Eksplorasi Senyawa Alami sebagai Lead Antikanker Payudara dengan Pendekatan In Silico
Abstract:
Purpose: This study aimed to explore the potential of natural compounds as lead candidates for breast cancer therapy through a medicinal chemistry framework using in silico methods, with the goal of identifying safer and more effective alternatives to conventional treatments.
Methodology: A qualitative library-based research design was employed using a systematic literature review of 15 primary national and international journal articles published between 2020 and 2025. The computational tools used in the study included AutoDock Vina and PyRx for molecular docking and virtual screening, SwissADME and pkCSM for ADMET predictions, and GROMACS for molecular dynamics simulations.
Results: Several natural compounds, including berberine, ellagic acid, camptothecin, and kaempferol, exhibited strong binding affinities toward key breast cancer molecular targets, such as estrogen receptor (ER), progesterone receptor (PR), HER2, and PD-L1. These compounds formed stable ligand–receptor complexes and showed favorable pharmacokinetic properties, conforming to Lipinski’s Rule of Five, thereby suggesting their viability as lead candidates for further development.
Conclusions: This study highlights the promising potential of selected natural compounds as lead structures for breast cancer drug development. The integration of molecular docking, pharmacokinetic prediction, and dynamic simulation provides a robust platform for early phase drug discovery.
Limitations: The primary limitation of this study is that in silico simulations do not fully capture complex biological interactions within the human body, including metabolic pathways and immune system responses.
Contribution: his study contributes to the fields of medicinal chemistry and pharmaceutical sciences by offering updated insights into the utility of natural compounds as anti-breast cancer agents.
Downloads

This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.
Amin, S., Abidin, A. T., & Fathurohman, M. (2024). Prediksi In silico Aktivitas Antikanker Payudara dari Metabolit Sekunder Tanaman Babandotan ( Ageratum conyzoides L .). 4, 267–282.
Amin, S., Aryanti, R., & Aprilia, A. Y. (2023). Studi In silico Senyawa yang Terkandung dalam Kulit Buah Manggis (Garcinia mangostana L.) Sebagai Antikanker Payudara. Prosiding Seminar Nasional Diseminasi Penelitian, 3(September), 2964–6154. https://zlab.umassmei
Amin, S., Hurry, Z. A. Z., Sumantri, T. A., & Fauzi, R. A. (2024). Studi Komputasional Senyawa Flavonoid Tanaman Obat sebagai Kandidat Agen Antidiabetik. Jurnal Ilmu Medis Indonesia, 4(1), 21-40. doi:10.35912/jimi.v4i1.4553
Amin, S., Muhtar, N. L. N., Sumardiawan, D. K., & Yulianingsih, T. S. Y. (2024). Studi In Silico Senyawa Daun Salam Sebagai Antidiabetes Melalui Mekanisme Inhibitor SGLT-2. Jurnal Ilmu Medis Indonesia, 4(1), 21-29. doi:10.35912/jimi.v4i1.4539
Amin, S., Supriatna, G. T., Ardian, M. I., & Abdurrahman, M. I. (2024). Potensi Senyawa Turunan Terpenoid sebagai Agen Anti-Kanker. Jurnal Ilmu Medis Indonesia, 4(1), 53-61. doi:10.35912/jimi.v4i1.4551
Amin, S., Wihdatunnisa, I., Aisyah, R., & Kurniawan, Y. S. (2024). Potensi Senyawa Kuersetin sebagai Antikanker Payudara melalui Pendekatan Molecular Docking. Jurnal Ilmu Medis Indonesia, 4(1), 41-51. doi:10.35912/jimi.v4i1.4565
Anandika Lestari, O., Sri Palupi, N., Setiyono, A., Kusnandar, F., & Dewi Yuliana, N. (2024). LC-MS metabolomics and molecular docking approaches to identify antihyperglycemic and antioxidant compounds from Melastoma malabathricum L. Leaf. Saudi Journal of Biological Sciences, 31(8), 104047. https://doi.org/10.1016/j.sjbs.2024.104047
Azmal, M., Paul, J. K., Prima, F. S., Talukder, O. F., & Ghosh, A. (2024). An in silico molecular docking and simulation study to identify potential anticancer phytochemicals targeting the RAS signaling pathway. PLoS ONE, 19(9 September), 1–27. https://doi.org/10.1371/journal.pone.0310637
Chhikara, B. S., & Parang, K. (2023). Global Cancer Statistics 2022: the trends projection analysis. Chemical Biology Letters, 10(1).
