Enhanced Anti-Lung Cancer Effects of Steamed Panacis Japonici Rhizoma: Insights from Metabolomics, Network Pharmacology and Molecular Dynamics Simulation
Abstract
1. Introduction
2. Results
2.1. Chemical Profiling and Multivariate Statistical Analysis of Distinctive Markers Between Raw and Steamed PJR
2.2. Network Analysis of the Increased Compounds
2.2.1. Target Prediction
2.2.2. Protein–Protein Interaction (PPI) Network Construction
2.2.3. Functional Enrichment Analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathways
2.2.4. The “Component-Target-Pathway” Network
2.3. Molecular Docking Analysis
2.4. MD Simulation Analysis
2.5. Gene Expression Omnibus (GEO) Database Validation
2.6. Cellular Viability Under Drug-Containing Serum Treatment
2.7. Cellular Morphology Alterations Induced by Drug-Containing Serum
3. Discussion
4. Materials and Methods
4.1. Chemicals and Reagents
4.2. Metabolomic Profiling of Raw and Steamed PJR
4.2.1. Preparation of Standard Solutions
4.2.2. Preparation of Test Products
4.2.3. UPLC-Q-TOF-MS Conditions
4.2.4. Data Processing and Analysis
4.3. Network Pharmacology
4.3.1. Acquisition of Targets for Differential Metabolites
4.3.2. Screening of Disease-Associated Targets
4.3.3. Construction of a Venn Diagram
4.3.4. Construction of the PPI Network
4.3.5. GO Functional Annotation and KEGG Pathway Enrichment Analysis
4.3.6. Construction of the Compound-Target-Pathway Network
4.4. Molecular Docking
4.5. MD Simulation
4.6. GEO Database Validation
4.7. Experimental Verification
4.7.1. Preparation of Experimental Liquid Medicine
4.7.2. Animal Grouping and Drug Administration
4.7.3. Preparation of Drug-Containing Serum
4.7.4. Cell Culture and Passage
4.7.5. Cell Proliferation Assay
4.7.6. Cell Morphology Observation
4.8. Statistical Analyses
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
| PJR | Panacis Japonici Rhizoma |
| UPLC-Q-TOF-MS | Ultra-high performance liquid chromatography-quadrupole/time-of-flight mass spectrometry |
| TCM | Traditional Chinese medicine |
| PCA | Principal component analysis |
| OPLS-DA | Orthogonal partial least squares-discriminant analysis |
| VIP | Variable importance in projection |
| PPI | Protein–protein interaction |
| GO | Gene Ontology |
| KEGG | Kyoto Encyclopedia of Genes and Genomes |
| DEGs | Differentially expressed genes |
| CMC-Na | Carboxymethyl cellulose sodium |
| RMSD | Root mean square deviation |
| RMSF | Root mean square fluctuation |
| Rg | Radius of gyration |
| SASA | Solvent accessible surface area |
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| Peak ID | RT (min) | Identification | Molecular Formula | Ions | Exact Mass | Error (ppm) | MS/MS Fragment | VIP | p | Trend |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 6.37 | Notoginsenoside J | C42H74O16 | [M−H]− | 833.4899 | 1.47 | 671.4501, 509.4091, 453.1986 | 1.61 | 2.69 × 10−2 | ↓ |
| 2 | 9.79 | Notoginsenoside R1 | C47H80O18 | [M−H]− | 931.5267 | 2.80 | 799.5081, 637.45000, 475.3922 | 4.61 | 4.04 × 10−5 | ↓ |
| 3 | 10.9 | Ginsenoside B2 | C48H82O18 | [M−H]− | 945.5400 | 3.10 | 783.5142, 637.4500, 475.3922 | 1.33 | 4.91 × 10−10 | ↓ |
| 4 | 17.97 | Notoginsenoside R4 | C59H100O27 | [M−H]− | 1239.6345 | 3.25 | 807.4406, 645.3884, 569.3983 | 2.85 | 3.39 × 10−8 | ↓ |
| 5 | 19.31 | Notoginsenoside Fa | C59H100O27 | [M−H]− | 1239.6345 | 2.68 | 879.5244, 623.3054, 593.2994 | 2.56 | 1.61 × 10−4 | ↓ |
