Studi In Silico Senyawa Fitokimia Tumbuhan Pasak Bumi (Eurycoma longifolia) sebagai Anti Malaria Plasmodium falciparum 

Authors

  • Dorce Bani Universitas Mulawarman
  • Dora Dayu Turista Universitas Mulawarman
  • Sri Purwari Universitas Mulawarman
  • Rusni Ernopita Ulan Universitas Mulawarman
  • Miningsih Universitas Mulawarman
  • Risty Geofani Universitas Mulawarman
  • Sintya Universitas Mulawarman

DOI:

https://doi.org/10.31539/qw8dpj63

Abstract

This study aimed to analyze the potential of pasak bumi (Eurycoma longifolia) phytochemical compounds as antimalarial candidates through an in silico approach targeting Plasmodium falciparum Plasmepsin X. The research methods included ligand and receptor preparation, receptor validation using Root Mean Square Deviation (RMSD), molecular docking, ligand-protein interaction analysis, drug-likeness evaluation, and toxicity prediction. The receptor validation produced an RMSD value of 0.371 Å, indicating that the docking protocol was valid. All tested compounds bound to the binding pocket of the target protein with varying binding affinity values. Niloticin showed the most negative binding affinity among the tested compounds at −11.404 kcal/mol. Eurycomalactone was not predicted to be hepatotoxic or carcinogenic. This study concludes that Niloticin has potential based on its binding affinity, while Eurycomalactone shows a better balance of binding affinity, drug-likeness characteristics, and predicted safety. However, the biological activity and safety of both compounds require confirmation through molecular dynamics simulations and in vitro and in vivo studies.

Keywords: Antimalarial, Eurycoma longifolia, In Silico, Molecular Docking, Phytochemicals, Plasmodium falciparum

References

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, Article 13398. https://doi.org/10.1038/s41598-023-40160-2

Al Azzam, K. (2022). SwissADME and pkCSM webservers predictors: An integrated online platform for accurate and comprehensive predictions for in silico ADME/T properties of artemisinin and its derivatives. Kompleksnoe Ispolzovanie Mineralnogo Syra, 325(2), 14–21. https://doi.org/10.31643/2023/6445.13

Banerjee, P., Kemmler, E., Dunkel, M., & Preissner, R. (2024). ProTox 3.0: A webserver for the prediction of toxicity of chemicals. Nucleic Acids Research, 52(W1), W513–W520. https://doi.org/10.1093/nar/gkae303

Bekono, B. D., Ntie-Kang, F., Onguéné, P. A., Lifongo, L. L., Sippl, W., Fester, K., & Owono, L. C. O. (2020). The potential of anti-malarial compounds derived from African medicinal plants: A review of pharmacological evaluations from 2013 to 2019. Malaria Journal, 19, Article 183. https://doi.org/10.1186/s12936-020-03231-7

Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7, Article 42717. https://doi.org/10.1038/srep42717

Farag, M. A., Ajayi, A. O., Taleb, M., Wang, K., & Ayoub, I. M. (2023). A multifaceted review of Eurycoma longifolia nutraceutical bioactives: Production, extraction, and analysis in drugs and biofluids. ACS Omega, 8(2), 1838–1850. https://doi.org/10.1021/acsomega.2c06340

Hassan, A. M., Gattan, H. S., Faizo, A. A., Alruhaili, M. H., Alharbi, A. S., Bajrai, L. H., Al-Zahrani, I. A., Dwivedi, V. D., & Azhar, E. I. (2024). Evaluating the binding potential and stability of drug-like compounds with the monkeypox virus VP39 protein using molecular dynamics simulations and free energy analysis. Pharmaceuticals, 17(12), Article 1617. https://doi.org/10.3390/ph17121617

Hodder, A. N., Christensen, J., Scally, S., Triglia, T., Ngo, A., Birkinshaw, R. W., Bailey, B., Favuzza, P., Dietrich, M. H., Tham, W. H., Czabotar, P. E., Lowes, K., Guo, Z., Murgolo, N., Lera Ruiz, M., McCauley, J. A., Sleebs, B. E., Olsen, D., & Cowman, A. F. (2022). Basis for drug selectivity of plasmepsin IX and X inhibition in Plasmodium falciparum and Plasmodium vivax. Structure, 30(6), 947–961.e6. https://doi.org/10.1016/j.str.2022.03.018

Ikhtiarudin, I., Dona, R., Frimayanti, N., Utami, R., Susianti, N., & Septama, A. W. (2022). Sintesis, karakterisasi struktur, dan kajian molecular docking senyawa turunan 4′-metoksi flavonol sebagai antagonis reseptor estrogen alfa pada kanker payudara. Jurnal Riset Kimia, 13(2), 236–248.

Kalontong, P. K., Safithri, M., & Tarman, K. (2022). Penambatan molekul senyawa aktif Spirulina platensis sebagai inhibitor TMPRSS2 untuk mencegah infeksi SARS-CoV-2. Jurnal Pengolahan Hasil Perikanan Indonesia, 25(2), 253–267.

