Therapeutic Potential of Gynostemma pentaphyllum (Thunb.) Makino Against COVID-19 Identified Through Network Pharmacology
Abstract
1. Introduction
2. Results
2.1. Network Pharmacology Analysis
2.2. Protein–Protein Interaction
2.3. GO and KEGG Pathway Enrichment Analysis
2.4. Compound–Target–Pathway (CTP) Network
2.5. Molecular Docking Analysis
2.6. Three-Dimensional Quantitative Structure-Activity Relationship (3D-QSAR) Analysis
2.7. Molecular Dynamics (MD) Simulation Analysis
3. Discussion
4. Materials and Methods
4.1. Screening for Active Compounds, Putative Target Proteins and COVID-19 Associated Genes
4.2. Network Construction
4.3. Gene Ontology (GO) Analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway Enrichment Analysis
4.4. Molecular Docking
4.5. Three-Dimensional Quantitative Structure-Activity Relationship (3D-QSAR)
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
References
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| Targets (kcal/mol) [RMSD] (Å) | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Type | Compounds (Code) | ACE [0.730] | AGTR2 [0.127] | ALOX5 [1.902] | EGFR [0.925] | F2 [0.919] | IL1B [0.885] | IL2 [2.137] | NOS2 [1.377] | PLA2G2A [N.C.] | PLG [0.599] | TNF [2.298] | VDR [0.790] | Mpro [2.173] | RdRp [0.340] | Spike Protein [0.356] |
| Triterpenoid | Damulin B (GPM24) | −10.3 ± 0.0 | −9.5 ± 0.5 | −9.2 ± 0.0 | −8.2 ± 0.2 | −7.9 ± 0.1 | −6.5 ± 0.1 | −6.5 ± 0.5 | −8.8 ± 0.1 | −6.5 ± 0.2 | −6.1 ± 0.2 | −8.1 ± 0.0 | −7.6 ± 0.0 | −7.3 ± 0.0 | −11.4 ± 0.0 | −6.8 ± 0.6 |
| Gypenoside LI (GPM32) | −10.2 ± 0.0 | −9.5 ± 0.0 | −9.5 ± 0.0 | −8.1 ± 0.0 | −7.7 ± 0.1 | −6.4 ± 0.0 | −6.5 ± 0.0 | −9.5 ± 0.0 | −6.8 ± 0.1 | −6.4 ± 0.1 | −7.7 ± 0.1 | −7.3 ± 0.1 | −7.4 ± 0.1 | −10.7 ± 0.0 | −6.9 ± 0.4 | |
| Gypensapogenin E (GPM30) | −10.0 ± 0.0 | −9.9 ± 0.0 | −10.6 ± 0.8 | −8.3 ± 0.0 | −7.8 ± 0.0 | −6.6 ± 0.0 | −7.5 ± 0.3 | −8.7 ± 0.1 | −7.0 ± 0.0 | −6.6 ± 0.2 | −8.7 ± 0.3 | −7.6 ± 0.3 | −8.0 ± 0.4 | −9.5 ± 0.1 | −7.2 ± 0.1 | |
| Flavonoid | Ombuin (GPM10) | −8.5 ± 0.0 | −7.9 ± 0.1 | −8.7 ± 0.0 | −8.0 ± 0.0 | −7.3 ± 0.0 | −8.2 ± 0.0 | −6.1 ± 0.0 | −8.2 ± 0.0 | −6.4 ± 0.0 | −6.3 ± 0.0 | −7.5 ± 0.0 | −8.6 ± 0.0 | −7.0 ± 0.0 | −8.4 ± 0.0 | −6.7 ± 0.1 |
| Ombuoside (GPM15) | −10.1 ± 0.0 | −9.3 ± 0.1 | −9.5 ± 0.0 | −8.1 ± 0.0 | −8.6 ± 0.0 | −6.5 ± 0.0 | −6.4 ± 0.4 | −9.7 ± 0.0 | −6.5 ± 0.3 | −7.2 ± 0.1 | −8.2 ± 0.0 | −7.5 ± 0.0 | −7.7 ± 0 | −10.4 ± 0.0 | −7.3 ± 0.1 | |
| Rutin (GPM23) | −9.8 ± 0.0 | −10.0 ± 0.0 | −9.3 ± 0.1 | −9.2 ± 0.0 | −9.0 ± 0 | −7.8 ± 0.0 | −6.8 ± 0.0 | −9.8 ± 0.0 | −7.2 ± 0.0 | −6.5 ± 0.5 | −7.8 ± 0.3 | −7.9 ± 0.1 | −7.7 ± 0.1 | −10.7 ± 0.0 | −7.7 ± 0.0 | |
| Reference | Lisinopril (ACE inhibitor) | −7.7 ± 0.1 | −7.1 ± 0.2 | −7.2 ± 0.1 | −6.4 ± 0.0 | −6.7 ± 0.1 | −6.3 ± 0.0 | −5.5 ± 0.0 | −7.8 ± 0.3 | −5.8 ± 0.1 | −5.1 ± 0.4 | −7.4 ± 0.1 | −6.8 ± 1.0 | −6.0 ± 0.1 | −7.6 ± 0.3 | −5.9 ± 0.1 |
| Remdesivir (RdRp inhibitor) | −6.0 ± 0.0 | −5.2 ± 0.0 | −6.2 ± 0.1 | −5.1 ± 0.0 | −5.6 ± 0.3 | −5.4 ± 0.1 | −4.7 ± 0.2 | −6.3 ± 0.1 | −4.8 ± 0.0 | −5.1 ± 0.1 | −5.1 ± 0.0 | −6.2 ± 0.2 | −5.7 ± 0.0 | −6.7 ± 0.0 | −5.1 ± 0.1 | |
