Uncovering Anti-Melanoma Mechanisms of Bambusa stenostachya Leaf Compounds via Network Pharmacology and Molecular Docking
Abstract
1. Introduction
2. Results
2.1. LCMS Analysis
2.2. Bioactive Compounds from B. stenostachya
2.3. Predicted Target Genes of B. stenostachya and Related Genes of Melanoma
2.4. Pathway and Process Enrichment Analysis
2.5. Ensemble Docking Results
3. Discussion
4. Materials and Methods
4.1. Materials and Sample Preparation
4.2. LCMS Analysis of B. stenostachya Leaf Crude Extract
4.3. Screening of Bioactive Compounds from B. stenostachya
4.4. Target Prediction of Bioactive Compounds from B. stenostachya
4.5. Pathway Enrichment Analysis
4.6. Molecular Docking Preparation
4.7. Ensemble Docking
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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PubChem ID | Chemical | Molecular Weight (g/mol) | Molecular Formula |
---|---|---|---|
6508 | Quinic acid | 192.17 | C7H12O6 |
1794427 | Chlorogenic acid | 354.31 | C16H18O9 |
5280441 | Vitexin | 432.4 | C21H20O10 |
162350 | Isovitexin | 432.4 | C21H20O10 |
114776 | Homoorientin | 448.38 | C21H20O11 |
5281675 | Orientin | 448.4 | C21H20O11 |
442428 | Naringin (Naringenin 7-rhamnoglucoside) | 580.5 | C27H32O14 |
Molecule | GI Absorption | Bioavailability Score | OB% | Structure |
---|---|---|---|---|
Chlorogenic acid | Low | 0.11 | 13.61 | |
Quinic acid | High | 0.56 | 63.53 | |
Homoorientin (isoorientin) | Low | 0.17 | 23.3 | |
Orientin | Low | 0.17 | 1.79 | |
Vitexin | Low | 0.55 | 3.05 | |
Isovitexin (rutin and ferulic acid) | Low | 0.55 | 31.29 | |
Naringin-7-rhamnoglucoside | Low | 0.17 | 6.92 |
Protein | Ligand | csMIN | csAVG | csMED | csTRIMMEAN |
---|---|---|---|---|---|
CDK2 | CHLOROGENIC ACID | −9.43000 | −4.92246 | −5.91150 | −5.18689 |
CDK2 | DACARBAZINE | −6.11900 | −3.67363 | −4.36200 | −3.87281 |
CDK2 | DOXORUBICIN | −86.06400 | −5.21502 | −5.88450 | −5.13361 |
CDK2 | HOMOORIENTIN | −9.63400 | −4.89919 | −5.75800 | −5.11512 |
CDK2 | ISOVITEXIN | −9.60300 | −4.81899 | −5.75450 | −5.03151 |
CDK2 | NARINGIN | −10.17400 | −5.26133 | −6.20200 | −5.48337 |
CDK2 | ORIENTIN | −12.12300 | −5.05633 | −5.98100 | −5.26331 |
CDK2 | QUINIC ACID | −8.12300 | −4.79348 | −5.66450 | −5.04931 |
CDK2 | VITEXIN | −10.40400 | −4.96989 | −5.93700 | −5.17481 |
MEK1 | CHLOROGENIC ACID | −8.99900 | −5.54884 | −6.07900 | −5.94549 |
MEK1 | DACARBAZINE | −6.33300 | −4.06540 | −4.46100 | −4.37759 |
MEK1 | DOXORUBICIN | −20.71700 | −5.71248 | −6.14900 | −6.01304 |
MEK1 | HOMOORIENTIN | −10.53400 | −5.63281 | −6.12200 | −5.99234 |
MEK1 | ISOVITEXIN | −11.00200 | −5.59132 | −6.09000 | −5.95523 |
MEK1 | NARINGIN | −15.06100 | −6.07004 | −6.59300 | −6.42142 |
MEK1 | ORIENTIN | −12.31800 | −5.77236 | −6.25400 | −6.15324 |
MEK1 | QUINIC ACID | −7.70700 | −5.18088 | −5.67900 | −5.58443 |
MEK1 | VITEXIN | −10.73900 | −5.69276 | −6.21200 | −6.06392 |
PDK1 | CHLOROGENIC ACID | −10.69600 | −5.84483 | −6.08850 | −6.12630 |