| 6 | 20.99 | Ginsenoside F1 | C36H62O9 | [M−H]− | 637.4299 | 0.49 | 597.2381, 461.2545, 345.1388 | 7.21 | 1.89 × 10−15 | ↑ |
| 7 | 23.78 | Vinaginsenoside R7 | C53H90O22 | [M−H]− | 1077.5820 | 3.38 | 955.5255, 793.4662, 569.4081 | 1.35 | 1.90 × 10−3 | ↓ |
| 8 | 30.21 | Ginsenoside Rd | C48H82O18 | [M+HCOO]− | 991.5454 | 3.16 | 793.4662, 725.4743, 419.2361 | 8.94 | 4.13 × 10−6 | ↓ |
| 9 | 30.34 | Ginsenoside Rs2 | C55H92O23 | [M+HCOO]− | 1165.5979 | 3.56 | 991.5887, 793.4662, 605.3209 | 1.8 | 1.90 × 10−2 | ↓ |
| 10 | 32.18 | Ginsenoside Rs1 | C55H92O23 | [M+HCOO]− | 1165.5979 | 3.16 | 605.3209, 592.2969 | 1.39 | 1.30 × 10−2 | ↓ |
| 11 | 32.45 | Gypenoside XVII | C48H82O18 | [M+HCOO]− | 991.5454 | 2.72 | 945.5776, 869.5281, 518.2928 | 3.98 | 5.47 × 10−4 | ↓ |
| 12 | 33.22 | Calenduloside H methyl ester | C49H78O19 | [M+HCOO]− | 1015.5091 | 2.92 | 853.4913, 530.2729, 455.3732 | 2.28 | 3.58 × 10−6 | ↓ |
| 13 | 33.23 | Calenduloside G methyl ester | C43H68O14 | [M+HCOO]− | 853.4566 | 1.94 | 609.4003, 455.3688, 153.0221 | 1.22 | 1.84 × 10−7 | ↓ |
| 14 | 34.87 | Ginsenoside F4/Rg6 | C42H70O12 | [M+HCOO]− | 811.4824 | 0.39 | 583.3910, 537.3824, 409.1258 | 4.81 | 2.24 × 10−14 | ↑ |
| 15 | 40.54 | Momordin I | C41H64O13 | [M−H]− | 763.4251 | 0.42 | 703.9182, 654.3607, 339.6309 | 1.46 | 4.98 × 10−3 | ↑ |
| 16 | 41.93 | (3b, 21b)-12-Oleanene-3,21,28-triol 28-[arabinosyl-(1→3)-arabinosyl-(1→3)-arabinoside] | C45H74O15 | [M−H]− | 853.4929 | 1.75 | 793.4778, 731.4792, 455.3732 | 1.12 | 4.11 × 10−12 | ↑ |
| 17 | 42.12 | Ginsenoside Rg3 | C42H72O13 | [M−H]− | 783.4875 | 1.24 | 621.4654, 459.4040, 161.0519 | 2.62 | 4.41 × 10−8 | ↑ |
| 18 | 47.70 | Vinaginsenoside R1 | C44H74O15 | [M−H]− | 841.4929 | 1.84 | 795.5377, 455.3732, 279.2435 | 1.05 | 2.93 × 10−4 | ↑ |
| 19 | 48.41 | Momordin Ia | C42H66O13 | [M−H]− | 777.4407 | 1.48 | 627.4192, 316.8525, 279.2469 | 1.12 | 2.78 × 10−3 | ↑ |
| 20 | 48.73 | Ginsenoside Rg5 | C41H68O10 | [M−H]− | 765.4770 | 0.69 | 603.4623, 501.3495, 113.0265 | 2.29 | 4.13 × 10−6 | ↑ |
| 21 | 50.75 | Ginsenoside Rh2 | C36H62O8 | [M+HCOO]− | 667.4404 | 0.81 | 569.3983393.2220, 146.9706 | 2.89 | 6.67 × 10−6 | ↑ |
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Zhang, Y.; Yang, J.; Qu, B.; Huang, J.; Wang, Y.; Yan, J. Enhanced Anti-Lung Cancer Effects of Steamed Panacis Japonici Rhizoma: Insights from Metabolomics, Network Pharmacology and Molecular Dynamics Simulation. Int. J. Mol. Sci. 2025, 26, 11999. https://doi.org/10.3390/ijms262411999
Zhang Y, Yang J, Qu B, Huang J, Wang Y, Yan J. Enhanced Anti-Lung Cancer Effects of Steamed Panacis Japonici Rhizoma: Insights from Metabolomics, Network Pharmacology and Molecular Dynamics Simulation. International Journal of Molecular Sciences. 2025; 26(24):11999. https://doi.org/10.3390/ijms262411999
Chicago/Turabian StyleZhang, Yijia, Jingxiao Yang, Binqing Qu, Jiacheng Huang, Yuanqing Wang, and Jianye Yan. 2025. "Enhanced Anti-Lung Cancer Effects of Steamed Panacis Japonici Rhizoma: Insights from Metabolomics, Network Pharmacology and Molecular Dynamics Simulation" International Journal of Molecular Sciences 26, no. 24: 11999. https://doi.org/10.3390/ijms262411999
APA StyleZhang, Y., Yang, J., Qu, B., Huang, J., Wang, Y., & Yan, J. (2025). Enhanced Anti-Lung Cancer Effects of Steamed Panacis Japonici Rhizoma: Insights from Metabolomics, Network Pharmacology and Molecular Dynamics Simulation. International Journal of Molecular Sciences, 26(24), 11999. https://doi.org/10.3390/ijms262411999

