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Submitted
September 11, 2021
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August 4, 2022
Published
December 30, 2022
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Abstract

Background: The community has known pasak bumi for generations to increase sexual desire in men (aphrodisiac). Besides, it can improve the performance of sports athletes and as an antistress, reduce tension, anger, and confusion.
Objective: This relatively large number of uses encourages researchers to want to do in silico screening of active compounds against antitumors by going through 2 stages, namely through online PASS and docking.
Method: Docking method to see the stability interaction of compounds with cyclin. In this test, Pyrx was used as a docking tool with various cell cycle-related targets, namely cyclin D3 (PDB ID: 3G33), cyclin A (PDB ID: IJSU), cyclin A (PDB ID, cyclin C (1ZP2), cyclin D (ID PDB: 2W9F), cyclin H (PDB ID: 1KXU), and cyclin T (PDB ID: 3BLR).
Results: The docking result showed that each cyclin showed the best interaction with these compounds: Cyclin A and 9-Methoxycanthin-6-one 3-N-oxide (-8.6 Kcal/mol), cyclin H and Niloticin (-8.0 Kcal/mol), cyclin D3 is 9-Methoxycanthin-6-one 3-N-oxide (-7.2 Kcal/mol), cyclin D is Eurycolactone F (-8.4 Kcal/mol), cyclin C is and Niloticin (-7.5 Kcal/mol), and cyclin T and Niloticin (-8.2 Kcal/mol).
Conclusion: Based on the docking score obtained, the stability of the interaction is predicted to occur in cyclin A and 9-Methoxycanthin-6-one 3-N-oxide (ΔG: -8.6 Kcal/mol).


Intisari


Latar belakang: Pasak bumi telah dikenal oleh masyarakat secara turun-temurun untuk meningkatkan gairah seksual pada pria (afrodisiaka). Disamping itu dapat meningkatkan performa atlet olahraga dan sebagai antistress, menurunkan tegangan, kemarahan, dan kebingungan.
Tujuan: Penggunaan yang relatif banyak ini mendorong peneliti berkeinginan melakukan skrining senyawa aktif terhadap antitumor secara in silico dengan melalui 2 tahap yaitu melalaui PASS online dan docking.
Metode: Metode docking dipakai untuk melihat interaksi stabilitas senyawa dengan cylin. Dalam pengujian ini, Pyrx digunakan sebagai alat docking dengan berbagai target yang berhubungan dengan siklus sel, yaitu cyclin D3 (PDB ID: 3G33), cyclin A (PDB ID: IJSU), cyclin C (PDB ID: 1ZP2), cyclin D (ID PDB: 2W9F), cyclin H (ID PDB: 1KXU), dan cyclin T (ID PDB: 3BLR).
Hasil: Hasil docking pada masing-masing cyclin menunjukkan interaksi terbaik dengan senyawa berikut ini: cyclin A dan 9-Methoxycanthin-6-one 3-N-oxide (-8,6 Kkal/mol), cyclin H dan Niloticin (-8,0 Kkal/mol), cyclin D3 dan 9-Methoxycanthin-6-one 3-N-oxide (-7,2 Kkal/mol), cyclin D dan Eurycolactone F (-8,4 Kkal/mol), cyclin C dan Niloticin (-7,5 Kkal/mol), serta cyclin T dan Niloticin (-8,2 Kkal/mol).
Kesimpulan: Berdasarkan skor docking yang diperoleh, kestabilan interaksi diprediksi akan terjadi pada cyclin A dengan 9-Methoxycanthin-6-one 3-N-oxide (ΔG: -8.6 Kkal/mol).

