In Silico Docking Analysis of Phaleria macrocarpa Fruit Phytochemicals in Inhibiting SARS-CoV-2

Authors

DOI:

https://doi.org/10.56532/mjsat.v6iS1.792

Keywords:

In silico, Phaleria macrocarpa, SARS-CoV-2 virus

Abstract

SARS-CoV-2 has caused significant global mortality, and while synthetic antivirals are used, their potential side effects highlight the need for safer natural alternatives. Phaleria macrocarpa contains antiviral flavonoids but remains underexplored against SARS-CoV-2. This study aimed to identify phytochemicals in P. macrocarpa fruit using GC-MS and phytochemical screening, evaluate their antiviral potential to inhibit SARS-CoV-2 through in silico docking, and assess their pharmacokinetic properties via SwissADME. Extraction was performed using maceration, followed by screening and GC-MS, which revealed flavonoids, terpenoids, phenolics, sterols, glycosides, and seven compounds, with only squalene showing antiviral activity. Thirteen compounds from databases were further analysed, yielding binding affinities ranging from -5.5 to -8.6 kcal/mol. Among these, sesamin, Mahkoside A, and Mahkoside B exhibited the strongest predicted binding interactions. These findings suggest P. macrocarpa phytochemicals may serve as natural alternatives to existing antiviral treatments, warranting further experimental validation.

References

Jinoni, D. A., Benjamin, M. A. Z., Mus, A. A., Goh, L. P. W., Rusdi, N. A., & Awang, M. A. (2024). Phaleria macrocarpa (Scheff.) Boerl. (Mahkota Dewa) seed essential oils: Extraction yield, volatile components, antibacterial, and antioxidant activities based on different solvents using Soxhlet extraction. Kuwait Journal of Science, 51(2), 100173. doi: https://doi.org/10.1016/j.kjs.2023.100173

Rahman, F., Tabrez, S., Ali, R., Alqahtani, A. S., Ahmed, M. Z., & Rub, A. (2021). Molecular docking analysis of rutin reveals possible inhibition of SARS-CoV-2 vital proteins. Journal of Traditional and Complementary Medicine, 11(2), 173–179. doi: https://doi.org/10.1016/j.jtcme.2021.01.006

Easmin, Mst. S., Sarker, Md. Z. I., Ferdosh, S., Shamsudin, S. H., Yunus, K. bin, Uddin, Md. S., Sarker, Md. M. R., Akanda, Md. J. H., Hossain, Md. S., & Khalil, H. A. (2014). Bioactive compounds and advanced processing technology: Phaleria macrocarpa (sheff.) Boerl, a review. Journal of Chemical Technology & Biotechnology, 90(6), 981–991. doi: https://doi.org/10.1002/jctb.4603

Celia Radita, D., & Widyarman, A. S. (2019). Mahkota Dewa (God's Crown) Fruit Extract Inhibits the Formation of Periodontal Pathogen Biofilms in vitro. Journal of Indonesian Dental Association, 2(2), 57. doi: https://doi.org/10.32793/jida.v2i2.404

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 diseases management. Scientific Reports, 13(1), 13398. doi: https://doi.org/10.1038/s41598-023-40160-2

Andrean, D., Prasetyo, S., Kristijarti, A. P., & Hudaya, T. (2014). The Extraction and Activity Test of Bioactive Compounds in Phaleria Macrocarpa as Antioxidants. Procedia Chemistry, 9, 94–101. doi: https://doi.org/10.1016/j.proche.2014.05.012

Christy Gnana Theeba P. & Sasi Kumar R.(2015). Phytochemical examination, antioxidant potential and in vitro antibacterial studies of crude extracts of Parthenium hysterophorus Linn. leavesPhytochemical examination, antioxidant potential and in vitro antibacterial studies of crude extracts of Parthenium hysterophorus Linn. Leaves. Journal of Chemical and Pharmaceutical Research, 2015, 7(4):219-225

Godlewska, K., Pacyga, P., Najda, A., & Michalak, I. (2023). Investigation of Chemical Constituents and Antioxidant Activity of Biologically Active Plant-Derived Natural Products. Molecules, 28(14), 5572. doi: https://doi.org/10.3390/molecules28145572

Dahanayake, J. M., Perera, P. K., Galappatty, P., Melshandi Perera, H. D. S., & Arawwawala, L. D. A. M. (2019). Comparative Phytochemical Analysis and Antioxidant Activities of Tamalakyadi Decoction with Its Modified Dosage Forms. Evidence-Based Complementary and Alternative Medicine, 2019, 1–9. doi: https://doi.org/10.1155/2019/6037137

