DIPEPTIDYL-PEPTIDASE-4 INHIBITORS FROM TINOSPORA CRISPA AS REVEALED BY METABOLOMICS STUDY, MOLECULAR DOCKING AND MOLECULAR DYNAMICS SIMULATION APPROACHES

Yıl 2025, Cilt: 49 Sayı: 3, 615 - 630, 19.09.2025

Andri Prasetiyo , Shirly Kumala , Esti Mumpuni , Raymond R. Tjandrawinata , Nancy Dewi Yuliana

https://doi.org/10.33483/jfpau.1526137

Öz

Objective: This study aims to identify potential compounds as inhibitors of DPP-4 from Tinospora crispa.
Material and Method: Tinospora crispa stem powder was extracted by ultrasonication. The DPP-4 inhibition test used the MAK 203 screening kit protocol. LC-MS/MS was used to determine the chemical profile. MetaboAnalyst5 and SIMCA were used to analyze the dataset. Molecular docking was performed using Molegro virtual docker, and molecular dynamics simulations were performed using YASARA dynamics employing the AMBER14 force field.
Result and Discussion: The percentage inhibition of DPP-4 results showed that the most active was 96% ethanol extract. Orthogonal projection to latent structure (OPLS) analysis provides that 6'-O-LactoylBorapetoside B correlates most with DPP-4 inhibitory activity based on VIP value and Y coefficient. In the docking molecular analysis, 6’-O-LactoylBorapetoside B was predicted to be active as DPP-4 inhibitors with a lower rerank score (−106.51 Kcal/Mol) than alogliptin as a reference (−96.02 Kcal/mol). In molecular dynamics simulation for 100 ns, 6’-O-LactoylBorapetoside B complex of binding with DPP-4 protein was stable with the movement of the RMSD value below 3Å. 6'-O-Lactoyl Borapetoside B has a potential of being a DPP-4-inhibitor. But these results must be tested in vitro and in vivo in order to confirm its activity as a DPP-4 inhibitor.

Anahtar Kelimeler

6’-O-LactoylBorapetoside B , computer-assisted drug discovery , DPP-4 , Tinospora crispa

Teşekkür

The author would like to thank Prof. Dr. Siswandono, Apt, Department of Pharmaceuticals Chemistry, Airlangga University, for permission and support in software facilities Molegro virtual docker.

METABOLOMİ ÇALIŞMALARI, MOLEKÜLER DOKUNMA VE MOLEKÜLER DİNAMİK SİMÜLASYON YAKLAŞIMLARIYLA ORTAYA ÇIKAN TİNOSPORA CRİSPA'DAN DİPEPTİDİL-PEPTİDAZ-4 İNHİBİTÖRLERİ

Öz

Amaç: Bu çalışmanın amacı, Tinospora Crispa'dan DPP 4'ün inhibitörleri olarak potansiyel bileşikleri tanımlamaktır.
Gereç ve Yöntem: Tinospora crispa sapının tozu ultrasonikasyonla ekstrakte edildi. DPP-4 inhibisyon testinde MAK 203 tarama kiti protokolü kullanıldı. Kimyasal profilin belirlenmesinde LC-MS/MS kullanıldı. Veri setinin analizinde MetaboAnalyst5 ve SIMCA kullanıldı. AMBER14 kuvvet alanını kullanan YASARA dinamikleri kullanılarak moleküler dinamik simülasyonları yapıldı.
Sonuç ve Tartışma: DPP-4'ün yüzde inhibisyonu sonuçları en aktif olanın %96 etanol ekstraktı olduğunu gösterdi. Latent yapıya dik projeksiyon (OPLS) analizi, 6'-O-LactoylBorapetoside B'nin, VIP değeri ve Y katsayısına dayalı olarak DPP-4 inhibitör aktivitesi ile en fazla korele olduğunu sağlar. Yerleştirme moleküler analizinde, 6'-O-LactoylBorapetoside B'nin, referans olarak alogliptin'den (−96.02 Kcal/mol) daha düşük bir yeniden sıralama skoru (−106.51 Kcal/Mol) ile DPP-4 inhibitörleri olarak aktif olduğu tahmin edildi. 100 ns'lik moleküler dinamik simülasyonunda, 6'-O-LactoylBorapetoside B kompleksinin DPP-4 proteini ile bağlanma kompleksi, RMSD değerinin 3Å'un altındaki hareketi ile stabildi. 6'-O-Lactoyl Borapetoside B, bir DPP-4 inhibitörü olma potansiyeline sahiptir. Ancak bu sonuçların, bir DPP-4 inhibitörü olarak aktivitesini doğrulamak için in vitro ve in vivo olarak test edilmesi gerekir.

