO ; Wenyuan LIU ; Wenting LIAO ; Lingfei HAN
Journal of Pharmaceutical Analysis 2025;15(3):564-576
Bacterial infection is a major threat to global public health,and can cause serious diseases such as bacterial skin infection and foodborne diseases.It is essential to develop a new method to rapidly di-agnose clinical multiple bacterial infections and monitor food microbial contamination in production sites in real-time.In this work,we developed a 4-mercaptophenylboronic acid gold nanoparticles(4-MPBA-AuNPs)-functionalized hydrogel microneedle(MPBA-H-MN)for bacteria detection in skin inter-stitial fluid.MPBA-H-MN could conveniently capture and enrich a variety of bacteria within 5 min.Surface enhanced Raman spectroscopy(SERS)detection was then performed and combined with ma-chine learning technology to distinguish and identify a variety of bacteria.Overall,the capture efficiency of this method exceeded 50%.In the concentration range of 1 × 10 7 to 1 × 10 10 colony-forming units/mL(CFU/mL),the corresponding SERS intensity showed a certain linear relationship with the bacterial concentration.Using random forest(RF)-based machine learning,bacteria were effectively distinguished with an accuracy of 97.87%.In addition,the harmless disposal of used MNs by photothermal ablation was convenient,environmentally friendly,and inexpensive.This technique provided a potential method for rapid and real-time diagnosis of multiple clinical bacterial infections and for monitoring microbial contamination of food in production sites.
4.Rapid enrichment and SERS differentiation of various bacteria in skin interstitial fluid by 4-MPBA-AuNPs-functionalized hydrogel microneedles.
Ying YANG ; Xingyu WANG ; Yexin HU ; Zhongyao LIU ; Xiao MA ; Feng FENG ; Feng ZHENG ; Xinlin GUO ; Wenyuan LIU ; Wenting LIAO ; Lingfei HAN
Journal of Pharmaceutical Analysis 2025;15(3):101152-101152
Bacterial infection is a major threat to global public health, and can cause serious diseases such as bacterial skin infection and foodborne diseases. It is essential to develop a new method to rapidly diagnose clinical multiple bacterial infections and monitor food microbial contamination in production sites in real-time. In this work, we developed a 4-mercaptophenylboronic acid gold nanoparticles (4-MPBA-AuNPs)-functionalized hydrogel microneedle (MPBA-H-MN) for bacteria detection in skin interstitial fluid. MPBA-H-MN could conveniently capture and enrich a variety of bacteria within 5 min. Surface enhanced Raman spectroscopy (SERS) detection was then performed and combined with machine learning technology to distinguish and identify a variety of bacteria. Overall, the capture efficiency of this method exceeded 50%. In the concentration range of 1 × 107 to 1 × 1010 colony-forming units/mL (CFU/mL), the corresponding SERS intensity showed a certain linear relationship with the bacterial concentration. Using random forest (RF)-based machine learning, bacteria were effectively distinguished with an accuracy of 97.87%. In addition, the harmless disposal of used MNs by photothermal ablation was convenient, environmentally friendly, and inexpensive. This technique provided a potential method for rapid and real-time diagnosis of multiple clinical bacterial infections and for monitoring microbial contamination of food in production sites.
5.Study on the mechanism of Xiongshi Shiwei Wendan decoction pro-moting RCT and treat AS based on network pharmacology,molecular docking and in vitro experiment
Xingyu MA ; Xuejiao XIE ; Chunqiao LI ; Zheng ZHANG
Chinese Journal of Clinical Pharmacology and Therapeutics 2025;30(8):1026-1036
AIM:Xiongshi Shiwei Wendan decoc-tion(SWD)comes from Xiong Jibai,a master of tra-ditional Chinese medicine,and has been widely used in the treatment of AS.ABCA1 is an important pathway for macrophages to export cholesterol and plays a protective role in the occurrence and development of AS.The purpose of this study was to study the effects of SWD on ABCA1 expression and cholesterol efflux through network pharmacol-ogy,molecular docking and in vitro experiments,and explore the pathway mechanism of promoting reverse cholesterol transport(RCT).METHODS:The active components of SWD drugs were screened by TCMSP and HERB databases,RCT targets were pre-dicted,the component-target network map was constructed,the PPI network was constructed and the GO and KEGG pathways were enriched and ana-lyzed by STRING database,and the key active com-ponents of SWD were selected for molecular dock-ing with ABCA1 protein and miR-33 by AutoDockVi-na.In vitro,RAW264.7 was used to establish foam cell model,oil red O staining,NBD-cholesterol staining and lentivirus overexpression cell miRNA-33 were used to study the effect of SWD on lipid accumulation and cholesterol outflow rate of RAW264.7 cells.Western blotting was used to de-tect the expression of ABCA1.RESULTS:According to network pharmacology,336 active components of SWD,267 targets of RCT and 46 targets of inter-section of RCT and SWD were obtained,which in-volved multiple signal pathways such as lipid and atherosclerosis.Molecular docking showed that the main active components had stable conforma-tion with ABCA1 and miR-33.In vitro experiment,it was found that the lipid content was significantly decreased(P<0.01),the cholesterol outflow rate was significantly increased(P<0.01)and the expres-sion of ABCA1 protein was up-regulated in SWD group(P<0.01),but the expression of ABCA1 in miR-33 overexpression group was significantly de-creased(P<0.01).CONCLUSION:SWD has the char-acteristics of multi-components and multi-targets,which can promote RCT and treat AS through miR-NA-33-ABCA1 pathway.