Kesari, P., Deshmukh, A., Pahelkar, N., Suryawanshi, A. B., Rathore, I., Mishra, V., Dupuis, J. H., Xiao, H., Gustchina, A., Abendroth, J., Labaied, M., Yada, R. Y., Wlodawer, A., Edwards, T. E., Lorimer, D. D., & Bhaumik, P. (2022). Structures of plasmepsin X from Plasmodium falciparum reveal a novel inactivation mechanism of the zymogen and molecular basis for binding of inhibitors in mature enzyme. Protein Science, 31(4), 882–899. https://doi.org/10.1002/pro.4279

Kleandrova, V. V., Cordeiro, M. N. D. S., & Speck-Planche, A. (2025). In silico approach for early antimalarial drug discovery: De novo design of virtual multi-strain antiplasmodial inhibitors. Microorganisms, 13(7), Article 1620. https://doi.org/10.3390/microorganisms13071620

Kovada, V., Withers-Martinez, C., Bobrovs, R., Cērule, H., Liepins, E., Grinberga, S., Hackett, F., Collins, C. R., Kreicberga, A., Jiménez-Díaz, M. B., Angulo-Barturen, I., Rasina, D., Suna, E., Jaudzems, K., Blackman, M. J., & Jirgensons, A. (2023). Macrocyclic peptidomimetic plasmepsin X inhibitors with potent in vitro and in vivo antimalarial activity. Journal of Medicinal Chemistry, 66(15), 10658–10680. https://doi.org/10.1021/acs.jmedchem.3c00812

Nhlapho, S., Nyathi, M. H. L., Ngwenya, B. L., Dube, T., Telukdarie, A., Munien, I., Vermeulen, A., & Chude-Okonkwo, U. A. K. (2024). Druggability of pharmaceutical compounds using Lipinski rules with machine learning. Sciences of Pharmacy, 3(4), 177–192. https://doi.org/10.58920/sciphar0304264

Pires, D. E. V., Blundell, T. L., & Ascher, D. B. (2015). pkCSM: Predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures. Journal of Medicinal Chemistry, 58(9), 4066–4072. https://doi.org/10.1021/acs.jmedchem.5b00104

Rahmasari, F. V., Asih, P. B. S., Dewayanti, F. K., Rotejanaprasert, C., Charunwatthana, P., Imwong, M., & Syafruddin, D. (2022). Drug resistance of Plasmodium falciparum and Plasmodium vivax isolates in Indonesia. Malaria Journal, 21, Article 354. https://doi.org/10.1186/s12936-022-04385-2

Ribeiro, G. J. G., Yan, S. L. R., Palmisano, G., & Wrenger, C. (2023). Plant extracts as a source of natural products with potential antimalarial effects: An update from 2018 to 2022. Pharmaceutics, 15(6), Article 1638. https://doi.org/10.3390/pharmaceutics15061638

Richardson, L. W., Ashton, T. D., Dans, M. G., Nguyen, N., Favuzza, P., Triglia, T., Hodder, A. N., Ngo, A., Jarman, K. E., Cowman, A. F., & Sleebs, B. E. (2022). Substrate peptidomimetic inhibitors of Plasmodium falciparum plasmepsin X with potent antimalarial activity. ChemMedChem, 17(18), Article e202200306. https://doi.org/10.1002/cmdc.202200306

Souza, J. A. C. R., Souza, T., Quintans, I. L. A. C. R., & Farias, D. (2023). Network toxicology and molecular docking to investigate the non-AChE mechanisms of organophosphate-induced neurodevelopmental toxicity. Toxics, 11(8), Article 710. https://doi.org/10.3390/toxics11080710

Teh, C.-H., Murugaiyah, V., & Chan, K.-L. (2011). Developing a validated liquid chromatography-mass spectrometric method for the simultaneous analysis of five bioactive quassinoid markers for the standardization of manufactured batches of Eurycoma longifolia Jack extract as antimalarial medicaments. Journal of Chromatography A, 1218(14), 1861–1877. https://doi.org/10.1016/j.chroma.2011.02.014

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. https://doi.org/10.1002/jcc.21334

White, N. J., & Chotivanich, K. (2024). Artemisinin-resistant malaria. Clinical Microbiology Reviews, 37(4), Article e00109-24. https://doi.org/10.1128/cmr.00109-24

Withers-Martinez, C., George, R., Ogrodowicz, R., Kunzelmann, S., Purkiss, A. G., Kjaer, S., Walker, P. A., Kovada, V., Jirgensons, A., & Blackman, M. J. (2025). Structural plasticity of Plasmodium falciparum plasmepsin X to accommodate binding of potent macrocyclic hydroxyethylamine inhibitors. Journal of Molecular Biology, 437, Article 169062. https://doi.org/10.1016/j.jmb.2025.169062

World Health Organization. (2024). World malaria report 2024: Addressing inequity in the global malaria response. https://www.who.int/teams/global-malaria-programme/reports/world-malaria-report-2024

Yogaswara, R., Pranowo, H. D., Prasetyo, N., & Pulung, M. L. (2025). Investigation of new 4-benzyloxy-2-trichloromethylquinazoline derivatives as Plasmodium falciparum dihydrofolate reductase-thymidylate synthase inhibitors: QSAR, ADME, drug-likeness, toxicity, molecular docking, and molecular dynamics simulation. Journal of Multidisciplinary Applied Natural Science, 5(2), 456–486. https://doi.org/10.47352/jmans.2774-3047.258

Downloads

Published

2026-08-31