skip to main content

Determination of the Activity of Bioactive Compounds from Biancaea sappan (L.) Tod. and Spatholobus ferrugineus (Zoll. and Moritzi) Benth Against Breast Cancer Cells: An In Silico Study

Faculty of Pharmacy, National Institute of Science and Technology, South Jakarta, Indonesia

Received: 7 Jan 2026; Revised: 5 Apr 2026; Accepted: 8 Apr 2026; Published: 25 May 2026.
Open Access Copyright 2026 Jurnal Kimia Sains dan Aplikasi under http://creativecommons.org/licenses/by-sa/4.0.

Citation Format:
Cover Image
Abstract
Breast cancer is one of the most prevalent malignancies worldwide, with subtypes expressing hormone receptors such as the Estrogen Receptor (ER), Progesterone Receptor (PR), and HER2 being primary therapeutic targets. This study explores the potential of natural compounds as inhibitors for these key proteins. This research aimed to evaluate the potential of bioactive compounds from sappanwood (Biancaea sappan (L.) Tod.), namely Brazilin and its derivative Brazilein, and from the stem of Spatholobus ferrugineus (Zoll. and Moritzi) Benth Variabilin, Medicarpin, and its derivative Vestitol, (-)- as candidate inhibitors against the target proteins of breast cancer (ERα, ERβ, PR, and HER2) using a molecular docking methodology. The analysis was performed by comparing the docking scores and interaction patterns of the test compounds against their native ligands and a reference ligand (lapatinib for HER2). Furthermore, in silico predictions of their pharmacokinetic (ADMET) profiles and drug-likeness were conducted. The docking results showed that Variabilin exhibited the highest binding affinity for HER2 among the test compounds and demonstrated a high predicted binding affinity for the antagonist conformations of both ERα and ERβ. The other test compounds also showed potential as ERα and ERβ inhibitors; however, none of the five compounds showed potential as PR antagonists. The ADMET analysis predicted that the majority of the compounds possess an acceptable pharmacokinetic profile. Variabilin shows favorable docking to the HER2 kinase site and to ER LBDs. Functional activity requires experimental confirmation.
Keywords: ADMET prediction; Biancaea sappan; Breast Cancer; In Silico; Spatholobus ferrugineus
Funding: Ministry of Higher Education, Science, and Technology of the Republic of Indonesia [Penelitian Dosen Pemula (PDP) 2025 for the research funding under contract 0917/LL3/AL.04/2025 , 007/SPK-HibahDikti/P/V/2025

Article Metrics:

