Virtual screening of Dioscorea alata active compound in the Sphingolipid metabolic pathway in endometriosis-related genes

Sri Nabawiyati Nurul Makiyah, Ivanna Beru Brahmana, Mulyoto Pangestu, Ahmad Hafidul Ahkam
In: Research Journal of Pharmacy and Technology · 2025 · pp. 1386–1393 · doi:10.52711/0974-360x.2025.00200 · W4409336925
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This study identified SGPP2 as an endometriosis-related gene and found that Dioscorea alata metabolites, diosgenin and prosapogenin, exhibit high binding affinity for it.

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The paper used endometriosis sample differentially expressed genes (DEGs) to identify endometriosis-related targets, then performed virtual screening of Dioscorea alata secondary metabolites for their ability to interact with genes in the sphingolipid metabolic pathway. It reports that SGPP2 is an endometriosis-related gene involved in sphingolipid metabolism and that diosgenin and prosapogenin showed high binding affinity with potential interactions affecting SGPP2 activity. The authors explicitly note a limitation of relying on in silico findings and recommend further research to validate SGPP2 as a marker and evaluate dioscorea metabolites as potential SGPP2 agonists or inhibitors. This paper is centrally about endometriosis — it uses endometriosis DEGs to nominate SGPP2 and models Dioscorea alata metabolites as potential modulators of that endometriosis-related target.

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Abstract

Endometriosis is a medical condition characterized by the growth of endometrial tissue outside the uterus, causing symptoms of pain and reproductive disorders in women. Expensive medical treatments open opportunities to explore herbal therapies with the potential for higher efficacy, lower side effects, and more affordable costs. Dioscorea alata is a food and herbal plant that has been used in several places. Therefore, this research aimed to evaluate the Dioscorea alata secondary metabolite potential for affecting endometriosis-related genes. The method used was to evaluate the differentially expressed genes (DEGs) from endometriosis samples, and then evaluate the potential of secondary metabolites of Dioscorea alata in influencing DEGs related to endometriosis. As a result, SGPP2 is known to be an endometriosis-related gene that plays a role in sphingolipid metabolism. Secondary metabolites of Dioscorea alata, namely diosgenin and prosapogenin, have high binding affinity and have the potential to interact with SGPP2. In conclusion, secondary metabolites of Dioscorea alata have a high potential to interact with SGPP2 and potentially influence its activity, which is an endometriosis-related gene. However, we recommend further research regarding SGPP2 as a marker for endometriosis and the potential of secondary metabolites of Dioscorea alata as SGPP2 agonists or inhibitors.
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Abstract

