Home⇛WVSU Research Journal⇛vol. 14 no. 2 (2025)

In Silico Screening of Flavonoids from Aratiles (Muntingia calabura L.) for Potential Anti-Angiogenic Activity

John Rowel S. Chavez | Leopoldo G. Ayukil Iii | Churney Maurice O. Dollolasa | Renz Nathaniel E. Asis | Bea Juliene G. Gambito | Rheivin Lourenzo B. Rodriguez | Shaira Daine A. Villuga

Discipline: health studies

 

Abstract:

In silico methods have been widely acknowledged by researchers as efficient and effective tools for accelerating drug discovery through computer modelling. This study explored the anti-angiogenic potential of flavonoids from Aratiles (Muntingia calabura L.) the first in silico screening of specific flavonoids against a panel of key angiogenic protein receptors, thereby providing a more precise evaluation of its anti-angiogenic potential than previously reported crude extract studies. PyRx software was used to assess each flavonoid ligand's binding score followed by BIOVIA Discovery Studio Visualizer Analysis to determine the binding site, docking pose, binding affinity score, and specific amino acid interactions of each flavonoid ligand within the receptor sites. Out of the forty (40) initial flavonoid ligands, twenty-three (23) were found to comply with Lipinski's Rule of 5, indicating favorable ADME properties (Absorption, Distribution, Metabolism, and Excretion). Using ProTox-3.0-2024 web server, seventeen (17) out of these twenty-three (23) flavonoid ligands have passed the toxicity screening being categorized as Class V- may be harmful and Class VInon-toxic. The selected flavonoid ligands were then analyzed for their binding affinity to five (5) angiogenic receptors: Vascular Endothelial Growth Factor Receptor 2 (VEGFR-2) (Kent, 2012), Fibroblast Growth Factor Receptor 2 (FGFR-2), Transforming Growth Factor Beta Receptor 1(TGF-βR-1), Insulin-like Growth Factor 1 Receptor (IGF -1R), and Endothelial Growth Factor Receptor (EGFR). Ultimately, flavonoid ligand 17 identified as 7-(benzyloxy)-6,8-dimethoxy-5-hydroxyflavone showed strong binding interactions ranging from -9 to -11 kcal/mol for all five (5) angiogenic receptors. These values were almost equal to, and in some instances, higher than those of the control inhibitors. By and large, flavonoid ligand 17 from Aratiles demonstrated a promising anti-angiogenic potential and may serve as a lead compound for further development in anti-cancer therapy.



References:

  1. Abotaleb, M., Samuel, S. M., Varghese, E., Varghese, S., Kubatka, P., Liskova, A., & Büsselberg, D. (2018). Flavonoids in cancer and apoptosis. Cancers, 11(1), Article 28. https://doi.org/10.3390/cancers11010028 MDPI+1
  2. Agu, P. C., Afiukwa, C. A., Orji, O. U., Ezeh, E. M., Ofoke, I. H., Ogbu, C. O., Ugwuja, E. I., & Aja, P. M. (2023). Molecular docking as a tool for the discovery of molecular targets of nutraceuticals in disease management. Scientific Reports, 13(1), Article 40160. https://doi.org/10.1038/s41598-023-40160-2
  3. Ansori, A. N. M., Kharisma, V. D., & Solikhah, T. I. (2021). Medicinal properties of Muntingia calabura L.: A review. Research Journal of Pharmacy and Technology, 14(5), 4509–4512. https://doi.org/10.52711/0974-360X.2021.00784
  4. Barquilha, C. E., & Braga, M. C. (2021). Adsorption of organic and inorganic pollutants onto biochars: Challenges, operating conditions, and mechanisms. Bioresource Technology Reports, 15, Article 100728. https://doi.org/10.1016/j.biteb.2021.100728
  5. Beyleveld, G., White, K. M., Ayllon, J., & Shaw, M. L. (2013). New-generation screening assays for detection of anti-influenza compounds targeting viral and host functions. Antiviral Research, 100(1), 120–132. https://doi.org/10.1016/j.antiviral.2013.07.018
  6. BiologyInsights Team. (2025, July 28). What is binding affinity and why is it important? Biology Insights. https://biologyinsights.com/what-is-binding-affinity-and-why-is-it-important/
  7. Brylinski, M. (2017). Aromatic interactions at the ligand–protein interface: Implications for the development of docking scoring functions. Chemical Biology & Drug Design, 91(2), 380–390. https://doi.org/10.1111/cbdd.13084
  8. Dassault Systèmes. (2024, September 25). BIOVIA Discovery Studio. https://www.3ds.com/products/biovia/discovery-studio
  9. Cheen, C. C. (2022, February). Phytochemical study of flavonoids from the leaves of Muntingia calabura, synthesis of flavonoid Mannich base derivatives and their anticancer activity against breast carcinoma cell lines [Unpublished master’s thesis, Universiti Tunku Abdul Rahman]. UTAR Institutional Repository. http://eprints.utar.edu.my/5734/
  10. Cooper, G. M. (2000). The development and causes of cancer. In The Cell [NCBI Bookshelf]. U.S. National Library of Medicine. https://www.ncbi.nlm.nih.gov/books/NBK9963/
  11. Dean, J. (2024, January 5). Philippine fruit Aratilis: Aratilis health benefits & why Aratilis fruit is beneficial. Antioxidant Fruits. https://antioxidant-fruits.com/fruit-of-the-philippines-aratilis.html#google_vignette
  12. Dias, M. C., Pinto, D. C. G. A., & Silva, A. M. S. (2021). Plant flavonoids: Chemical characteristics and biological activity. Molecules, 26(17), Article 5377. https://doi.org/10.3390/molecules26175377
  13. 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. https://doi.org/10.1038/sj.bjp.0707305
  14. Eth Zurich. (n.d.). Databases. Infozentrum. Retrieved, from https://infozentrum.ethz.ch/en/databases-tools/databases
  15. Ferlay, J., Ervik, M., Lam, F., Laversanne, M., Colombet, M., Mery, L., Piñeros, M., Znaor, A., Soerjomataram, I., & Bray, F. (2024). Global Cancer Observatory: Cancer Today (GLOBOCAN 2022). International Agency for Research on Cancer. Retrieved March 25, 2025, from https://gco.iarc.who.int/media/globocan/factsheets/populations/608-philippines-fact-sheet.pdf
  16. Gautam, R., Singh, M., Gautam, S., Rawat, J. K., Saraf, S. A., & Kaithwas, G. (2016). Rutin attenuates intestinal toxicity induced by methotrexate linked with anti-oxidative and anti-inflammatory effects. BMC Complementary and Alternative Medicine, 16, Article 99. https://doi.org/10.1186/s12906-016-1069-1