  1. Hyuna Sung, Jacques Ferlay, Rebecca L. Siegel, Mathieu Laversanne, Isabelle Soerjomataram, Ahmedin Jemal, Freddie Bray, Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries, CA: A Cancer Journal for Clinicians, 71, 3, (2021), 209-249 https://doi.org/10.3322/caac.21660
  2. Aleix Prat, Estela Pineda, Barbara Adamo, Patricia Galván, Aranzazu Fernández, Lydia Gaba, Marc Díez, Margarita Viladot, Ana Arance, Montserrat Muñoz, Clinical implications of the intrinsic molecular subtypes of breast cancer, The Breast, 24, (2015), 26-35 https://doi.org/10.1016/j.breast.2015.07.008
  3. Jindal Arpita, Gothwal Priyanka, Solanki Ranjana, A Study of Molecular Subtypes of Carcinoma Breast by Immunohistochemistry at Tertiary Care Center, Jaipur, Asian Pacific Journal of Cancer Biology, 7, 3, (2022), 219-223 https://doi.org/10.31557/apjcb.2022.7.3.219-223
  4. Xiaoqing Cheng, A Comprehensive Review of HER2 in Cancer Biology and Therapeutics, Genes, 15, 7, (2024), 216 https://doi.org/10.3390/genes15070903
  5. Gottfried E. Konecny, Mark D. Pegram, Natarajan Venkatesan, Richard Finn, Guorong Yang, Martina Rahmeh, Michael Untch, David W. Rusnak, Glenn Spehar, Robert J. Mullin, Barry R. Keith, Tona M. Gilmer, Mark Berger, Karl C. Podratz, Dennis J. Slamon, Activity of the Dual Kinase Inhibitor Lapatinib (GW572016) against HER-2-Overexpressing and Trastuzumab-Treated Breast Cancer Cells, Cancer Research, 66, 3, (2006), 1630-1639 https://doi.org/10.1158/0008-5472.CAN-05-1182
  6. Patrick J. Medina, Susan Goodin, Lapatinib: A Dual Inhibitor of Human Epidermal Growth Factor Receptor Tyrosine Kinases, Clinical Therapeutics, 30, 8, (2008), 1426-1447 https://doi.org/10.1016/j.clinthera.2008.08.008
  7. M. Washiyama, Y. Sasaki, T. Hosokawa, S. Nagumo, Anti-inflammatory constituents of Sappan Lignum, Biological and Pharmaceutical Bulletin, 32, 5, (2009), 941-944 https://doi.org/10.1248/bpb.32.941
  8. Xihua Yang, Lili Zhao, Tingting Zhang, Junfeng Xi, Shuze Liu, Liansheng Ren, Yaqin Zheng, Huanhu Zhang, Protosappanin B promotes apoptosis and causes G1 cell cycle arrest in human bladder cancer cells, Scientific Reports, 9, (2019), 1-10 https://doi.org/10.1038/s41598-018-37553-z
  9. Ratih Dewi Saputri, Muhammad Fadjar Aldin, Tjitjik Srie Tjahjandarie, Eva Marliana, Mulyadi Tanjung, Aktivitas Antikanker Senyawa Pterokarpan dari Kulit Batang Aka Kalesi (Spatholobus ferrugineus), Jurnal Kimia Mulawarman, 20, 2, (2023), 69-74 https://doi.org/10.30872/jkm.v20i2.920
  10. P. C. Agu, C. A. Afiukwa, O. U. Orji, E. M. Ezeh, I. H. Ofoke, C. O. Ogbu, E. I. Ugwuja, P. M. Aja, Molecular docking as a tool for the discovery of molecular targets of nutraceuticals in diseases management, Scientific Reports, 13, (2023), 13398 https://doi.org/10.1038/s41598-023-40160-2
  11. Jordy Homing Lam, Vsevolod Katritch, Navigating structure-based drug discovery with emerging innovations in approaches, Drug Discovery Today, 2, (2025), 29 https://doi.org/10.1038/s44386-025-00031-4
  12. Resti Wulan Dari, Rosario Trijuliamos Manalu, Erwi Putri Setyaningsih, Penentuan Aktivitas dan Potensi Senyawa Kalkon Daun Jambu Air (Eugenia aquea Burm f) Terhadap Sel T47D Kanker Payudara Secara In Silico, Sainstech Farma: Jurnal Ilmu Kefarmasian, 18, 1, (2025), 1-9
  13. Xuan-Yu Meng, Hong-Xing Zhang, Mihaly Mezei Mezei, Meng Cui, Molecular Docking: A Powerful Approach for Structure-Based Drug Discovery, Current Computer-Aided Drug Design, 7, 2, (2011), 146-157 http://dx.doi.org/10.2174/157340911795677602
  14. Zhiyan Xiao, Susan L. Morris-Natschke, Kuo-Hsiung Lee, Strategies for the Optimization of Natural Leads to Anticancer Drugs or Drug Candidates, Medicinal Research Reviews, 36, 1, (2017), 32-91 https://doi.org/10.1002/med.21377