Keywords

Docking Eurycoma longifolia cyclin

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Author Biography

Samsul Hadi, universitas lambung mangkurat

biochemistry

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References

  1. Arwansyah, A., Ambarsari, L., & Sumaryada, T. I. (2014). Simulasi docking senyawa kurkumin dan analognya sebagai inhibitor reseptor androgen pada kanker prostat. Jurnal Dinamika, 5(2), 60–75.
  2. Baumli, S., Lolli, G., Lowe, E. D., Troiani, S., Rusconi, L., Bullock, A. N., Debreczeni, J. E., Knapp, S., & Johnson, L. N. (2008). The structure of P-TEFb (CDK9/cyclin T1), its complex with flavopiridol and regulation by phosphorylation. Embo j, 27(13), 1907-1918. https://doi.org/10.1038/emboj.2008.121
  3. ChemAxon. (2016). ChemAxon - Software Solutions and Services for Chemistry and Biology MarvinSketch, Version 16.10.31. https://chemaxon.com/
  4. Chen, C. K., Mohamad, W. M., Ooi, F. K., Ismail, S. B., Abdullah, M. R., & George, A. (2014). Supplementation of Eurycoma longifolia Jack extract for 6 weeks does not affect urinary testosterone: epitestosterone ratio, liver and renal functions in male recreational athletes. Int J Prev Med, 5(6), 728-733.
  5. Dallakyan, S., & Olson, A. J. (2015). Small-molecule library screening by docking with PyRx. Methods Mol Biol, 1263, 243-250. https://doi.org/10.1007/978-1-4939-2269-7_19
  6. Day, P. J., Cleasby, A., Tickle, I. J., O'Reilly, M., Coyle, J. E., Holding, F. P., McMenamin, R. L., Yon, J., Chopra, R., Lengauer, C., & Jhoti, H. (2009). Crystal structure of human CDK4 in complex with a D-type cyclin. Proc Natl Acad Sci U S A, 106(11), 4166-4170. https://doi.org/10.1073/pnas.0809645106
  7. Hamzah, S. H., & Yusof, A. (2003). The Ergogenic Effect of Eurycoma longifolia Jack: A Pilot Study
  8. Haneef, M., Lohani, M., Dhasmana, A., Jamal, Q. M., Shahid, S. M., & Firdaus, S. (2014). Molecular docking of known carcinogen 4- (Methyl-nitrosamino)-1-(3-pyridyl)-1-butanone (NNK) with cyclin dependent kinases towards its potential role in cell cycle perturbation. Bioinformation, 10(8), 526-532. https://doi.org/10.6026/97320630010526
  9. Hoeppner, S., Baumli, S., & Cramer, P. (2005). Structure of the mediator subunit cyclin C and its implications for CDK8 function. J Mol Biol, 350(5), 833-842. https://doi.org/10.1016/j.jmb.2005.05.041
  10. Issa, N. T., Badiavas, E. V., & Schürer, S. (2019). Research techniques made simple: molecular docking in dermatology - a foray into in silico drug discovery. Journal of Investigative Dermatology, 139(12), 2400-2408.e2401. https://doi.org/https://doi.org/10.1016/j.jid.2019.06.129
  11. Ivanov, S. M., Lagunin, A. A., Rudik, A. V., Filimonov, D. A., & Poroikov, V. V. (2018). ADVERPred-Web Service for prediction of adverse effects of drugs. J Chem Inf Model, 58(1), 8-11. https://doi.org/10.1021/acs.jcim.7b00568
  12. Jayaraman, A., & Jamil, K. (2014). Drug targets for cell cycle dysregulators in leukemogenesis: in silico docking studies. PLoS One, 9(1), e86310. https://doi.org/10.1371/journal.pone.0086310
  13. Jendele, L., Krivak, R., Skoda, P., Novotny, M., & Hoksza, D. (2019). PrankWeb: a web server for ligand binding site prediction and visualization. Nucleic Acids Res, 47(W1), W345-w349. https://doi.org/10.1093/nar/gkz424
  14. Kim, K. K., Chamberlin, H. M., Morgan, D. O., & Kim, S. H. (1996). Three-dimensional structure of human cyclin H, a positive regulator of the CDK-activating kinase. Nat Struct Biol, 3(10), 849-855. https://doi.org/10.1038/nsb1096-849
  15. Rekha, U. V., Anita, M., Jayamathi, G., Sadhana, K., Deepa, S., Hussain, S., Bhuvaneswari, J., Ramya, V., Selvaraj, J., & Naveenraj, N. S. (2020). Molecular docking analysis of piperine with CDK2,CDK4,Cyclin D and Cyclin T proteins. Bioinformation, 16(5), 359-362. https://doi.org/10.6026/97320630016359
  16. Russo, A. A., Jeffrey, P. D., Patten, A. K., Massagué, J., & Pavletich, N. P. (1996). Crystal structure of the p27Kip1 cyclin-dependent-kinase inhibitor bound to the cyclin A-Cdk2 complex. Nature, 382(6589), 325-331. https://doi.org/10.1038/382325a0
  17. Sutomo, S., & Pratama, M. R. F. (2020). Measuring the potential antioxidant activity of methyl gallate: Molecular docking study. Thai Journal of Pharmaceutical Sciences, 44(1), 14–22.
  18. Systèmes, D. (2020). Free Download: BIOVIA Discovery Studio Visualizer - Dassault Systèmes. https://discover.3ds.com/discovery-studio-visualizer-download#_ga=2.4935860.685747970.1587999055-a5d1c1c0-3176-11e9-a86f-e302515d21c8
  19. Takaki, T., Echalier, A., Brown, N. R., Hunt, T., Endicott, J. A., & Noble, M. E. (2009). The structure of CDK4/cyclin D3 has implications for models of CDK activation. Proc Natl Acad Sci U S A, 106(11), 4171-4176. https://doi.org/10.1073/pnas.0809674106
  20. Talbott, S. M., Talbott, J. A., George, A., & Pugh, M. (2013). Effect of Tongkat Ali on stress hormones and psychological mood state in moderately stressed subjects. J Int Soc Sports Nutr, 10(1), 28. https://doi.org/10.1186/1550-2783-10-28
  21. Tambi, M. I., Imran, M. K., & Henkel, R. R. (2012). Standardised water-soluble extract of Eurycoma longifolia, Tongkat ali, as testosterone booster for managing men with late-onset hypogonadism? Andrologia, 44 Suppl 1, 226-230. https://doi.org/10.1111/j.1439-0272.2011.01168.x