Chunarkar-Patil, P., Kaleem, M., Mishra, R., Ray, S., Ahmad, A., Verma, D., Bhayye, S., Dubey, R., Singh, H. N., & Kumar, S. (2024). Anticancer Drug discovery Based on Natural Products: From Computational Approaches to Clinical Studies. Biomedicines, 12(1), 1–35. https://doi.org/10.3390/biomedicines12010201
Dai, S. X., Li, W. X., Han, F. F., Guo, Y. C., Zheng, J. J., Liu, J. Q., Wang, Q., Gao, Y. D., Li, G. H., & Huang, J. F. (2016). In silico identification of anti-cancer compounds and plants from traditional Chinese medicine database. Scientific Reports, 6(December 2015), 1–11. https://doi.org/10.1038/srep25462
Effiong, M. E., Bella-Omunagbe, M., Afolabi, I. S., & Chinedu, S. N. (2024). In silico evaluation of potential breast cancer receptor antagonists from GC-MS and HPLC identified compounds in Pleurotus ostreatus extracts. RSC Advances, 14(33), 23744–23771. https://doi.org/10.1039/d4ra03832k
Hashemi, S. M. J., Barzegar, A., Akhtari, J., & Mellati, A. (2024). In Silico Discovery of Multi-Target Natural Ligands and Efficient siRNA Design for Overcoming Drug Resistance in Breast Cancer via Local Therapy. bioRxiv, 2024.2011. 2010.622866. doi:https://doi.org/10.1101/2024.11.10.622866
Jabir, M., Balakrishnan, V., Krishnamoorthy, K., Kumar, A., & Abraham, P. R. (2024). Factors influencing participation of elderly population in mass drug administration for lymphatic filariasis: a cross-sectional study. Frontiers in Pharmacology, 15(November), 1–11. https://doi.org/10.3389/fphar.2024.1429653
Millan-Casarrubias, E. J., García-Tejeda, Y. V., González-De la Rosa, C. H., Ruiz-Mazón, L., Hernández-Rodríguez, Y. M., & Cigarroa-Mayorga, O. E. (2025). Molecular docking and Pharmacological In silico Evaluation of Camptothecin and Related Ligands as Promising HER2-Targeted Therapies for Breast cancer. Current Issues in Molecular Biology, 47(3), 1–20. https://doi.org/10.3390/cimb47030193
Othman, B., Beigh, S., Albanghali, M. A., Sindi, A. A. A., Shanawaz, M. A., Ibahim, M. A. E. M., Marghani, D., Kofiah, Y., Iqbal, N., & Rashid, H. (2025). Comprehensive pharmacokinetic profiling and molecular docking analysis of natural bioactive compounds targeting oncogenic biomarkers in breast cancer. Scientific Reports, 15(1), 1–19. https://doi.org/10.1038/s41598-024-84401-4
Park, Y., Jeong, J., Seong, S., & Kim, W. (2021). In silico evaluation of natural compounds for an acidic extracellular environment in human breast cancer. Cells, 10(10), 1–13. https://doi.org/10.3390/cells10102673
Putri, A. R. C., Ladesvita, F., & Burmanajaya, B. (2024). Relationship between Lifestyle with Quality of Life in Breast cancer Patients. Jurnal Berita Ilmu Keperawatan, 17(2), 170–179. https://doi.org/10.23917/bik.v17i2.5256
Setyoningrum, R. A., Lestari, S. R., Sari, R. K., Visuddho, V., Hapsari, R., & Chafid, A. P. P. (2024). White Blood Cell Count and Neutrophil-Lymphocyte Ratio in Children with Complicated and Uncomplicated Pneumonia. Jurnal Ilmu Medis Indonesia, 4(1), 1-7.