  17. Gilbis, T. P., Yasmin, Y. (2022). Phytochemicals and antibacterial activity of Muntingia calabura leaves-based product. Journal of Research in Medical and Dental Science, 10(11), 259–263. https://www.jrmds.in/articles/phytochemicals-and-antibacterial-activity-of-muntingia-calabura-leaves-based-product-96528.html
  18. Jisha, N., Vysakh, A., Vijeesh, V., & Latha, M. (2020). Ethyl acetate fraction of Muntingia calabura L. exerts anti-colorectal cancer potential via regulating apoptotic and inflammatory pathways. Journal of Ethnopharmacology, 261, Article 113064. https://doi.org/10.1016/j.jep.2020.113064
  19. Kathirvel, P., & Sundar Kumar, V. (2025). Exploring the medicinal potential of Muntingia calabura Linn. fruit: A comprehensive overview. In Pomotherapeutic Insights on Wild Edible Fruits (pp. 37–52). Springer. https://doi.org/10.1007/978-981-96-0543-9_3
  20. Khater, M., Greco, F., & Osborn, H. M. (2020). Antiangiogenic activity of flavonoids: A systematic review and meta-analysis. Molecules, 25(20), Article 4712. https://doi.org/10.3390/molecules25204712
  21. Kent, D. (2012, May 14). Cell therapy for diabetic retinopathy — a work in progress. touchENDOCRINOLOGY. https://touchendocrinology.com/diabetes/journal-articles/cell-therapy-for-diabetic-retinopathy-a-work-in-progress/
  22. Kuchekar, M., Upadhye, M., Pujari, R., Kadam, S., & Gunjal, P. (2021). Muntingia calabura: A comprehensive review. Journal of Pharmaceutical and Biological Sciences, 9(2), 81–87. https://doi.org/10.18231/j.jpbs.2021.011
  23. Lazatin, H. (2019, May 31). 16-year-old Filipino discovers the Aratiles plant can be used to prevent type 2 diabetes. Esquire. https://www.esquiremag.ph/the-good-life/mavericks/maria-isable-layson-aratiles-research-a00184-20190531?s=kdmvbosmovn6eldste891toraa
  24. Liskova, A., Samec, M., Koklesova, L., Brockmueller, A., Zhai, K., Abdellatif, B., Siddiqui, M., Biringer, K., Kudela, E., Pec, M., Gadanec, L. K., Šudomová, M., Hassan, S. T. S., Zulli, A., Shakibaei, M., Giordano, F. A., Büsselberg, D., Golubnitschaja, O., & Kubatka, P. (2021). Flavonoids as an effective sensitizer for anti-cancer therapy: Insights into multi-faceted mechanisms and applicability toward individualized patient profiles. The EPMA Journal, 12(2), 155–176. https://doi.org/10.1007/s13167-021-00242-5
  25. Long, K., Kostman, S. J., Fernandez, C., Burnett, J., & Huryn, D. (2019). Do zebrafish obey Lipinski rules? Retrieved from https://www.semanticscholar.org/paper/Do-Zebrafish-Obey-Lipinski-Rules-Long-Kostman/18afbbc645b0b1dcb2a340ef10632be3f4d5d1a9
  26. Mahmood, N. D., Nasir, N. L. M., Rofiee, M. S., Tohid, S. F. M., Ching, S. M., Teh, L. K., Salleh, M. Z., & Zakaria, Z. A. (2014). Muntingia calabura: A review of its traditional uses, chemical properties, and pharmacological observations. Pharmaceutical Biology, 52(12), 1598–1623. https://doi.org/10.3109/13880209.2014.908397
  27. Martin, Y. (2005, June). A bioavailability score. ResearchGate. https://www.researchgate.net/publication/7881216_A_Bioavailability_Score
  28. Nas, J. S. (2020). Screening of flavonoids from Muntingia calabura aqueous leaf extract and its potential influence on different metabolic enzymes in Danio rerio. AACL Bioflux, 13(5), 3046–3055. https://bioflux.com.ro/docs/2020.3046-3055.pdf
  29. Nasir, N. L. M., Kamsani, N. E., Mohtarrudin, N., Othman, F., Tohid, S. F. M., & Zakaria, Z. A. (2017). Anticarcinogenic activity of Muntingia calabura leaves methanol extract against the azoxymethane-induced colon cancer in rats involves modulation of the colonic antioxidant system partly by flavonoids. Pharmaceutical Biology, 55(1), 2102–2109. https://doi.org/10.1080/13880209.2017.1371769
  30. Nussinov, R., Tsai, C.-J., Xin, F., & Radivojac, P. (2012, October). Allosteric post-translational modification codes. Retrieved from https://www.khoury.northeastern.edu/home/radivojac/papers/nussinov_trendsbiochemsci_2012.pdf