PDK1 | DACARBAZINE | −6.55200 | −4.26388 | −4.47700 | −4.47145 |
PDK1 | DOXORUBICIN | −17.18300 | −5.94061 | −6.16500 | −6.18560 |
PDK1 | HOMOORIENTIN | −9.87300 | −5.88804 | −6.12450 | −6.14669 |
PDK1 | ISOVITEXIN | −9.52400 | −5.83747 | −6.06300 | −6.08772 |
PDK1 | NARINGIN | −10.60100 | −6.29952 | −6.54000 | −6.57658 |
PDK1 | ORIENTIN | −10.18200 | −6.00952 | −6.27700 | −6.26988 |
PDK1 | QUINIC ACID | −8.24700 | −5.43671 | −5.70000 | −5.69214 |
PDK1 | VITEXIN | −10.14200 | −5.94927 | −6.18250 | −6.19803 |
PIM1 | CHLOROGENIC ACID | −9.54600 | −5.52084 | −6.11100 | −5.92045 |
PIM1 | DACARBAZINE | −6.72500 | −4.09535 | −4.45800 | −4.39848 |
PIM1 | DOXORUBICIN | −50.59300 | −5.57615 | −6.08800 | −5.86939 |
PIM1 | HOMOORIENTIN | −10.45500 | −5.58319 | −6.20750 | −5.94528 |
PIM1 | ISOVITEXIN | −10.69600 | −5.52624 | −6.13400 | −5.88888 |
PIM1 | NARINGIN | −17.22900 | −5.91897 | −6.54600 | −6.30309 |
PIM1 | ORIENTIN | −11.47800 | −5.60748 | −6.28100 | −5.98845 |
PIM1 | QUINIC ACID | −8.51000 | −5.33340 | −5.89500 | −5.73615 |
PIM1 | VITEXIN | −10.43800 | −5.53094 | −6.14600 | −5.91048 |
PDB | PDB ID | Protein Name | Resolution |
---|---|---|---|
3A99 | pdb_00003a99 | proto-oncogene serine/threonine-protein kinase | 1.60 A |
2R3Q | pdb_00002r3q | mitogen-activated protein kinase | 1.35 A |
5LVO | pdb_00005lvo | cyclin-dependent kinase 2 | 1.09 A |
7B7R | pdb_00007b7r | phosphoinositide-dependent kinase-1 | 1.70 A |
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Darilag, G.M.C.; Liu, H.-C.; Hsieh, C.-Y.; Tayo, L.L.; Talubo, N.D.D.; Yang, S.-C.; Chang, C.-H.; Huang, Y.-P.; Lee, S.-C.; Liu, Y.-C.; et al. Uncovering Anti-Melanoma Mechanisms of Bambusa stenostachya Leaf Compounds via Network Pharmacology and Molecular Docking. Int. J. Mol. Sci. 2025, 26, 6120. https://doi.org/10.3390/ijms26136120
Darilag GMC, Liu H-C, Hsieh C-Y, Tayo LL, Talubo NDD, Yang S-C, Chang C-H, Huang Y-P, Lee S-C, Liu Y-C, et al. Uncovering Anti-Melanoma Mechanisms of Bambusa stenostachya Leaf Compounds via Network Pharmacology and Molecular Docking. International Journal of Molecular Sciences. 2025; 26(13):6120. https://doi.org/10.3390/ijms26136120
Chicago/Turabian StyleDarilag, Gen Maxxine C., Hsuan-Chieh Liu, Cheng-Yang Hsieh, Lemmuel L. Tayo, Nicholas Dale D. Talubo, Shu-Ching Yang, Ching-Hui Chang, Ying-Pin Huang, Shih-Chi Lee, Yung-Chuan Liu, and et al. 2025. "Uncovering Anti-Melanoma Mechanisms of Bambusa stenostachya Leaf Compounds via Network Pharmacology and Molecular Docking" International Journal of Molecular Sciences 26, no. 13: 6120. https://doi.org/10.3390/ijms26136120
APA StyleDarilag, G. M. C., Liu, H.-C., Hsieh, C.-Y., Tayo, L. L., Talubo, N. D. D., Yang, S.-C., Chang, C.-H., Huang, Y.-P., Lee, S.-C., Liu, Y.-C., & Tsai, P.-W. (2025). Uncovering Anti-Melanoma Mechanisms of Bambusa stenostachya Leaf Compounds via Network Pharmacology and Molecular Docking. International Journal of Molecular Sciences, 26(13), 6120. https://doi.org/10.3390/ijms26136120