In silico Evaluation of Physicochemical and ADMET Properties of Bioactive Compounds from Marchantia paleacea.
DOI:
https://doi.org/10.24114/jpgmn753Keywords:
Drug- likeness, Lipinski's Rule of Five, Marchantia paleacea, Pharmacokinetic prediction, Toxicity.Abstract
Marchantia paleacea is a liverwort with diverse secondary metabolites of pharmacological interest. This study aimed to evaluate the physicochemical and ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) properties of eighteen bioactive compounds previously identified from M. paleacea by GC-MS analysis using an in silico approach. Physicochemical parameters were analyzed using SwissADME, ADMET predictions were performed using pKCSM and ProTox 3.0 for toxicity class analysis. Results showed that most compounds complied with Lipinski’s Rule of Five (RO5), demonstrating good oral drug-likeness. All compounds exhibited high human intestinal absorption (86-95%), favorable BBB permeability, and CNS permeability values remained low. Most compounds did not significantly interact with major CYP450 isoenzymes or P-glycoprotein. Toxicity prediction revealed that the majority of compounds were non-mutagenic (Ames-negative), non-hepatotoxic, and did not inhibit the hERG channel, suggesting a relatively safe pharmacological profile. Exceptions included 2-nitro-cyclohexanone (positive Ames test) and thymol (hepatotoxicity). Compounds such as linalool, dodecanoic acid, n-decanoic acid, and bicyclo[2.2.2]hept5-en2-ol demonstrated particularly favorable drug-like characteristics, warranting further experimental validation. These findings provide a computational foundation for prioritizing M. paleacea bioactive compounds for future drug development.
References
Asakawa, Y. (2017). NPC Natural Product Communications. Natural Product Communications. Vol 12, No.8. 1335–1349. doi.org/10.1177/1934578X1701200845
Banerjee, P., Kemmler, E., Dunkel, M., & Preissner, R. (2024). ProTox 3 . 0 : a w ebserv er f or the prediction of t oxicity of chemicals. Nucleic Acid Research. Vol. 52: 513–520. doi.org/10.1093/nar/gkae303
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. Vol. 7: 42717. doi.org/10.1038/srep42717
Đorđević, V., Balanč, B., Belščak-Cvitanović, A., Lević, S., Trifković, K., Kalušević, A., Kostić, I., Komes, D., Bugarski, B., & Nedović, V. (2020). Natural Macromolecules as Carriers for Essential Oils: From Extraction to Biomedical Application. Frontiers in Bioengineering and Biotechnology. Vol. 8, No.563. doi.org/10.3389/fbioe.2020.00563
Fadhilla, R., Iskandar, E. A., & Kusumaningrum, H. D. (2012). Tumbuhan lumut hati (Marchantia paleacea) terhadap bakteri patogen dan perusak pangan. Jurnal Teknologi dan Industri Pangan. Vol. 23, No.2: 126–131. doi.org/10.6066/jtip.2012.23.2.126
Gonzales, A. L., Huang, S. K. H., Sevilla, U. T. A., Hsieh, C. Y., & Tsai, P. W. (2023). In silico Analysis of Anti-Inflammatory and Antioxidant Properties of Bioactive Compounds from Crescentia cujete L. Molecules. Vol. 28, No.8. https://doi.org/10.3390/molecules28083547
Honma, M., Kitazawa, A., Cayley, A., Williams, R. V., Barber, C., Hanser, T., Saiakhov, R., Chakravarti, S., Myatt, G. J., Cross, K. P., Benfenati, E., Raitano, G., Mekenyan, O., Petkov, P., Bossa, C., Benigni, R., Battistelli, C. L., Giuliani, A., Tcheremenskaia, O., Demo, C., Norinder, U., Koga, H., Jose, C., Jeliazkova, N., Kochev, N., Paskaleva, V., Yang, C., Daga, P.R., Clark, R.D., & Rathman, J. (2019). Improvement of quantitative structure–activity relationship (QSAR) tools for predicting Ames mutagenicity: outcomes of the Ames/QSAR International Challenge Project. Mutagenesis, Vol 34, No.1:3–16. https://doi.org/10.1093/mutage/gey031
Huang, S., Ren, Y., Peng, X., Qian, P., & Meng, L. (2019). Computer-aid drug design, synthesis, and anticoagulant activity evaluation of novel dabigatran derivatives as thrombin inhibitors. European Journal of Pharmaceutical Sciences. Vol. 137: 104965. doi.org/10.1016/j.ejps.2019.104965
Lagorce, D., Douguet, D., Miteva, M. A., & Villoutreix, B. O. (2017). Computational analysis of calculated physicochemical and ADMET properties of protein-protein interaction inhibitors. Scientific Reports. Vol. 7: 1–15. doi.org/10.1038/srep46277
Lammari, N., Louaer, O., Meniai, A. H., & Elaissari, A. (2022). Essential Oils as Multicomponent Mixtures and Their Potential for Human Health and Well-Being. Frontiers in Pharmacology. Vol. 13: 956541. doi.org/10.3389/fphar.2022.956541