  31. Osakwe, O. (2016). The significance of discovery screening and structure optimization studies. In Elsevier eBooks (pp. 109–128). https://doi.org/10.1016/B978-0-12-802220-7.00005-3
  32. Osorno, R. D., Osorno, I. M. G., & Ferrater-Gimena, J. A. O. (2024). Development of a nutritious mocktail using “Aratiles” (Muntingia calabura Linn.) as a modifier and natural sweetener. American Journal of Multidisciplinary Research & Development, 6(12), 54–62. https://www.ajmrd.com/wp-content/uploads/2024/12/D6125462.pdf
  33. Pan, D., Gong, X., Wang, X., & Li, M. (2021). Role of active components of medicinal food in the regulation of angiogenesis. Frontiers in Pharmacology, 11, Article 594050. https://doi.org/10.3389/fphar.2020.594050
  34. Pandey, P., Lakhanpal, S., Mahmood, D., Kang, H. N., Kim, B., Kang, S., Choi, J., Choi, M., Pandey, S., Bhat, M., Sharma, S., Khan, F., Park, M. N., & Kim, B. (2025). An updated review summarizing the anticancer potential of flavonoids via targeting NF-κB pathway. Frontiers in Pharmacology, 15, Article 1513422. https://doi.org/10.3389/fphar.2024.1513422
  35. Patil, R., Das, S., Stanley, A., Yadav, L., Sudhakar, A., & Varma, A. K. (2010). Optimized hydrophobic interactions and hydrogen bonding at the target–ligand interface lead the pathways of drug design. PLoS ONE, 5(8), e12029. https://doi.org/10.1371/journal.pone.0012029
  36. Pillai, O., Dhanikula, A. B., & Panchagnula, R. (2001). Drug delivery: An odyssey of 100 years. Current Opinion in Chemical Biology, 5(4), 439–446. https://doi.org/10.1016/S1367-5931(00)00226-X
  37. Pratiwi, E. D., & Dewi, N. P. (2022). Screening of phytochemical secondary metabolites of Muntingia calabura: A potential as hepatoprotector. Journal of Fundamental and Applied Pharmaceutical Science, 2(2), 59–65. https://journal.umy.ac.id/index.php/jfap/article/view/12364
  38. Protein Data Bank. (1971). RCSB PDB: Homepage. https://www.rcsb.org/
  39. ProTox-3.0 – Prediction of TONicity of chemicals. (2004). https://tox.charite.de/protox3/
  40. PubChem. (2015). National Center for Biotechnology Information. https://pubchem.ncbi.nlm.nih.gov/
  41. PyRx – Python Prescription – Virtual Screening Tool. (n.d.). https://pyrx.sourceforge.io/
  42. Rad, E. (2015). Identification of biomarkers for development of NF1-associated malignant peripheral nerve sheath tumours (Doctoral dissertation, Cardiff University). Retrieved from https://core.ac.uk/download/444023529.pdf
  43. Raval, N., Maheshwari, R., Kalyane, D., Youngren-Ortiz, S. R., Chougule, M. B., & Tekade, R. K. (2019). Importance of physicochemical characterization of nanoparticles in pharmaceutical product development. In Elsevier eBooks (pp. 369–400). https://doi.org/10.1016/B978-0-12-817909-3.00010-8
  44. Riganti, C., & Contino, M. (2019). New strategies to overcome resistance to chemotherapy and immune system in cancer. International Journal of Molecular Sciences, 20(19), Article 4783. https://doi.org/10.3390/ijms20194783
  45. Roney, M., & Aluwi, M. F. F. M. (2024). The importance of in-silico studies in drug discovery. Intelligent Pharmacy. https://doi.org/10.1016/j.ipha.2024.01.010
  46. Sangande, F., Julianti, E., & Tjahjono, D. H. (2020). Ligand-based pharmacophore modeling, molecular docking, and molecular dynamic studies of dual tyrosine kinase inhibitor of EGFR and VEGFR2. International Journal of Molecular Sciences, 21(20), Article 7779. https://doi.org/10.3390/ijms21207779
  47. Saud, B., Geetha, K. M., Dubey, S., Singh, P. K., Shrivastava, S., Singh, D., & Tiwari, P. (2023). Traditional, current and prospective therapeutic uses of Muntingia calabura: A comprehensive literature review. Research Journal of Medicinal Plants. https://doi.org/10.3923/rjmp.2023.09.22