Anahtar Kelimeler

6 , bilgisayar destekli ilaç keşf , DPP-4 , Tinospora crispa

Kaynakça

• 1. International Diabetes Federation. (2021). International Diabetes Federation. In E.J. Boyko, D.J. Magliano, S. Karuranga, L. Piemonte, P. Riley, P. Saeedi and S. Hong (Eds.), IDF Diabetes Atlas, 10th edition. Ireland: Elsevier. [CrossRef]
• 2. Chaudhury, A., Duvoor, C., Reddy Dendi, V.S., Kraleti, S., Chada, A., Ravilla, R., Marco, A., Shekhawat, N.S., Montales, M.T., Kuriakose, K., Sasapu, A., Beebe, A., Patil, N., Musham, C.K., Lohani, G.P., Mirza, W. (2017). Clinical review of antidiabetic drugs: implications for type 2 diabetes mellitus management. Frontiers in Endocrinology, 8(6), 1-12. [CrossRef]
• 3. Nauck, M.A., Meier, J.J. (2018). Incretin hormones: Their role in health and disease. Diabetes, Obesity and Metabolism, 20, 5-21. [CrossRef]
• 4. Nauck, M. (2016). Incretin therapies: Highlighting common features and differences in the modes of action of glucagon-like peptide-1 receptor agonists and dipeptidyl peptidase-4 inhibitors. Diabetes, Obesity and Metabolism, 18(3), 203-216. [CrossRef]
• 5. Omar, B., Ahrén, B. (2014). Pleiotropic mechanisms for the glucose-lowering action of DPP-4 inhibitors. Diabetes, 63(7), 2196-2202. [CrossRef]
• 6. Muhammed, M.T., Aksoy, N., Kirilmaz, A., Türkmen, E. (2024). Towards understanding natural alpha-glucosidase inhibitors: A computational study. Journal of Faculty of Pharmacy of Ankara University, 48(1), 205-14. [CrossRef]
• 7. Gooßen, K., Gräber, S. (2012). Longer term safety of dipeptidyl peptidase-4 inhibitors in patients with type 2 diabetes mellitus: systematic review and meta-analysis. Diabetes, Obesity and Metabolism, 14(12), 1061-1072. [CrossRef]
• 8. Karagiannis, T., Paschos, P., Paletas, K., Matthews, D.R., Tsapas, A. (2012). Dipeptidyl peptidase-4 inhibitors for treatment of type 2 diabetes mellitus in the clinical setting: Systematic review and meta-analysis. BMJ (Online), 344, 1-15. [CrossRef]
• 9. Deacon, C.F. (2018). A review of dipeptidyl peptidase-4 inhibitors. Hot topics from randomized controlled trials. Diabetes, Obesity and Metabolism, 20, 34-46. [CrossRef]
• 10. Buse, J.B., Wexler, D.J., Tsapas, A., Rossing, P., Mingrone, G., Mathieu, C., D’alessio, D.A., Davies, M.J. (2020). 2019 Update to: Management of hyperglycemia in type 2 diabetes, 2018. A consensus report by the American Diabetes Association (ADA) and the European Association for the Study of Diabetes (EASD). Diabetes Care, 43(7), 1-7. [CrossRef]
• 11. McGuire, H., Longson, D., Adler, A., Farmer, A., Lewin, I. (2016). Management of type 2 diabetes in adults: Summary of updated NICE guidance. BMJ (Online), 353, 1-3. [CrossRef]
• 12. Geng, J., Yu, H., Mao, Y., Zhang, P., Chen, Y. (2015). Cost effectiveness of Dipeptidyl Peptidase-4 Inhibitors for type 2 diabetes. PharmacoEconomics, 33(6), 581-597. [CrossRef]
• 13. Thomas, A., Rajesh, E.K., Kumar, D.S. (2016). The significance of Tinospora crispa in treatment of diabetes mellitus. Phytotherapy Research, 30(3), 357-366. [CrossRef]
• 14. Ahmad, W., Jantan, I., Bukhari, S.N.A. (2016). Tinospora crispa (L.) Hook. F. & Thomson: A review of its ethnobotanical, phytochemical, and pharmacological aspects. Frontiers in Pharmacology, 7, 1-19. [CrossRef]
• 15. Riyanti, S., Suganda, A.G., Sukandar, E.Y. (2016). Dipeptidyl peptidase-IV inhibitory activity of some Indonesian medicinal plants. Asian Journal of Pharmaceutical and Clinical Research, 9(2), 375-377.
• 16. Chi, S., She, G., Han, D., Wang, W., Liu, Z., Liu, B. (2016). Genus tinospora: Ethnopharmacology, phytochemistry, and pharmacology. Evidence-Based Complementary and Alternative Medicine, 2016 (1). [CrossRef]