Lipinski, C.A. (2004). Lead- and drug-like compounds: The rule-of-five revolution. Drug Discovery Today: Technologies. Vol. 1, No.4: 337–341. doi.org/10.1016/j.ddtec.2004.11.007
Lipinski, C.A., Lombardo, F., Dominy, B.W., & Feeney, P.J. (2001). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews. Vol. 46, No.1–3: 3–26. doi.org/10.1016/S0169-409X(00)00129-0
M ˛aczka, W. . D.-M., & A.; Grabarczyk, M.; Wi´nska, K. (2022). Natural Compounds in the Battle against. Molecules. Vol. 27: 6928. doi.org/10.3390/molecules27206928
Maser, W. H., Purwoko, A., Yuliana, N. D., Lubis, L. M., & Khatib, A. (2022). GC-MS Based Metabolite Profiling and Antibacterial Activity of Torch Ginger Etlingera elatior Flowers Extract. Indonesian Journal of Chemistry. Vol. 22, No.4: 1014–1024. doi.org/10.22146/ijc.72583
Moroy, G., Martiny, V.Y., Vayer, P., Villoutreix, B.O., & Miteva, M.A. (2012). Toward in silico structure-based ADMET prediction in drug discovery. Drug Discovery Today. Vol. 17, No.1–2: 44–55. doi.org/10.1016/j.drudis.2011.10.023
Olasupo, S. B., Uzairu, A., Shallangwa, G. A., & Uba, S. (2021). Unveiling novel inhibitors of dopamine transporter via in silico drug design, molecular docking, and bioavailability predictions as potential antischizophrenic agents. Future Journal of Pharmaceutical Sciences. Vol 7, No 1. doi.org/10.1186/s43094-021-00198-3
Pajouhesh, H., & Lenz, G. R. (2005). Medicinal chemical properties of successful central nervous system drugs. NeuroRx. Vol. 2, No.4: 541–553. https://doi.org/10.1602/neurorx.2.4.541
Pardridge, W.M. (2012). Drug transport across the blood-brain barrier. Journal of Cerebral Blood Flow & Metabolism. Vol. 32, No.11: 1959–1972. doi.org/10.1038/jcbfm.2012.126
Pirvu, L. C., Stefaniu, A., Nita, S., Radu, N., & Neagu, G. (2025). In silico and in vitro analyses of strawberry-derived extracts in relation to key compounds' metabolic and anti-tumor effects. International Journal of Molecular Sciences. Vol. 26, No.8: 3492. doi.org/10.3390/ijms26083492
Purkon, D. B., Iwo, M. I., Soemardji, A. A., Rahmawati, S. F., Fadhlillah, F. M., & Nadhifah, A. (2021). Immunostimulant Activity of Marchantia paleacea Bertol . Herb Liverwort Ethanol Extract in BALB / c Mice. Vol. 32, No.4: 464–473.
Purkon, D. M., Hidayat, A., & Kaplan, A. (2022). Phytochemical, use in ethnomedicine, and therapeutic activities of Marchantia genus. Journal of Vocational Health Studies. Vol. 5, No.3: 115–128. doi.org/10.20473/jvhs.V5.I3.2022.174-185
Rukmana, R. M., Silfarohana, R., Putra, A. D. P., Safrina, D., Susanti, D., Wijaya, N. R., Adi, M. B. S., Prastiyanto, M. E., Cahyaningrum, Y. A., Nurmaulawati, R., & Bhagawan, W. S. (2025). Phytochemical profile, antioxidant activity and anticancer activity of gamma-irradiated black rice bran (Oryza sativa L.) ethanolic extract: In-vitro and in-silico study. Science and Technology Indonesia. Vol.10, No.2. 628–643. doi.org/10.26554/sti.2025.10.2.628-643
Sharma, A., Sharma, S., Gupta, M., Fatima, S., Saini, R., & Agarwal, S. M. (2018). Pharmacokinetic profiling of anticancer phytocompounds using computational approach. Phytochemical Analysis. Vol. 29, No.6: 559–568. doi.org/10.1002/pca.2767
Siregar, E. S., Situmorang, P. C., Pasaribu, N., Hairima, H., & Hasibuan, M. R. (2025). Profiling and potential of Marchantia paleacea Bertol. extract for breast anticancer candidate: GC-MS, LC-MS/MS, and in silico analysis. Journal of Pharmacy and Pharmacognosy Research. Vol. 13: S371–S393. doi.org/10.56499/jppres25.2531_13.s1.371
Smith, D. A., Beaumont, K., Maurer, T. S., & Di, L. (2015). Volume of distribution in drug design: Miniperspective. Journal of Medicinal Chemistry. Vol. 58, No.15: 5691–5698. doi.org/10.1021/acs.jmedchem.5b00201
Veber, D. F., Johnson, S. R., Cheng, H.-Y., Smith, B. R., Ward, K. W., & Kopple, K. D. (2002). Molecular properties that influence the oral bioavailability of drug candidates. Journal of Medicinal Chemistry. Vol 45. No 12: 2615–2623. doi.org/10.1021/jm020017n
Yin L, Liang C, Wei W, H. S., Ren Y, Geng Y, Huang X, C. D., Guo H, Fang J, Deng H, Lai W, Y. S., & P, and O. (2022). The Antibacterial Activity of Thymol Against Drug-Resistant Streptococcus iniae and Its Protective Effect on Channel Catfish ( Ictalurus punctatus) . Front. Microbiol. Vol. 13: 914868. doi.org/10.3389/fmicb.2022.914868
Zanger, U. M., & Schwab, M. (2013). Cytochrome P450 enzymes in drug metabolism: Regulation of gene expression, enzyme activities, and impact of genetic variation. Pharmacology & Therapeutics. Vol. 138, No.1: 103–141. doi.org/10.1016/j.pharmthera.2012.12.007
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