  48. Shana, E. (2023). Protein-ligand interactions: Its biological process and molecular choreography for drug development to cell signaling. Enzyme Engineering, 12(3). https://doi.org/10.35248/2329-6674.12.223
  49. Shaker, B., Ahmad, S., Lee, J., Jung, C., & Na, D. (2021). In silico methods and tools for drug discovery. Computers in Biology and Medicine, 137, Article 104851. https://doi.org/10.1016/j.compbiomed.2021.104851
  50. Stuart, G., & Santiago, A. (1998). Aratiles (Muntingia calabura Linn) / Cherry tree: Philippine medicinal herbs / Philippine alternative medicine. Retrieved from https://www.stuartxchange.org/Aratiles
  51. Subbaraj, G. K., Kumar, Y. S., & Kulanthaivel, L. (2021). Antiangiogenic role of natural flavonoids and their molecular mechanism: An update. The Egyptian Journal of Internal Medicine, 33(1). https://doi.org/10.1186/s43162-021-00056-x
  52. SwissADME. (2017). http://www.swissadme.ch/
  53. Tang, Y., Zhu, W., Chen, K., & Jiang, H. (2006). New technologies in computer-aided drug design: Toward target identification and new chemical entity discovery. Drug Discovery Today: Technologies, 3(3), 307–313. https://doi.org/10.1016/j.ddtec.2006.09.004
  54. Uribe, M. L., Marrocco, I., & Yarden, Y. (2021). EGFR in cancer: signaling mechanisms, drugs, and acquired resistance. Cancers, 13(11), Article 2748. https://doi.org/10.3390/cancers13112748
  55. Tinrat, S., & Jiraprasertwong, O. (2023). An assessment of in vitro antibacterial, anti-biofilm, anti-diabetic and antioxidant activities of bioactive compounds from Muntingia calabura Linn. leaves extracts. Pharmaceutical Sciences Asia, 50(4), 337–346. https://doi.org/10.29090/psa.2023.04.23.922
  56. Volate, S. R., Davenport, D. M., Muga, S. J., & Wargovich, M. J. (2005). Modulation of aberrant crypt foci and apoptosis by dietary herbal supplements (quercetin, curcumin, silymarin, ginseng, and rutin). Carcinogenesis, 26(8), 1450–1456.
  57. Wang, J., Xiang, H., Lu, Y., & Wu, T. (2021). Role and clinical significance of TGF-β1 and TGF-βR1 in malignant tumors (Review). International Journal of Molecular Medicine, 47(4). https://doi.org/10.3892/ijmm.2021.4888
  58. Wenthur, C. J., Gentry, P. R., Mathews, T. P., & Lindsley, C. W. (2011). Drugs for allosteric sites on receptors. Annual Review of Pharmacology and Toxicology, 54(1), 165–184. https://doi.org/10.1146/annurev-pharmtox-010611-134525
  59. Weroha, S. J., & Haluska, P. (2012). The insulin-like growth factor system in cancer. Endocrinology and Metabolism Clinics of North America, 41(2), 335–350. https://doi.org/10.1016/j.ecl.2012.04.014
  60. Wei, Q., & Zhang, Y. (2024). Flavonoids with anti-angiogenesis function in cancer. Molecules, 29(7), Article 1570. https://doi.org/10.3390/molecules29071570
  61. Wong, C. H., Sia, K. W., & Lo, A. W. (2018). Estimation of clinical trial success rates and related parameters. Biostatistics, 20(2), 273–286. https://doi.org/10.1093/biostatistics/kxx069
  62. Zakaria, Z. A., Mohamed, A. M., Jamil, N. S., Rofiee, M., Fatimah, C. A., Mat Jais, A., Sulaiman, M. R., & Somchit, M. N. (2008). In vitro anticancer activity of various extracts of the Malaysian, available but neglected, plants (Muntingia calabura and Dicranopteris linearis) against MCF-7 and HT-29 cancer cell lines. E-Pharmanexus, 1, 10–17. https://www.researchgate.net/publication/308335188_In_vitro_anticancer_activity_of_various_extracts_of_the_Malaysian_available_but_neglected_plants_Muntingia_Calabura_And_Dicranopteris_Linearis_against_Mcf-7_And_Ht-29_cancer_cell_lines/citation/download
  63. Zhang, R., Yao, Y., Gao, H., & Hu, X. (2024). Mechanisms of angiogenesis in tumors. Frontiers in Oncology, 14, Article 135906. https://doi.org/10.3389/fonc.2024.135906

 


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