  15. Y. Zheng, M. Zhu, S. Srinivasan, J. C. Nwachukwu, V. Cavett, J. Min, K. E. Carlson, P. Wang, C. Dong, J. A. Katzenellenbogen, K. W. Nettles, H. B. Zhou, Development of selective estrogen receptor modulator (SERM)-like activity through an indirect mechanism of estrogen receptor antagonism: defining the binding mode of 7-oxabicyclo[2.2.1]hept-5-ene scaffold core ligands, ChemMedChem, 7, 6, (2012), 1094-1100 https://doi.org/10.1002/cmdc.201200048
  16. Daniel P. McDougal, Jordan L. Pederick, Scott J. Novick, Blagojce Jovcevski, Annmaree K. Warrender, Bruce D. Pascal, Patrick R. Griffin, John B. Bruning, A ternary switch model governing ERα ligand binding domain conformation, Nature Communications, 16, (2025), 10363 https://doi.org/10.1038/s41467-025-65323-9
  17. Natthakan Thongon, Nittaya Boonmuen, Kanoknetr Suksen, Patsorn Wichit, Arthit Chairoungdua, Patoomratana Tuchinda, Apichart Suksamrarn, Wipawee Winuthayanon, Pawinee Piyachaturawat, Selective Estrogen Receptor Modulator (SERM)-like Activities of Diarylheptanoid, a Phytoestrogen from Curcuma comosa, in Breast Cancer Cells, Pre-osteoblast Cells, and Rat Uterine Tissues, Journal of Agricultural and Food Chemistry, 65, 17, (2017), 3490-3496 https://doi.org/10.1021/acs.jafc.7b00769
  18. Paweł Śliwa, Magdalena Dziurzyńska, Rafał Kurczab, Katarzyna Kucwaj-Brysz, The Pivotal Distinction between Antagonists’ and Agonists’ Binding into Dopamine D4 Receptor—MD and FMO/PIEDA Studies, International Journal of Molecular Sciences, 25, 2, (2024), 746 https://doi.org/10.3390/ijms25020746
  19. Scott J. Lusher, Hans C. A. Raaijmakers, Diep Vu-Pham, Koen Dechering, Tsang Wai Lam, Angus R. Brown, Niall M. Hamilton, Olaf Nimz, Rolien Bosch, Ross McGuire, Arthur Oubrie, Jacob de Vlieg, Structural Basis for Agonism and Antagonism for a Set of Chemically Related Progesterone Receptor Modulators, Journal of Biological Chemistry, 286, 40, (2011), 35079-35086 https://doi.org/10.1074/jbc.M111.273029
  20. Luca Pinzi, Giulio Rastelli, Molecular Docking: Shifting Paradigms in Drug Discovery, International Journal of Molecular Sciences, 20, 18, (2019), 4331 https://doi.org/10.3390/ijms20184331
  21. Douglas B. Kitchen, Hélène Decornez, John R. Furr, Jürgen Bajorath, Docking and scoring in virtual screening for drug discovery: methods and applications, Nature Reviews Drug Discovery, 3, (2004), 935-949 https://doi.org/10.1038/nrd1549
  22. Christopher A. Lipinski, Franco Lombardo, Beryl W. Dominy, Paul J. Feeney, Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings, Advanced Drug Delivery Reviews, 46, 1-3, (2001), 3-26 https://doi.org/10.1016/S0169-409X(00)00129-0
  23. Lakshmi Kumari, Yash Choudhari, Preeti Patel, Ghanshyam Das Gupta, Dilpreet Singh, Jessica M. Rosenholm, Kuldeep Kumar Bansal, Balak Das Kurmi, Advancement in Solubilization Approaches: A Step towards Bioavailability Enhancement of Poorly Soluble Drugs, Life, 13, 5, (2023), 1099 https://doi.org/10.3390/life13051099
  24. Kalirajan Rajagopal, Anandarajagopal Kalusalingam, Anubhav Raj Bharathidasan, Aadarsh Sivaprakash, Krutheesh Shanmugam, Monall Sundaramoorthy, Gowramma Byran, In Silico Drug Design of Anti-Breast Cancer Agents, Molecules, 28, 10, (2023), 4175 https://doi.org/10.3390/molecules28104175
  25. Laila Khamsatul Muharrami, Mardi Santoso, Sri Fatmawati, Chemical profiles, in silico pharmacokinetic and toxicity prediction of bioactive compounds from Boesenbergia rotunda, Case Studies in Chemical and Environmental Engineering, 10, (2024), 100992 https://doi.org/10.1016/j.cscee.2024.100992

Last update:

No citation recorded.

Last update: 2026-05-31 12:56:55

No citation recorded.