Characterization and Anti-Allergic Mechanisms of Bioactive Compounds in a Traditional Chinese Medicine Prescription Using UHPLC-Q-TOF-MS/MS, Network Pharmacology and Computational Simulations
Abstract
1. Introduction
2. Results
2.1. Qualitative Study of Chemical Constituents in ACP Based on UHPLC–Q–TOF–MS Technology
2.1.1. Flavonoids
2.1.2. Amino Acids
2.1.3. Phenolic Acids
2.1.4. Saponins
2.1.5. Nucleosides
2.1.6. Iridoids
2.1.7. Other Compounds
2.2. Target Analysis Results
2.3. Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway Enrichment Analysis Results
2.4. Network Analysis
2.5. Molecular Docking Analysis
2.6. MD Simulation
3. Discussion
4. Materials and Methods
4.1. Materials and Reagents
4.2. Preparation for Water-Extraction of ACP
4.3. Chromatography Conditions and MS Parameters
4.4. Network Pharmacology Analysis
4.4.1. Collection of ACP Compound Targets and ACP-Disease Targets
4.4.2. Collection of Anti-Allergic Drugs and Their Targets
4.4.3. Target Intersection
4.4.4. KEGG Pathway Enrichment Analysis
4.4.5. Network Construction
4.5. Molecular Docking
4.6. Molecular Dynamics (MD) Simulation
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
TCM | Traditional Chinese Medicine |
ACP | Allergic constitution prescription |
UHPLC-Q-TOF-MS/MS | Ultra-high performance liquid chromatography quadrupole time-of-flight tandem mass spectrometry |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
WAO | World Allergy Organization |
WHO | World Health Organization |
MD | Molecular dynamics |
RMSD | Root mean squared deviation |
Rg | Radius of gyration |
RMSF | Root mean squared fluctuations |
SASA | Solvent accessible surface area |
QAMS | Quantitative analysis of multi-components by single-marker |
DRS | Digital reference standard |
TRSDMC | Two reference substances for determination of multiple components |
QASRE | Quantitative analysis by standardized reference extract |
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No.-Unique | Gene Nane | Degree | No.-Common | Gene Nane | Degree |
---|---|---|---|---|---|
1 | Mitogen-activated protein kinase 1 (MAPK1) | 9 | 1 | Alpha-1D adrenergic receptor (ADRA1D) | 4 |
2 | Mitogen-activated protein kinase 3 (MAPK3) | 9 | 2 | Beta-1 adrenergic receptor (ADRB1) | 4 |
3 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform (PIK3CD) | 9 | 3 | Alpha-1A adrenergic receptor (ADRA1A) | 4 |
4 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit beta isoform (PIK3CB) | 9 | 4 | Alpha-2B adrenergic receptor (ADRA2B) | 1 |
5 | RAC-alpha serine/threonine-protein kinase (AKT1) | 8 | 5 | Alpha-2A adrenergic receptor (ADRA2A) | 1 |
6 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform (PIK3CA) | 8 | 6 | Hematopoietic prostaglandin D synthase (HPGDS) | 1 |
7 | Phosphatidylinositol 3-kinase regulatory subunit alpha (PIK3R1) | 8 | 7 | Polyunsaturated fatty acid 5-lipoxygenase (ALOX5) | 1 |
8 | Transcription factor p65 (RELA) | 8 | 8 | Thromboxane-A synthase (TBXAS1) | 1 |
9 | Nuclear factor NF-kappa-B p105 subunit (NFKB1) | 8 | 9 | Thromboxane A2 receptor (TBXA2R) | 1 |
10 | Mitogen-activated protein kinase 8 (MAPK8) | 8 |
No.-Unique | Mol ID | Degree | Compounds | No.-Common | Mol ID | Degree | Compounds |
---|---|---|---|---|---|---|---|
1 | M12 | 7 | Lyoniresinol | 1 | M90 | 5 | Naringin-3-O-(3-hydroxy-3-methylglutarate)-glucoside |
2 | M54 | 5 | Limonin | 2 | M93 | 4 | Glycyrrhizic acid |
3 | M26 | 5 | 7-Acetoxy-2-methylisoflavone | 3 | M20 | 4 | Heptopyranosides |
4 | M92 | 4 | Apiole | 4 | M89 | 4 | Licorice-saponin G2 |
5 | M88 | 4 | Phellopterin | 5 | M94 | 3 | Uralsaponin A |
6 | M87 | 4 | Byakangelicol | 6 | M11 | 3 | Phenylalanine |
7 | M30 | 3 | Caffeic acid | 7 | M17 | 2 | Tryptophan |
8 | M64 | 2 | Nomilin | 8 | M73 | 2 | Diosmin |
9 | M71 | 2 | Naringenin | 9 | M50 | 2 | Luteolin-7-O-β-D-glucoside |
10 | M45 | 2 | Dillapiol | 10 | M59 | 2 | Hyperoside |
11 | M86 | 2 | Nortangeretin | 11 | M55 | 2 | Leucoside |
12 | M80 | 2 | Luteolin | 12 | M65 | 2 | Kaempferol 3-O-robinobioside |
13 | M81 | 2 | Kaempferol | 13 | M57 | 2 | Rutin |
14 | M85 | 2 | Quercetin | 14 | M72 | 2 | Genistein |
15 | M82 | 2 | Daidzein |
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Hong, L.; Qin, Y.; Ip, C.; Xu, W.; Zeng, H.; Duan, X.; Wang, J.; Zhao, J.; Wang, Q.; Li, S. Characterization and Anti-Allergic Mechanisms of Bioactive Compounds in a Traditional Chinese Medicine Prescription Using UHPLC-Q-TOF-MS/MS, Network Pharmacology and Computational Simulations. Pharmaceuticals 2025, 18, 1444. https://doi.org/10.3390/ph18101444
Hong L, Qin Y, Ip C, Xu W, Zeng H, Duan X, Wang J, Zhao J, Wang Q, Li S. Characterization and Anti-Allergic Mechanisms of Bioactive Compounds in a Traditional Chinese Medicine Prescription Using UHPLC-Q-TOF-MS/MS, Network Pharmacology and Computational Simulations. Pharmaceuticals. 2025; 18(10):1444. https://doi.org/10.3390/ph18101444
Chicago/Turabian StyleHong, Liang, You Qin, Chiwai Ip, Wenfei Xu, Haoxuan Zeng, Xiu Duan, Ji Wang, Jing Zhao, Qi Wang, and Shaoping Li. 2025. "Characterization and Anti-Allergic Mechanisms of Bioactive Compounds in a Traditional Chinese Medicine Prescription Using UHPLC-Q-TOF-MS/MS, Network Pharmacology and Computational Simulations" Pharmaceuticals 18, no. 10: 1444. https://doi.org/10.3390/ph18101444
APA StyleHong, L., Qin, Y., Ip, C., Xu, W., Zeng, H., Duan, X., Wang, J., Zhao, J., Wang, Q., & Li, S. (2025). Characterization and Anti-Allergic Mechanisms of Bioactive Compounds in a Traditional Chinese Medicine Prescription Using UHPLC-Q-TOF-MS/MS, Network Pharmacology and Computational Simulations. Pharmaceuticals, 18(10), 1444. https://doi.org/10.3390/ph18101444