Endometriosis is a medical condition characterized by the growth of endometrial tissue outside the uterus, causing symptoms of pain and reproductive disorders in women. Expensive medical treatments open opportunities to explore herbal therapies with the potential for higher efficacy, lower side effects, and more affordable costs. Dioscorea alata is a food and herbal plant that has been used in several places. Therefore, this research aimed to evaluate the Dioscorea alata secondary metabolite potential for affecting endometriosis-related genes. The method used was to evaluate the differentially expressed genes (DEGs) from endometriosis samples, and then evaluate the potential of secondary metabolites of Dioscorea alata in influencing DEGs related to endometriosis. As a result, SGPP2 is known to be an endometriosis-related gene that plays a role in sphingolipid metabolism. Secondary metabolites of Dioscorea alata, namely diosgenin and prosapogenin, have high binding affinity and have the potential to interact with SGPP2. In conclusion, secondary metabolites of Dioscorea alata have a high potential to interact with SGPP2 and potentially influence its activity, which is an endometriosis-related gene. However, we recommend further research regarding SGPP2 as a marker for endometriosis and the potential of secondary metabolites of Dioscorea alata as SGPP2 agonists or inhibitors. Cite this article: Sri Nabawiyati Nurul Makiyah, Ivanna Beru Brahmana, Mulyoto Pangestu, Ahmad Hafidul Ahkam. Virtual screening of Dioscorea alata active compound in the Sphingolipid metabolic pathway in endometriosis-related genes. Research Journal of Pharmacy and Technology. 2025;18(3):1386-3. doi: 10.52711/0974-360X.2025.00200 Cite(Electronic): Sri Nabawiyati Nurul Makiyah, Ivanna Beru Brahmana, Mulyoto Pangestu, Ahmad Hafidul Ahkam. Virtual screening of Dioscorea alata active compound in the Sphingolipid metabolic pathway in endometriosis-related genes. Research Journal of Pharmacy and Technology. 2025;18(3):1386-3. doi: 10.52711/0974-360X.2025.00200 Available on: https://www.rjptonline.org/AbstractView.aspx?PID=2025-18-3-61

References

1. Wolfman W, Leyland N, Heywood M, Singh SS, Rittenberg DA, Soucy R, et al. Asymptomatic endometrial thickening. J Obstet Gynaecol Can. 2010; 32(10): 990–9. doi: 10.1016/s1701-2163(16)34690-4. 2. Gaia‑Oltean AI, Braicu C, Gulei D, Ciortea R, Mihu D, Roman H, et al. Ovarian endometriosis, a precursor of ovarian cancer: Histological aspects, gene expression and microRNA alterations (Review). Experimental and Therapeutic Medicine. 2021; 21(3): 1–1. doi: 10.3892/etm.2021.9674 3. Bedaiwy MA, Alfaraj S, Yong P, Casper R. New developments in the medical treatment of endometriosis. Fertility and Sterility. 2017; 107(3): 555–65. doi: 10.1016/j.fertnstert.2016.12.025. 4. Coxon L, Horne AW, Vincent K. Pathophysiology of endometriosis-associated pain: A review of pelvic and central nervous system mechanisms. Best Practice and Research Clinical Obstetrics and Gynaecology. 2018; 51: 53–67. doi: 10.1016/j.bpobgyn.2018.01.014. 5. Ulyarti, Nazarudin, Lisani. Optimization of Anthocyanin Content in Uwi Flour (Dioscorea alata) Using Response Surface Methodology. Indonesian Food Science and Technology Journal. 2018; 1(2): 61–4. https://doi.org/10.22437/ifstj.v1i2.6006 6. Kumar S, Das G, Shin HS, Patra JK. Dioscorea spp. (A Wild Edible Tuber): A Study on Its Ethnopharmacological Potential and Traditional Use by the Local People of Similipal Biosphere Reserve, India. Front Pharmacol. 2017; 8: 52. doi: 10.3389/fphar.2017.00052 7. Makiyah SNN, Djati MS, Rifa’i M, Widodo. Lymphocyte Proliferation on Hypersensitivity of BALB/c Mice after Given Ethanol Extract Tuber of Dioscorea alata L. KnE Life Sciences. 2015; Sep 20; 107–11. DOI: 10.18502/kls.v2i1.125 8. Lavlinesia, Ulyarti, Yulia A, Pransisca I, Purnawati Z. Comparative Analysis of Flour Properties of Dioscorea alata Tuber And Its Utilization On Wet Noodle. Indonesian Food Science and Technology Journal. 