Network Pharmacology and Molecular Docking-Based Investigation of Herbal Compounds Against Cancer-Related Signaling Pathways

Authors

  • Bnaind Maliek Department of Computer Science, University of Houston, Houston, TX, USA.
  • Parth Kapoor Department of Computer Science, University of New Hampshire, Durham, NH, USA.
  • Krish Trivedi Department of Computer Science, University of North Texas, Denton, TX, USA.

Keywords:

network pharmacology, molecular docking, cancer signaling, herbal compounds, systems architecture, reproducibility, governance, fairness

Abstract

Cancer is a heterogeneous family of diseases characterized by the progressive dysregulation of intracellular and intercellular signaling networks. The limitations of single-target therapeutic strategies, including acquired resistance and systemic toxicity, have motivated the search for multicomponent interventions that can modulate multiple nodes within cancer-related pathways. Herbal medicines represent a rich source of structurally diverse compounds with potential polypharmacological activity, yet their mechanistic complexity poses substantial challenges for evidence-based investigation. This paper examines the integration of network pharmacology and molecular docking as a systems-level computational framework for investigating herbal compounds against cancer-related signaling pathways. The discussion is oriented toward architectural design, data integration, computational trade-offs, validation robustness, reproducibility, governance, and translational sustainability. Network pharmacology provides a high-level topological representation of compound-target-disease relationships, while molecular docking contributes structural filters for evaluating binding plausibility. The combined pipeline enables prioritization of herbal constituents for experimental and clinical follow-up, but it also introduces systemic vulnerabilities related to data bias, pathway incompleteness, scoring function uncertainty, and regulatory ambiguity. This paper argues that the utility of such platforms depends not only on algorithmic accuracy but also on transparent data provenance, interoperable infrastructure, rigorous external validation, and ethically aligned deployment. Future developments should emphasize adaptive learning architectures, federated data governance, cross-domain knowledge graphs, and robust frameworks for translating computational predictions into sustainable and equitable cancer therapeutic research.

References

1. Hopkins, A. L. (2008). Network pharmacology: The next paradigm in drug discovery. Nature Chemical Biology, 4(11), 682-690.

2. Barabasi, A.-L., & Oltvai, Z. N. (2004). Network biology: Understanding the cell's functional organization. Nature Reviews Genetics, 5(2), 101-113.

3. Li, S., & Zhang, B. (2013). Traditional Chinese medicine network pharmacology: Theory, methodology and application. Chinese Journal of Natural Medicines, 11(2), 110-120.

4. Kanehisa, M., Furumichi, M., Tanabe, M., Sato, Y., & Morishima, K. (2017). KEGG: New perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Research, 45(D1), D353-D361.

5. Szklarczyk, D., Gable, A. L., Nastou, K. C., Lyon, D., Kirsch, R., Pyysalo, S., Doncheva, N. T., Legeay, M., Fang, T., Bork, P., Jensen, L. J., & von Mering, C. (2021). The STRING database in 2021: Protein-protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Research, 49(D1), D605-D612.

6. Ru, J., Li, P., Wang, J., Zhou, W., Li, B., Huang, C., Li, P., Guo, Z., Tao, W., Yang, Y., Xu, X., Li, Y., Wang, Y., & Yang, L. (2014). TCMSP: A database of systems pharmacology for drug discovery from herbal medicines. Journal of Cheminformatics, 6, 13.

7. Wishart, D. S., Feunang, Y. D., Guo, A. C., Lo, E. J., Marcu, A., Grant, J. R., Sajed, T., Johnson, D., Li, C., Sayeeda, Z., Assempour, N., Iynkkaran, I., Liu, Y., Maciejewski, A., Gale, N., Wilson, A., Chin, L., Cummings, R., Le, D., Pon, A., Knox, C., & Wilson, M. (2018). DrugBank 5.0: A major update to the DrugBank database for 2018. Nucleic Acids Research, 46(D1), D1074-D1082.

8. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., & Bourne, P. E. (2000). The Protein Data Bank. Nucleic Acids Research, 28(1), 235-242.