Deshmukh, M. A., & Theng, M. A. (2018). Phytochemical Screening, Quantitative Analysis Of Primary And Secondary Metabolites Of Acacia Arabica Bark. International Journal of Current Pharmaceutical Research, 10(2), 35. doi: https://doi.org/10.22159/ijcpr.2018v10i2.25889

Aqeel, M. T., Nisar-Ur-Rahman, Khan, A., Ashraf, Z., Khan, S., & Arif, M. (2022). In silico approach for the development of phenolic derivatives as potential anti-angiogenic agents against lysyl oxidase-like 2 enzyme. Future Journal of Pharmaceutical Sciences, 8(1), 32. doi: https://doi.org/10.1186/s43094-022-00422-8

Boopathi, V., Nahar, J., Murugesan, M., Subramaniyam, S., Kong, B. M., Choi, S.-K., Lee, C.-S., Ling, L., Yang, D. U., Yang, D. C., Mathiyalagan, R., & Chan Kang, S. (2023). In silico and in vitro inhibition of host-based viral entry targets and cytokine storm in COVID-19 by ginsenoside compound K. Heliyon, 9(9), e19341. doi: https://doi.org/10.1016/j.heliyon.2023.e19341

Adedayo, A., & Famuti, A. (2023). In-silico studies of Momordica charantia extracts as potential candidates against SARS-CoV-2 targeting human main protease enzyme (Mpro). Informatics in Medicine Unlocked, 38, 101216. doi: https://doi.org/10.1016/j.imu.2023.101216

Ebrahimi, M., Farhadian, N., Amiri, A. R., Hataminia, F., Soflaei, S. S., & Karimi, M. (2022). Evaluating the efficacy of extracted squalene from seed oil in the form of microemulsion for the treatment of COVID‐19: A clinical study. Journal of Medical Virology, 94(1), 119–130. doi: https://doi.org/10.1002/jmv.27273

Fisher, K. J., Kinsey, R., Mohamath, R., Phan, T., Liang, H., Orr, M. T., Lykins, W. R., Guderian, J. A., Bakken, J., Argilla, D., Ramer-Denisoff, G., Larson, E., Qi, Y., Sivananthan, S., Smolyar, K., Carter, D., Paddon, C. J., & Fox, C. B. (2023). Semi-synthetic terpenoids with differential adjuvant properties as sustainable replacements for shark squalene in vaccine emulsions. Npj Vaccines, 8(1), 14. doi: https://doi.org/10.1038/s41541-023-00608-y

Stavenga, D. G., Leertouwer, H. L., Dudek, B., & van der Kooi, C. J. (2021). Coloration of Flowers by Flavonoids and Consequences of pH Dependent Absorption. Frontiers in Plant Science, 11. doi: https://doi.org/10.3389/fpls.2020.600124

Ibrahim, Z. Y., Uzairu, A., Shallangwa, G. A., & Abechi, S. E. (2021). Pharmacokinetic predictions and docking studies of substituted aryl amine- based triazolopyrimidine designed inhibitors of Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH). Future Journal of Pharmaceutical Sciences, 7(1), 133. doi: https://doi.org/10.1186/s43094-021-00288-2

Tue-ngeun, P., Rakitikul, W., Thinkumrob, N., Hannongbua, S., Meelua, W., & Jitonnom, J. (2024). Binding interactions and in silico ADME prediction of isoconessimine derivatives as potent acetylcholinesterase inhibitors. Journal of Molecular Graphics and Modelling, 129, 108746. doi: https://doi.org/10.1016/j.jmgm.2024.108746

Kenny, P. (2022). Hydrogen bond donors in drug design. doi: https://doi.org/10.1021/acs.jmedchem.2c01147

Lina Agustin, S., Widiandani, T., Hardjono, S., & Tri Purwanto, B. (2022). QSAR of Acyl pinostrobin derivatives as Anti-breast cancer against HER-2 receptor and their ADMET properties based on in silico Study. Research Journal of Pharmacy and Technology, 4641 doi: https://doi.org/10.52711/0974-360x.2022.00779

Miebs, G., Mielniczuk, A., Kadziński, M., & Bachorz, R. A. (2024). Beyond the Arbitrariness of Drug-Likeness Rules: Rough Set Theory and Decision Rules in the Service of Drug Design. Applied Sciences, 14(21), 9966. doi: https://doi.org/10.3390/app14219966