2018; 1(2): 70–5. https://doi.org/10.22437/ifstj.v1i2.5342 9. Makiyah SNN, Christina YI, Ahkam AH. Dioscorea alata Extract as Anti-Cancer Agent by Regulating Genetic Mutations, Apoptosis, and Cell Proliferation: In Vitro and in Silico Studies. JSM. 2023; 52(9): 2657–71. http://doi.org/10.17576/jsm-2023-5209-15 10. Makiyah SNN, Djati MS. Potency of Purple Yam (Dioscorea alata L) as an Immunomodulatory Agent. J Berk Ked. 2018; Feb 24; 14(1): 89. http://dx.doi.org/10.20527/jbk.v14i1.4589 11. Kaur B, Khatun S, Suttee A. Current Highlights on Biochemical and Pharmacological Profile of Dioscorea alata: A Review. Plant Archives. 2021; 21(Suppliment-1): 552–9. DOI:10.51470/PLANTARCHIVES.2021.V21.S1.085 12. Jose A, Nizar S, Mr V, M AK. Antioxidant Potential in Relation to Total Phenolics and Pigment Contents among The Selected Landraces of Dioscorea alata L. in Kerala, India. JEBAS. 2019; 7(4): 403–10. DOI: 10.18006/2019.7(4).403.410 13. Behl T, Kaur I, Sehgal A, Singh S, Bhatia S, Al-Harrasi A, et al. Bioinformatics Accelerates the Major Tetrad: A Real Boost for the Pharmaceutical Industry. International Journal of Molecular Sciences. 2021; 22(12): 6184. doi: 10.3390/ijms22126184 14. Chakraborty A, Mukherjee P, Chakraborty M, Singha D Kumar. An Updated Review on Bioinformatics and Pharmacogenomics in Drug Discovery and Development Process. Asian Journal of Pharmaceutical Research and Development. 2021; 9(3): 62–5. https://doi.org/10.22270/ajprd.v9i3.942 15. Hooda R. Bioinformatics As An Emerging Field of Data Science. International Journal of Scientific and Technology Research. 2019; 8(4): 375–377. https://www.ijstr.org/final-print/aug2019/Bioinformatics-As-An-Emerging-Field-Of-Data-Science.pdf 16. Natarajan PM. Dental Bioinformatics – Current Scope and Future Perspectives. Research Journal of Pharmacy and Technology. 2022; 15(5): 2351–6. DOI: 10.52711/0974-360X.2022.00391 17. Kumari PVK, Rao YS. Personalized Medicine-A Review. Rese Jour of Pharm and Technol. 2019; 12(8): 3989. DOI: 10.5958/0974-360X.2019.00687.5 18. Suganya J, Radha M, Hubert. Computational studies on Differential gene Expression in Malaria Microarray Dataset. Research Journal of Pharmacy and Technology. 2020; Mar 1; 13(3): 1368–76. DOI: 10.5958/0974-360X.2020.00252.8 19. Suganya J, Radha M, Manoharan S, V V, Francis A. Virtual Screening and Analysis of Bioactive Compounds of Momordica charantia against Diabetes using Computational Approaches. Research Journal of Pharmacy and Technology. 2017; Oct 30; 10(10): 3353–60. DOI: 10.5958/0974-360X.2017.00596.0 20. Heberle H, Meirelles GV, da Silva FR, Telles GP, Minghim R. InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams. BMC Bioinformatics. 2015; May 22; 16(1): 169. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0611-3 21. Wang J, Zhong J, Chen G, Li M, Wu F Xiang, Pan Y. ClusterViz: A Cytoscape APP for Cluster Analysis of Biological Network. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2015; Jul; 12(4): 815–22. DOI: 10.1109/TCBB.2014.2361348 22. Xue J min, Liu Y, Wan L hong, Zhu Y xi. Comprehensive Analysis of Differential Gene Expression to Identify Common Gene Signatures in Multiple Cancers. Med Sci Monit. 2020; Feb 8; 26: e919953-1- e919953-13. doi: 10.12659/MSM.919953 23. Makiyah SNN, Usman S, Dwijayanti DR. In Silico Toxicity Prediction of Bioactive Compounds of Dioscorea alata L. TJNPR. 