9. Trott, O., & Olson, A. J. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455-461.

10. Kitchen, D. B., Decornez, H., Furr, J. R., & Bajorath, J. (2004). Docking and scoring in virtual screening for drug discovery: Methods and applications. Nature Reviews Drug Discovery, 3(11), 935-949.

11. Wang, Y., Yao, J., Sui, Y., Jiang, H., Ma, B., Lai, S., ... & Tan, N. (2026). HerbSyner_Finder: a network community-based model for identifying synergistic combinations from herbal medicines and complex systems. Targetome, 2(2).

12. Pinzi, L., & Rastelli, G. (2019). Molecular docking: Shifting paradigms in drug discovery. International Journal of Molecular Sciences, 20(18), 4331.

13. O'Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. Journal of Cheminformatics, 3, 33.

14. Baell, J. B., & Holloway, G. A. (2010). New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays. Journal of Medicinal Chemistry, 53(7), 2719-2740.

15. Lipinski, C. A. (2001). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 46(1-3), 3-26.

16. Wilkinson, M. D., Dumontier, M., Aalbersberg, I. J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J.-W., da Silva Santos, L. B., Bourne, P. E., Bouwman, J., Brookes, A. J., Clark, T., Crosas, M., Dillo, I., Dumon, O., Edmunds, S., Evelo, C. T., Finkers, R., Gonzalez-Beltran, A., Gray, A. J. G., Groth, P., Goble, C., Grethe, J. S., Heringa, J., 't Hoen, P. A. C., Hooft, R., Kuhn, T., Kok, R., Kok, J., Lusher, S. J., Martone, M. E., Mons, A., Packer, A. L., Persson, B., Rocca-Serra, P., Roos, M., van Schaik, R., Sansone, S.-A., Schultes, E., Sengstag, T., Slater, T., Strawn, G., Swertz, M. A., Thompson, M., van der Lei, J., van Mulligen, E., Velterop, J., Waagmeester, A., Wittenburg, P., Wolstencroft, K., Zhao, J., & Mons, B. (2016). The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data, 3, 160018.

17. Weinstein, J. N., Collisson, E. A., Mills, G. B., Shaw, K. R. M., Ozenberger, B. A., Ellrott, K., Shmulevich, I., Sander, C., & Stuart, J. M. (2013). The Cancer Genome Atlas Pan-Cancer analysis project. Nature Genetics, 45(10), 1113-1120.

18. Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., & Mesirov, J. P. (2005). Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences, 102(43), 15545-15550.

19. Mendez, D., Gaulton, A., Bento, A. P., Chambers, J., De Veij, M., Felix, E., Magarinos, M. P., Mosquera, J. F., Mutowo, P., Nowotka, M., Gordillo-Maranon, M., Hunter, F., Junco, L., Mugumbate, G., Rodriguez-Lopez, M., Atkinson, F., Bosc, N., Radoux, C. J., Segura-Cabrera, A., Hersey, A., & Leach, A. R. (2019). ChEMBL: Towards direct deposition of bioassay data. Nucleic Acids Research, 47(D1), D930-D940.

20. Irwin, J. J., & Shoichet, B. K. (2005). ZINC: A free database of commercially available compounds for virtual screening. Journal of Chemical Information and Modeling, 45(1), 177-182.

21. Ekins, S., Mestres, J., & Testa, B. (2007). In silico pharmacology for drug discovery: Methods for virtual ligand screening and profiling. British Journal of Pharmacology, 152(1), 9-20.

22. Hao, D. C., & Xiao, P. G. (2014). Network pharmacology: A Rosetta Stone for traditional Chinese medicine. Drug Development Research, 75(5), 299-312.

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Published

2026-07-19

How to Cite

Bnaind Maliek, Parth Kapoor, & Krish Trivedi. (2026). Network Pharmacology and Molecular Docking-Based Investigation of Herbal Compounds Against Cancer-Related Signaling Pathways. Bioinformatics Insights and Analytics, 1(2). Retrieved from https://bioinfia.org/index.php/home/article/view/180