| Category | Disease | Pathways | Key Target | Refs. |
|---|---|---|---|---|
| Liver | NAFLD and NASH | Apoptosis; Non-alcoholic fatty liver disease; PI3K-Akt signaling pathway; Lipid and atherosclerosis | AKT1, GSK3B | [25] |
| Hepatic fibrosis | Proteoglycans in cancer; PI3K–Akt signaling pathway; EGFR tyrosine kinase inhibitor resistance; EGFR signaling pathway | AKT1, IL6, STAT3, EGFR | [26,27] | |
| Liver injury | Apoptosis signaling pathway | STAT3, HIF1A, PTGS2, EGFR, PPARG, MTOR, AKT1, ESR1, TNF | [28] | |
| Metabolism-associated fatty liver disease | NF-κB signaling pathway; PI3K-Akt signaling pathway; TNF signaling pathway; HIF-1 signaling pathway | TNF, IL6, PTGS2, TP53, CCL2, VEGFA | [29] | |
| Non-alcoholic fatty liver disease | HIF-1 signaling pathway; AGE-RAGE signaling pathway in diabetic complications; Chagas disease; Beta-oxidation pathway | IL6, PTGS2, NFKB1, CDK6, SERPINE1, ADRB2, PCNA, TOP2A, TYMS, PPARA | [30,31] | |
| Heart | Heart failure | PI3K/Akt signaling pathway; MAPK signaling pathway; Ras signaling pathway | MAPK, EGFR, PI3KCA, MCL1 | [32] |
| Lung | Non-small-cell lung cancer | Chemical carcinogenesis receptor activation; Lipid and atherosclerosis; Human cytomegalovirus infection; Pyrimidine metabolism; Pantothenate and CoA biosynthesis | MMP9, STAT3, TYMS, MYC, ESR1, HIF1A | [33,34] |
| Acute lung injury | TNF-α signaling pathway; NF-κB signaling pathway | CXCL2, CXCL1, CXCL10, CCL2, TNFAIP3, SOCS3, IFIT2, TLR2, IL1, IL6, IRF7, | [35] | |
| Lung cancer | MAPK14/STAT3 signaling pathway | STAT3, MAPK14, EGFR, TYMS | [36] | |
| Brain/nervous system | Alzheimer’s disease | Amoebiasis; African trypanosomiasis; Cytokine-cytokine receptor interaction | EGFR, IL1B, IL6, NOS3, PON1 | [37] |
| Depression | HIF-1 signaling pathway; PI3K-Akt signaling pathway; TNF signaling pathway | SIRT1 | [38] | |
| Glioma | EGFR tyrosine kinase inhibitor resistance; Prolactin signaling pathway; VEGF signaling pathway | STAT3, HSP90AA1, IL6, ESR1, PIK3CA, MTOR, PTPN11, MAPK3, BCL2L1, PTGS2 | [39] | |
| Cancer | Breast cancer | PI3K-Akt signaling pathway; Breast cancer pathway; EGFR tyrosine kinase inhibitor resistance | ALB, EGFR, ESR1, AR, PGR, HSP90AA1 | [40] |
| Osteosarcoma | PI3K-Akt signaling pathway; MAPK signaling pathway; Cellular senescence | CCND1, RELA, TNF | [41] | |
| Esophageal cancer | PI3K-Akt signaling pathway; MAPK signaling pathway; IL-17 signaling pathway | AKT1, TP53, VEGFA | [42] | |
| Cervical intraepithelial neoplasia | Cancer; Fluid shear stress and atherosclerosis; Lipid and atherosclerosis | IL6, IL1B, TNF, TP53, PTGS2 | [43] | |
| Renal cell carcinoma | Cancer; Prolactin signaling pathway; PI3K-Akt signaling pathway, Ras/MAPK pathways | VEGFA, PIK3CA, JAK2, CCND1, MAPK3, EGFR, CASP3, HRAS, STAT3, SRSC | [44,45] | |
| Anaplastic thyroid cancer | Cancer; PI3K-Akt signaling pathway; Proteoglycans in cancer | HSP90AA1, SRC, CASP3 | [46] | |
| Bladder cancer | PI3K-Akt signaling pathway; Pathway in cancer; Proteoglycans in cancer | VEGFA, STAT3, PI3KCA | [47] | |