2022; 6(10): 1587–96. http://www.doi.org/10.26538/tjnpr/v6i10.5 24. Makiyah S, Kita M, Setyawati I, Tasminatun S. Dioscorea alata L. Tubers Improve Diabetes through Anti- hyperglycemia, Anti-inflammation, Ameliorate Insulin Resistance and Mitochondrial Dysfunction. The Indonesian Biomedical Journal. 2022; Dec 1; 14: 365–75. https://doi.org/10.18585/inabj.v14i4.1966 25. O’Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR. Open Babel: An open chemical toolbox. Journal of Cheminformatics. 2011; 3(1): 33. https://jcheminf.biomedcentral.com/articles/10.1186/1758-2946-3-33 26. Dallakyan S, Olson AJ. Small-molecule library screening by docking with PyRx. Methods Mol Biol. 2015; 1263: 243–50. https://doi.org/10.1007/978-1-4939-2269-7_19 27. Wu Q, Peng Z, Zhang Y, Yang J. COACH-D: improved protein-ligand binding sites prediction with refined ligand-binding poses through molecular docking. Nucleic Acids Research. 2018; Jul 2; 46(W1): W438–42. doi: 10.1093/nar/gky439. 28. Li X, Wang X, Yu Q. Combined Proteomics and Transcriptomics Identifies Serpin Family C Member 1 Associated Protein as a Biomarker of Endometriosis [Internet]. Peking Union Medical College Hospital; 2023 [cited 2023 Dec 9]. Available from: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE232713 29. Chen J, He K, Wang K, Wang Z. A comprehensive analysis of the mechanism of FOS in the progression of endometrial cyst of ovary to endometriosis-associated ovarian cancer [Internet]. Changchun: The second hospital of Jilin University; 2023 [cited 2023 Dec 9]. Available from: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi 30. Yana A, Daniil N, Andrew G, Maria S, Maxim S, Anton B. Gene expression signature of endometrial samples from women with and without endometriosis. [Internet]. Moscow: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry; 2019 [cited 2023 Dec 9]. Available from: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi 31. Bredeson JV, Lyons JB, Oniyinde IO, Okereke NR, Kolade O, Nnabue I, et al. Chromosome evolution and the genetic basis of agronomically important traits in greater yam. Nat Commun. 2022; Apr 14; 13(1): 2001. doi: 10.1038/s41467-022-29114-w. 32. Obidiegwu JE, Lyons JB, Chilaka CA. The Dioscorea Genus (Yam)—An Appraisal of Nutritional and Therapeutic Potentials. Foods. 2020; Sep; 9(9): 1304. doi: 10.3390/foods9091304 33. Liu SF, Chang SY, Lee TC, Chuang LY, Guh JY, Hung CY, et al. Dioscorea alata Attenuates Renal Interstitial Cellular Fibrosis by Regulating Smad- and Epithelial-Mesenchymal Transition Signaling Pathways. PLOS ONE. 2012; Nov 8; 7(11): e47482. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0047482 34. Chen T, Hu S, Zhang H, Guan Q, Yang Y, Wang X. Anti-inflammatory effects of Dioscorea alata L. anthocyanins in a TNBS-induced colitis model. Food Funct. 2017; Feb 23; 8(2): 659–69. DOI: 10.1039/c6fo01273f 35. Koninckx PR, Ussia A, Adamyan L, Wattiez A, Gomel V, Martin DC. Pathogenesis of endometriosis: the genetic/epigenetic theory. Fertility and Sterility. 2019; Feb 1; 111(2): 327–40. DOI: 10.1016/j.fertnstert.2018.10.013 36. Dinsdale N, Nepomnaschy P, Crespi B. The evolutionary biology of endometriosis. Evolution, Medicine, and Public Health. 2021; Jan 1;9(1): 174–91. DOI: 10.1093/emph/eoab008 37. Sancakli Usta C, Turan G, Bulbul CB, Usta A, Adali E. Differential expression of Oct-4, CD44, and E- cadherin in eutopic and ectopic endometrium in ovarian endometriomas and their correlations with clinicopathological variables. Reproductive Biology and Endocrinology. 