6.Anti-inflammatory effects and related mechanisms of naringenin in human periodontal ligament stem cells under lipopolysaccharide stimulation based on RNA sequencing
Junyu LI ; Xiaomei XU ; Xingyu LIU ; Ting ZENG ; Li ZHANG ; Qian ZHENG
West China Journal of Stomatology 2024;42(4):512-520
Objective RNA sequencing(RNA-seq)and bioinformatic analysis were combined and used to explore the anti-inflammatory effects and mechanisms of naringenin(Nar)in lipopolysaccharide(LPS)-stimulated human peri-odontal ligament stem cells(hPDLSCs).Methods Cell counting kit-8,quantitative real-time reverse transcription poly-merase chain reaction(qRT-PCR),and enzyme-linked immunosorbent assay(ELISA)were adopted to detect the effects of Nar on the proliferation and expression of inflammatory factors in LPS-stimulated hPDLSCs,screening for the opti-mal anti-inflammatory concentration of Nar.Differentially expressed genes(DEGs)were screened using|log2FC|≥1 and P≤0.05 as criteria.Volcano plot analysis,Kyoto En-cyclopedia of Genes and Genomes(KEGG)pathway en-richment analysis,the String database,and the MCODE module of Cytoscape were utilized to select core genes and enriched pathways.The effects on the nuclear factor κB(NF-κB)signaling pathway were verified using ELISA,qRT-PCR,and Western blot.Results Appropriate concentrations of Nar could alleviate the expression of inflammatory fac-tors and promote the proliferation of hPDLSCs stimulated by LPS.The best anti-inflammatory effect was achieved with 20 μmol/L Nar.RNA-seq showed significant enrichment of inflammation-related signaling pathways.The anti-inflamma-tory effect of Nar was mediated by inhibiting the NF-κB signaling pathway,similar to the effect of the NF-κB inhibitor BAY 11-7802.Conclusion Nar could exert its anti-inflammatory effects by inhibiting the NF-κB signaling pathway,making it a potential therapeutic option for the adjuvant treatment of periodontitis.
7.IDO1-mediated immune escape mechanisms in endometrial cancer and related clinical progress
Wang TIANQI ; Zheng XINGYU ; Zhao SHUANGSHUANG ; Wang YINGMEI
Chinese Journal of Clinical Oncology 2024;51(22):1159-1163
Endometrial cancer (EC) is a common malignant tumor within the female reproductive system,and its incidence is increasing. The prognosis for patients with early EC is good,but the prognosis for patients with advanced and recurrent EC is extremely poor. In recent years,immune checkpoint inhibitors have shown significant promise in tumor therapy,including therapy for patients with advanced and re-current EC. Some of these patients experience disease progression during immunotherapy,and the mechanism of tumor immune escape is not thoroughly understood. Indoleamine 2,3-dioxyfenase-1 (IDO1) catalyzes the conversion of tryptophan to kynurenine,which is the first and rate-limiting step in the major pathway of tryptophan catabolism. IDO1 overexpression in a tumor microenvironment results in trypto-phan depletion and kynurenine metabolites overproduction,facilitating cancer immune escape. We review the primary mechanisms by which the IDO1 pathway facilitates immune escape in EC,and describe research progress into EC therapy targeting the IDO1 pathway.
8.IDO1-mediated immune escape mechanisms in endometrial cancer and related clinical progress
Wang TIANQI ; Zheng XINGYU ; Zhao SHUANGSHUANG ; Wang YINGMEI
Chinese Journal of Clinical Oncology 2024;51(22):1159-1163
Endometrial cancer (EC) is a common malignant tumor within the female reproductive system,and its incidence is increasing. The prognosis for patients with early EC is good,but the prognosis for patients with advanced and recurrent EC is extremely poor. In recent years,immune checkpoint inhibitors have shown significant promise in tumor therapy,including therapy for patients with advanced and re-current EC. Some of these patients experience disease progression during immunotherapy,and the mechanism of tumor immune escape is not thoroughly understood. Indoleamine 2,3-dioxyfenase-1 (IDO1) catalyzes the conversion of tryptophan to kynurenine,which is the first and rate-limiting step in the major pathway of tryptophan catabolism. IDO1 overexpression in a tumor microenvironment results in trypto-phan depletion and kynurenine metabolites overproduction,facilitating cancer immune escape. We review the primary mechanisms by which the IDO1 pathway facilitates immune escape in EC,and describe research progress into EC therapy targeting the IDO1 pathway.