| Gastric cancer | Glycerophospholipid metabolism; Alanine, aspartate and glutamate metabolism; Central carbon metabolism in cancer; PD-L1 checkpoint in cancer; T-cell receptor signaling pathway; Th17 differentiation | ALB, EGFR, HSP90AA1, MMP9, ESR1, IGF1, PPARG, ANXA5 | [48,49] | |
| Ophthalmopathy | JAK–STAT signaling pathway | STAT1, STAT3, STAT4 | [50] | |
| Retinitis Pigmentosa | Cancer; HIF-1 signaling pathway; TNF signaling pathway; PI3K-Akt signaling pathway | FGF2, IL6, MAPK14, MMP2, MMP9, SLC2A1 | [51] | |
| Pancreatic cancer | Cancer; AGE-RAGE signaling pathway in diabetic complications; hepatitis C; IL-17 signaling pathway; Platinum drug resistance | MET, SPP1, ADRA1A, HMOX1, CCL2, ICAM1, VCAM1, BCL2, PRKCB, NCF1, | [52] | |
| Metabolic/Endocrine | Type II Diabetes | Insulin resistance; PI3K-Akt signaling pathway; FOXO signaling pathway | STAT3, PIK3CA, AKT1, EGFR, VEGFA, INSR | [53] |
| Hyperlipidemia | Lipid metabolism and atherosclerosis; TNF signaling pathway; PI3K-Akt signaling pathway | NCOA2, NR3C2, PGR, PPARG, IL6, PPARG, VEGFA | [54] | |
| Diabetic cataracts | AGE-RAGE signaling pathway in diabetic complications; Fluid shear stress and atherosclerosis; Pathways in cancer | IL6, IL1B, TNF, CASP3, MMP9, AKT1, TGFB1, HIF1A, PTGS2, JUN | [55] | |
| Glucose metabolic disorders | AGE-RAGE signaling pathway | SRC, PIK3CA, HRAS, AKT1 | [56] | |
| Obesity | AGE-RAGE signaling pathway; glycerolipid metabolism; lipid and atherosclerosis metabolism; Cholesterol metabolism | HMGCR, ACE, LIPC, LIPG, PPARA, PPARD, PPARG | [57] | |
| Immune/Inflammatory | Acute Pharyngitis | Cancer; PI3K-Akt signaling pathway; JAK–STAT signaling pathway | EGFR, STAT3, MAPK3, SRC, AKT1 | [58] |
| Diarrhea | Cancer; PI3K-Akt pathway; MAPK pathway | AKT1, STAT3, SRC, ESR1, EGFR, HSP90AA1 | [59] | |
| Respiratory system | COVID-19 | Coronavirus disease; renin–angiotensin system | NOS2, F2, REN *, IL1B, IL6, TNF, ACE, EGFR | This study |
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Kim, M.H.; Won, J.A.; Yu, J.S.; Kim, S.M.; Lee, D.K.; Piao, X.-L.; Yoo, H.H. Therapeutic Potential of Gynostemma pentaphyllum (Thunb.) Makino Against COVID-19 Identified Through Network Pharmacology. Pharmaceuticals 2025, 18, 1851. https://doi.org/10.3390/ph18121851
Kim MH, Won JA, Yu JS, Kim SM, Lee DK, Piao X-L, Yoo HH. Therapeutic Potential of Gynostemma pentaphyllum (Thunb.) Makino Against COVID-19 Identified Through Network Pharmacology. Pharmaceuticals. 2025; 18(12):1851. https://doi.org/10.3390/ph18121851
Chicago/Turabian StyleKim, Min Ho, Jin Ah Won, Jun Sang Yu, Su Min Kim, Dong Keun Lee, Xiang-Lan Piao, and Hye Hyun Yoo. 2025. "Therapeutic Potential of Gynostemma pentaphyllum (Thunb.) Makino Against COVID-19 Identified Through Network Pharmacology" Pharmaceuticals 18, no. 12: 1851. https://doi.org/10.3390/ph18121851
APA StyleKim, M. H., Won, J. A., Yu, J. S., Kim, S. M., Lee, D. K., Piao, X.-L., & Yoo, H. H. (2025). Therapeutic Potential of Gynostemma pentaphyllum (Thunb.) Makino Against COVID-19 Identified Through Network Pharmacology. Pharmaceuticals, 18(12), 1851. https://doi.org/10.3390/ph18121851