• 17. Lam, S., Ruan, C., Hsieh, P., Su, M., Lee, S. (2012). Hypoglycemic diterpenoids from Tinospora crispa. Journal of Natural Products, 75(2), 153-159. [CrossRef]
• 18. Xu, L.L., Guo, F.X., Chi, S.S., Wang, Z.J., Jiang, Y.Y., Liu, B., Zhang, J.Y. (2017). Rapid screening and identification of diterpenoids in Tinospora sinensis based on high-performance liquid chromatography coupled with linear ion trap-orbitrap mass spectrometry. Molecules, 22(6), 1-17. [CrossRef]
• 19. Avogaro, A., Dardano, A., de Kreutzenberg, S.V., Del Prato, S. (2015). Dipeptidyl peptidase-4 inhibitors can minimize the hypoglycaemic burden and enhance safety in elderly people with diabetes. Diabetes, Obesity and Metabolism, 17(2), 107-115. [CrossRef]
• 20. Chambers, M.C., MacLean, B., Burke, R. Amodei D, Ruderman D.L., Neumann, S., Gatto, L., Fischer, B., Pratt, B., Egertson, J., Hoff, K., Kessner, D., Tasman, N., Shulman, N., Frewen, B., Baker, T.A., Brusniak, M.Y., Paulse, C., Creasy, D., Flashner, L., Kani, K., Moulding, C., Seymour, S.L., Nuwaysir, L.M., Lefebvre, B., Kuhlmann, F., Roark, J., Rainer, P., Detlev, S., Hemenway, T., Huhmer, A., Langridge, J., Connolly, B., Chadick, T., Holly, K., Eckels, J., Deutsch, E.W., Moritz, R.L., Katz, J.E., Agus, D.B., MacCoss, M., Tabb, D.L., Mallick, P. (2012). A Cross-platform toolkit for mass spectrometry and proteomicszwane’s mining charter lunacy. Nature Biotechnology, 30(10), 1. [CrossRef]
• 21. Pang, Z., Chong, J., Zhou, G., De Lima Morais, D.A., Chang, L., Barrette, M., Gauthier, C., Jacques, P.É., Li, S., Xia, J. (2021). MetaboAnalyst 5.0: Narrowing the gap between raw spectra and functional insights. Nucleic Acids Research, 49(W1), W388-W396. [CrossRef]
• 22. Mihaleva,V.V., Vorst, O., Maliepaard, C., Verhoeven, H.A., de Vos, R.C.H., Hall, R.D., van Ham, R.C.H.J. (2008). Accurate mass error correction in liquid chromatography time-of-flight mass spectrometry based metabolomics. Metabolomics, 4, 171-82. [CrossRef]
• 23. Mahadevan, S., Shah, S.L., Marrie, T.J., Slupsky, C.M. (2008). Analysis of metabolomic data using support vector machines. Analytical Chemistry, 80(19), 7562-7570. [CrossRef]
• 24. Zhang, Z., Wallace, M.B., Feng, J., Stafford, J.A., Skene, R.J., Shi, L., Lee, B., Aertgeerts, K., Jennings, A., Xu, R., Kassel, D.B., Kaldor, S.W., Navre, M., Webb, D.R., Gwaltney, S.L. (2011). Design and synthesis of pyrimidinone and pyrimidinedione inhibitors of dipeptidyl peptidase IV. Journal of Medicinal Chemistry, 54(2), 510-524. [CrossRef]
• 25. RSCB Website. (2021). From https://www.rcsb.org/. Accessed date: 13.07.2021.
• 26. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Wessig, H., Shindyalov, I.N., Bourne, P.E. (2000). The protein data bank. Nucleic Acid Research, 28, 235-242. [CrossRef]
• 27. Prasetiyo, A., Kumala, S., Mumpuni, E., Tjandrawinata, R.R. (2022). Validation of structural-based virtual screening protocols with the PDB Code 3G0B and prediction of the activity of Tinospora crispa compounds as inhibitors of dipeptidyl-peptidase-IV. Research Results in Pharmacology, 8(1), 95-102. [CrossRef]
• 28. Krieger, E., Vriend, G. (2015). New ways to boost molecular dynamics simulations. Journal of Computational Chemistry, 36(13), 996-1007. [CrossRef]
• 29. Krieger, E., Ozvoldik, K. (2003). Yasara Biosciences. From http://www.yasara.org/md run. mcr. Accessed date: 13.07.2021.
• 30. Mahmud, S., Biswas, S., Paul, G.K., Mita, M.A., Afrose, S., Hasan, Md. R., Shimu, Mst. S.S., Uddin, M.A.R., Uddin, Md. S., Zaman, S., Kibria, K.M.K., Khan, Md. A., Bin Emran, T., Saleh, Md. A. (2021). Antiviral peptides against the main protease of SARS-CoV-2: A molecular docking and dynamics study. Arabian Journal of Chemistry, 14(9), 103315.