9.In vivo antioxidant activity of rabbiteye blueberry (Vaccinium ashei cv. 'Brightwell') anthocyanin extracts.
Jing WANG ; Xingyu ZHAO ; Jiawei ZHENG ; Daniela D HERRERA-BALANDRANO ; Xiaoxiao ZHANG ; Wuyang HUANG ; Zhongquan SUI
Journal of Zhejiang University. Science. B 2023;24(7):602-616
Blueberries are rich in phenolic compounds including anthocyanins which are closely related to biological health functions. The purpose of this study was to investigate the antioxidant activity of blueberry anthocyanins extracted from 'Brightwell' rabbiteye blueberries in mice. After one week of adaptation, C57BL/6J healthy male mice were divided into different groups that were administered with 100, 400, or 800 mg/kg blueberry anthocyanin extract (BAE), and sacrificed at different time points (0.1, 0.5, 1, 2, 4, 8, or 12 h). The plasma, eyeball, intestine, liver, and adipose tissues were collected to compare their antioxidant activity, including total antioxidant capacity (T-AOC), superoxide dismutase (SOD) activity and glutathione-peroxidase (GSH-PX/GPX) content, and the oxidative stress marker malondialdehyde (MDA) level. The results showed that blueberry anthocyanins had positive concentration-dependent antioxidant activity in vivo. The greater the concentration of BAE, the higher the T-AOC value, but the lower the MDA level. The enzyme activity of SOD, the content of GSH-PX, and messenger RNA (mRNA) levels of Cu,Zn-SOD, Mn-SOD, and GPX all confirmed that BAE played an antioxidant role after digestion in mice by improving their antioxidant defense. The in vivo antioxidant activity of BAE indicated that blueberry anthocyanins could be developed into functional foods or nutraceuticals with the aim of preventing or treating oxidative stress-related diseases.
Male
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Mice
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Animals
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Antioxidants/pharmacology*
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Blueberry Plants
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Anthocyanins/pharmacology*
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Mice, Inbred C57BL
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Superoxide Dismutase
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Plant Extracts/pharmacology*
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Superoxide Dismutase-1
10.Effects of Acupuncture on Gut Microbiota and Central Iinflammation in Rat Model of Migraine based on"Gut-Brain"Theory
Mingsheng SUN ; Xingyu CHEN ; Mengdi ZHOU ; Yi LIU ; Yuqi ZHENG ; Siying HUANG ; Dingjun CAI ; Ling ZHAO
World Science and Technology-Modernization of Traditional Chinese Medicine 2023;25(8):2726-2734
Objective Based on the theory of"gut-brain",this study explored the effect of acupuncture on the gut microbiota and central inflammation in migraine model rats,in order to explore the mechanism of acupuncture in the treatment of migraine from the perspective of"gut-brain".Methods The migraine rat model was established by subcutaneous injection of nitroglycerin.They were randomly divided into a model group and an acupuncture group,with 6 rats in each group,and a control group with 6 rats for conventional binding and fixation.Before modeling and on the 1st,5th,and 9th days after modeling,each group used electronic VonFrey to measure the plantar mechanical pain threshold of rats.After the experiment,Elisa was used to detect the expression levels of inflammatory factors IL-6 and TNF-α in the central trigeminal spinal nucleus of the rats in each group.Three-generation Pacbio full-length microbial diversity sequencing was used to perform 16S full-length rDNA sequencing on each group of fecal samples to detect the operational taxonomic unit(OTU)clustering and its abundance,Alpha diversity index,Beta diversity index,species among the samples in each group.differences in abundance.Results In migraine model rats,plantar mechanical pain threshold was significantly decreased(P<0.01),central IL-6 and TNF-α contents were significantly increased(P<0.01),and the structure and abundance of gut microbiota were abnormal.change(P<0.01).Continuous acupuncture treatment can significantly increase the plantar mechanical pain threshold in migraine rats(P<0.01),regulate the diversity of gut microbiota in migraine rats,increase Lactobacillus murine,and reduce the abundance of Lactobacillus enterobacteriaceae.degree(P<0.05),and decreased the levels of IL-6 and TNF-α in the central nervous system of migraine model rats(P<0.01).Conclusion Acupuncture can exert the"gut-brain"anti-inflammatory and analgesic effect of acupuncture in the treatment of migraine by regulating the gut microbiota structure and the expression of central IL-6 and TNF-α inflammatory factors in migraine model rats.

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