Babalola, B. A., & Adegboyega, A. E. (2024). Computational Discovery of Novel Imidazole Derivatives as Inhibitors of SARS-CoV-2 Main Protease: An Integrated Approach Combining Molecular Dynamics and Binding AffinityAnalysis. COVID, 4(6), 672–695. doi: https://doi.org/10.3390/covid4060046

Gangadhar Y, Al Turaifi AR, Naveen NR, Goudanavar P, Fattepur S, et al. Bio-Simulation Studies of Valganciclovir Hydrochloride: Molecular Descriptor-Based QSAR Modelling and Swiss ADME Analysis Using in silico Models. Indian J of Pharmaceutical Education and Research. 2025;59(1):1-10 doi: https://doi.org/10.5530/ijper.20251137

Price, G., & Patel, D. A. (2025). Drug Bioavailability. National Library of Medicine. StatPearls Publishing LLC. url: https://www.ncbi.nlm.nih.gov/books/NBK557852/

Lin, J. H., & Yamazaki, M. (2003). Role of P-Glycoprotein in Pharmacokinetics. Clinical Pharmacokinetics, 42(1), 59–98. doi: https://doi.org/10.2165/00003088-200342010-00003

Huang, L., Li, B., Li, X., Liu, G., Liu, R., Guo, J., Xu, B., Li, Y., & Fang, W. (2019). Significance and Mechanisms of P-glycoprotein in Central Nervous System Diseases. Current Drug Targets, 20(11), 1141–1155. doi: https://doi.org/10.2174/1389450120666190308144448

Nur Hannani Ahmad Rozani, Fatahiya Mohamed Tap, Fadzilah Adibah Abd Majid, Nur 'Ainun Mokhtar, & Nurul Bahiyah Ahmad Khairudin. (2024). Molecular Docking of Phytochemicals from M. Charantia Targeting SARS-CoV-2 Main Protease. Journal of Advanced Research in Applied Sciences and Engineering Technology, 47(1), 152–165. doi: https://doi.org/10.37934/araset.47.1.152165

Amelia, M. A., Kesuma, D., Kirtishanti, A., Sumartha, I. G. A., & Claudya, M. (2024). Molecular Docking: Study of Chalcone Derivatives from Boesenbergia pandurata Targeting Estrogen Receptor Alpha (ER–a) for Breast Cancer. Jurnal Penelitian Pendidikan IPA, 10(11), 8376–8386. doi: https://doi.org/10.29303/jppipa.v10i11.8734

Akhtar, N., Verma, H., Silkari, O. M., Upadhyay, A. K., Kaushik, V., & Amin-ul Mannan, M. (2022). Drummondin E and Flinderole B are potential inhibitors of RNA-dependent RNA polymerase of SARS-CoV-2: an in silico study. BioTechnologia, 103(1), 53–70. doi: https://doi.org/10.5114/bta.2022.113915

Kawsar, S. M. A., Hosen, M. A., el Bakri, Y., Ahmad, S., Affi, S. T., & Goumri-Said, S. (2022). In silico approach for potential antimicrobial agents through antiviral, molecular docking, molecular dynamics, pharmacokinetic and bioactivity predictions of galactopyranoside derivatives. Arab Journal of Basic and Applied Sciences, 29(1), 99–112. doi: https://doi.org/10.1080/25765299.2022.2068275

Harisna, A. H., Nurdiansyah, R., Syaifie, P. H., Nugroho, D. W., Saputro, K. E., Firdayani, Prakoso, C. D., Rochman, N. T., Maulana, N. N., Noviyanto, A., & Mardliyati, E. (2021). In silico investigation of potential inhibitors to main protease and spike protein of SARS-CoV-2 in propolis. Biochemistry and Biophysics Reports, 26, 100969. doi: https://doi.org/10.1016/j.bbrep.2021.100969

Zhu, M., Pan, J., Hu, X., & Zhang, G. (2021). Epicatechin Gallate as Xanthine Oxidase Inhibitor: Inhibitory Kinetics, Binding Characteristics, Synergistic Inhibition, and Action Mechanism. Foods, 10(9), 2191. doi: https://doi.org/10.3390/foods10092191

In Silico Docking Analysis of Phaleria macrocarpa Fruit Phytochemicals in Inhibiting SARS-CoV-2

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Published

2026-08-21

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Section

Special Issue: The 3rd International Science and Technology Colloquium 2025

How to Cite

[1]
“In Silico Docking Analysis of Phaleria macrocarpa Fruit Phytochemicals in Inhibiting SARS-CoV-2”, Malaysian J. Sci. Adv. Tech., pp. 80–93, Aug. 2026, doi: 10.56532/mjsat.v6iS1.792.