• 31. Lokman, F.E., Gu, H.F., Wan Mohamud, W.N., Yusoff, M.M., Chia, K.L., Östenson, C.G. (2013). Antidiabetic effect of oral borapetol B compound, isolated from the plant Tinospora crispa, by stimulating insulin release. Evidence-Based Complementary and Alternative Medicine, 2013, Article ID 727602. [CrossRef]
• 32. Ruan, C.T., Lam, S.H., Chi, T.C., Lee, S.S., Su, M.J. (2012). Borapetoside C from Tinospora crispa improves insulin sensitivity in diabetic mice. Phytomedicine, 19(8–9), 719–724. [CrossRef]
• 33. Xu, Y., Niu, Y., Gao, Y., Wang, F., Qin, W., Lu, Y., Hu, J., Peng, L., Liu, J., Xiong, W. (2017). Borapetoside E, a clerodane diterpenoid extracted from Tinospora crispa, improves hyperglycemia and Hyperlipidemia in high-fat-diet-induced type 2 diabetes mice. Journal of Natural Products, 80(8), 2319-2327. [CrossRef]
• 34. Ruan, C., Lam, S., Lee, S., Su, M. (2013). Hypoglycemic action of borapetoside A from the plant Tinospora crispa in mice. International Journal of Phytotherapy and Phytopharmacology, 20(8-9), 667-675. [CrossRef]
• 35. METLIN Website. (2021). From https://metlin.scripps.edu. Accessed date: 10.09.2021.
• 36. Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., Li, Q., Shoemaker, B.A., Thessen, P.A., Yu, B., Zaslavsky, L., Zhang, J., Bolton, E. E. (2021). PubChem in 2021: New data content and improved web interfaces. Nucleic Acids Research. 49(D1), D1388-D1395. [CrossRef]
• 37. Triba, M.N., Le Moyec, L., Amathieu, R., Goossens, C., Bouchemal, N., Nahon, P., Rutledge, D.N., Savarin, P. (2015). PLS/OPLS models in metabolomics: The impact of permutation of dataset rows on the K-fold cross-validation quality parameters. Molecular BioSystems, 11(1), 13-19. [CrossRef]
• 38. Yang, Y., Wu, Z., Li, S., Yang, M., Xiao, X., Lian, C., Wen, W., He, H., Zeng, J., Wang, J., Zhang, G. (2020). Targeted blood metabolomic study on retinopathy of prematurity. Investigative Ophthalmology and Visual Science, 61(2), 12. [CrossRef]
• 39. Chong, I.G., Jun, C.H. (2005). Performance of some variable selection methods when multicollinearity is present. Chemometrics and Intelligent Laboratory Systems, 78(1), 103-112. [CrossRef]
• 40. Dhananjayan, K. (2015). Molecular docking study characterization of rare flavonoids at the nac-binding site of the first bromodomain of BRD4 (BRD4 BD1). Journal of Cancer Research, 2015, 1-15. [CrossRef]
• 41. Nabeno, M., Akahoshi, F., Kishida, H., Miyaguchi, I., Tanaka, Y., Ishii, S., Kadowaki, T. (2013). A comparative study of the binding modes of recently launched dipeptidyl peptidase IV inhibitors in the active site. Biochemical and Biophysical Research Communications, 434(2), 191-196. [CrossRef]
• 42. Li, D., Zhang, Y., Zhao, R. N., Fan, S., Han, J.G. (2014). Investigation on the mechanism for the binding and drug resistance of wild type and mutations of G86 residue in HIV-1 protease complexed with Darunavir by molecular dynamic simulation and free energy calculation. Journal of Molecular Modeling, 20, 2122. [CrossRef]
• 43. Biswas, P., Dey, D., Rahman, A., Islam, M.A., Susmi, T.F., Kaium, M.A., Hasan, M.N., Rahman, M.H., Mahmud, S., Saleh, M.A., Paul, P., Rahman, M.R., Al Saber, M., Song, H., Rahman, M.A., Kim, B. (2021). Analysis of SYK gene as a prognostic biomarker and suggested potential bioactive phytochemicals as an alternative therapeutic option for colorectal cancer: An in-silico pharmaco-informatics investigation. Journal of Personalized Medicine, 11, 888. [CrossRef]