Sohrab, S. S., & Kamal, M. A. (2022). Screening, Docking, and Molecular dynamics Study of Natural compounds as an Anti-HER2 for the Management of Breast cancer. Life, 12(11). https://doi.org/10.3390/life12111729
Sung, H., Ferlay, J., Siegel, R. L., Laversanne, M., Soerjomataram, I., Jemal, A., & Bray, F. (2021). 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), 209–249. https://doi.org/10.3322/caac.21660
Tran, L. T. T., Dang, N. Y. T., Nguyen Le, N. T., Nguyen, H. T., Ho, D. V., Do, T. T., Tran, M. H., Nguyen, T. K., & Pham, P. T. V. (2022). In silico and in Vitro Evaluation of Alkaloids from Goniothalamus elegans Ast. for Breast cancer Treatment. Natural Product Communications, 17(3). https://doi.org/10.1177/1934578X221088110
Vernanda, G. A., & Sari, I. W. W. (2024). Studi Komparatif: Manajemen Diri pada Pasien Diabetes Mellitus Tipe II di Wilayah Perkotaan dan Pedesaan. Jurnal Ilmu Medis Indonesia, 3(2), 47-57. doi:10.35912/jimi.v3i2.2996
Widyananda, M. H., Fatchiyah, F., Muflikhah, L., Ulfa, S. M., & Widodo, N. (2023). Computational examination to reveal Kaempferol as the most potent active compound from Euphorbia hirta against breast cancer by targeting AKT1 and ER?. Egyptian Journal of Basic and Applied Sciences, 10(1), 753-767. doi:http://dx.doi.org/10.1080/2314808X.2023.2272385
Yeni, Y. T. N., Wardana, F. A., & Pawana, I. P. A. (2025). Pengaruh Circuit Training terhadap Peningkatan Agility pada Pemain Futsal. Jurnal Ilmu Medis Indonesia, 4(1), 9-20. doi:10.35912/jimi.v4i1.4393
- Amin, S., Abidin, A. T., & Fathurohman, M. (2024). Prediksi In silico Aktivitas Antikanker Payudara dari Metabolit Sekunder Tanaman Babandotan ( Ageratum conyzoides L .). 4, 267–282.
- Amin, S., Aryanti, R., & Aprilia, A. Y. (2023). Studi In silico Senyawa yang Terkandung dalam Kulit Buah Manggis (Garcinia mangostana L.) Sebagai Antikanker Payudara. Prosiding Seminar Nasional Diseminasi Penelitian, 3(September), 2964–6154. https://zlab.umassmei
- Amin, S., Hurry, Z. A. Z., Sumantri, T. A., & Fauzi, R. A. (2024). Studi Komputasional Senyawa Flavonoid Tanaman Obat sebagai Kandidat Agen Antidiabetik. Jurnal Ilmu Medis Indonesia, 4(1), 21-40. doi:10.35912/jimi.v4i1.4553
- Amin, S., Muhtar, N. L. N., Sumardiawan, D. K., & Yulianingsih, T. S. Y. (2024). Studi In Silico Senyawa Daun Salam Sebagai Antidiabetes Melalui Mekanisme Inhibitor SGLT-2. Jurnal Ilmu Medis Indonesia, 4(1), 21-29. doi:10.35912/jimi.v4i1.4539
- Amin, S., Supriatna, G. T., Ardian, M. I., & Abdurrahman, M. I. (2024). Potensi Senyawa Turunan Terpenoid sebagai Agen Anti-Kanker. Jurnal Ilmu Medis Indonesia, 4(1), 53-61. doi:10.35912/jimi.v4i1.4551
- Amin, S., Wihdatunnisa, I., Aisyah, R., & Kurniawan, Y. S. (2024). Potensi Senyawa Kuersetin sebagai Antikanker Payudara melalui Pendekatan Molecular Docking. Jurnal Ilmu Medis Indonesia, 4(1), 41-51. doi:10.35912/jimi.v4i1.4565
- Anandika Lestari, O., Sri Palupi, N., Setiyono, A., Kusnandar, F., & Dewi Yuliana, N. (2024). LC-MS metabolomics and molecular docking approaches to identify antihyperglycemic and antioxidant compounds from Melastoma malabathricum L. Leaf. Saudi Journal of Biological Sciences, 31(8), 104047. https://doi.org/10.1016/j.sjbs.2024.104047
- Azmal, M., Paul, J. K., Prima, F. S., Talukder, O. F., & Ghosh, A. (2024). An in silico molecular docking and simulation study to identify potential anticancer phytochemicals targeting the RAS signaling pathway. PLoS ONE, 19(9 September), 1–27. https://doi.org/10.1371/journal.pone.0310637
- Chhikara, B. S., & Parang, K. (2023). Global Cancer Statistics 2022: the trends projection analysis. Chemical Biology Letters, 10(1).