2020; Nov 20;18(1): 116. https://rbej.biomedcentral.com/articles/10.1186/s12958-020-00673-1 38. Filby CE, Rombauts L, Montgomery GW, Giudice LC, Gargett CE. Cellular Origins of Endometriosis: Towards Novel Diagnostics and Therapeutics. Semin Reprod Med. 2020; May;38(02/03): 201–15. DOI: 10.1055/s-0040-1713429 39. Ferrero S, Remorgida V, Maganza C, Venturini PL, Salvatore S, Papaleo E, et al. Aromatase and endometriosis: estrogens play a role. Annals of the New York Academy of Sciences. 2014; 1317(1): 17–23. DOI: 10.1111/nyas.12411 40. Pluchino N, Poppi G, Yart L, Marci R, Wenger JM, Tille JC, et al. Effect of local aromatase inhibition in endometriosis using a new chick embryo chorioallantoic membrane model. Journal of Cellular and Molecular Medicine. 2019; 23(8): 5808–12. doi: 10.1111/jcmm.14372 41. Maceyka M, Spiegel S. Sphingolipid metabolites in inflammatory disease. Nature. 2014; Jun; 510(7503): 58–67. https://www.nature.com/articles/nature13475 42. Zhou N, Liu L, Zou R, Zou M, Zhang M, Cao F, et al. Circular Network of Coregulated Sphingolipids Dictates Chronic Hypoxia Damage in Patients with Tetralogy of Fallot. Frontiers in Cardiovascular Medicine [Internet]. 2022 [cited 2023 Dec 28];8. Available from: https://www.frontiersin.org/articles/10.3389/fcvm.2021.780123 43. Song C, Qiao Z, Chen L, Ge J, Zhang R, Yuan S, et al. Identification of Key Genes as Early Warning Signals of Acute Myocardial Infarction Based on Weighted Gene Correlation Network Analysis and Dynamic Network Biomarker Algorithm. Frontiers in Immunology [Internet]. 2022 [cited 2023 Dec 28];13. Available from: https://www.frontiersin.org/articles/10.3389/fimmu.2022.879657 44. Huang WC, Liang J, Nagahashi M, Avni D, Yamada A, Maceyka M, et al. Sphingosine-1-phosphate phosphatase 2 promotes disruption of mucosal integrity and contributes to ulcerative colitis in mice and humans. The FASEB Journal. 2016; 30(8): 2945–58. doi: 10.1096/fj.201600394R. 45. Barnawi J, Tran H, Jersmann H, Pitson S, Roscioli E, Hodge G, et al. Potential Link between the Sphingosine-1-Phosphate (S1P) System and Defective Alveolar Macrophage Phagocytic Function in Chronic Obstructive Pulmonary Disease (COPD). PLOS ONE. 2015; Oct 20;10(10): e0122771. doi: 10.1371/journal.pone.0122771. 46. Reardon BJ, Hansen JG, Crystal RG, Houston DK, Kritchevsky SB, Harris T, et al. Vitamin D-responsive SGPP2 variants associated with lung cell expression and lung function. BMC Medical Genetics. 2013; Nov 25;14(1): 122. https://bmcmedgenet.biomedcentral.com/articles/10.1186/1471-2350-14-122 47. Taguchi Y, Allende ML, Mizukami H, Cook EK, Gavrilova O, Tuymetova G, et al. Sphingosine-1- phosphate Phosphatase 2 Regulates Pancreatic Islet β-Cell Endoplasmic Reticulum Stress and Proliferation. Journal of Biological Chemistry. 2016; Jun 3;291(23): 12029–38. doi: 10.1074/jbc.M116.728170. 48. Proia RL, Hla T. Emerging biology of sphingosine-1-phosphate: its role in pathogenesis and therapy. J Clin Invest. 2015; Apr 1;125(4): 1379–87. doi: 10.1172/JCI76369. 49. Zhang Y, Kong X, Xin S, Bi L, Sun X. Discovery of Lipid Metabolism-Related Genes for Predicting Tumor Immune Microenvironment Status and Prognosis in Prostate Cancer. Journal of Oncology. 2022; Sep 5;2022: e8227806. doi: 10.1155/2022/8227806. Research Journal of Pharmacy and Technology (RJPT) is an international, peer-reviewed, multidisciplinary journal.... Read more >>> RNI: CHHENG00387/33/1/2008-TCDOI: 10.52711/0974-360X 1.3 2021CiteScore 56th percentile Powered by

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