- Chunarkar-Patil, P., Kaleem, M., Mishra, R., Ray, S., Ahmad, A., Verma, D., Bhayye, S., Dubey, R., Singh, H. N., & Kumar, S. (2024). Anticancer Drug discovery Based on Natural Products: From Computational Approaches to Clinical Studies. Biomedicines, 12(1), 1–35. https://doi.org/10.3390/biomedicines12010201
- Dai, S. X., Li, W. X., Han, F. F., Guo, Y. C., Zheng, J. J., Liu, J. Q., Wang, Q., Gao, Y. D., Li, G. H., & Huang, J. F. (2016). In silico identification of anti-cancer compounds and plants from traditional Chinese medicine database. Scientific Reports, 6(December 2015), 1–11. https://doi.org/10.1038/srep25462
- Effiong, M. E., Bella-Omunagbe, M., Afolabi, I. S., & Chinedu, S. N. (2024). In silico evaluation of potential breast cancer receptor antagonists from GC-MS and HPLC identified compounds in Pleurotus ostreatus extracts. RSC Advances, 14(33), 23744–23771. https://doi.org/10.1039/d4ra03832k
- Hashemi, S. M. J., Barzegar, A., Akhtari, J., & Mellati, A. (2024). In Silico Discovery of Multi-Target Natural Ligands and Efficient siRNA Design for Overcoming Drug Resistance in Breast Cancer via Local Therapy. bioRxiv, 2024.2011. 2010.622866. doi:https://doi.org/10.1101/2024.11.10.622866
- Jabir, M., Balakrishnan, V., Krishnamoorthy, K., Kumar, A., & Abraham, P. R. (2024). Factors influencing participation of elderly population in mass drug administration for lymphatic filariasis: a cross-sectional study. Frontiers in Pharmacology, 15(November), 1–11. https://doi.org/10.3389/fphar.2024.1429653
- Millan-Casarrubias, E. J., García-Tejeda, Y. V., González-De la Rosa, C. H., Ruiz-Mazón, L., Hernández-Rodríguez, Y. M., & Cigarroa-Mayorga, O. E. (2025). Molecular docking and Pharmacological In silico Evaluation of Camptothecin and Related Ligands as Promising HER2-Targeted Therapies for Breast cancer. Current Issues in Molecular Biology, 47(3), 1–20. https://doi.org/10.3390/cimb47030193
- Othman, B., Beigh, S., Albanghali, M. A., Sindi, A. A. A., Shanawaz, M. A., Ibahim, M. A. E. M., Marghani, D., Kofiah, Y., Iqbal, N., & Rashid, H. (2025). Comprehensive pharmacokinetic profiling and molecular docking analysis of natural bioactive compounds targeting oncogenic biomarkers in breast cancer. Scientific Reports, 15(1), 1–19. https://doi.org/10.1038/s41598-024-84401-4
- Park, Y., Jeong, J., Seong, S., & Kim, W. (2021). In silico evaluation of natural compounds for an acidic extracellular environment in human breast cancer. Cells, 10(10), 1–13. https://doi.org/10.3390/cells10102673
- Putri, A. R. C., Ladesvita, F., & Burmanajaya, B. (2024). Relationship between Lifestyle with Quality of Life in Breast cancer Patients. Jurnal Berita Ilmu Keperawatan, 17(2), 170–179. https://doi.org/10.23917/bik.v17i2.5256
- Setyoningrum, R. A., Lestari, S. R., Sari, R. K., Visuddho, V., Hapsari, R., & Chafid, A. P. P. (2024). White Blood Cell Count and Neutrophil-Lymphocyte Ratio in Children with Complicated and Uncomplicated Pneumonia. Jurnal Ilmu Medis Indonesia, 4(1), 1-7.
- Sohrab, S. S., & Kamal, M. A. (2022). Screening, Docking, and Molecular dynamics Study of Natural compounds as an Anti-HER2 for the Management of Breast cancer. Life, 12(11). https://doi.org/10.3390/life12111729
- Sung, H., Ferlay, J., Siegel, R. L., Laversanne, M., Soerjomataram, I., Jemal, A., & Bray, F. (2021). 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), 209–249. https://doi.org/10.3322/caac.21660
- Tran, L. T. T., Dang, N. Y. T., Nguyen Le, N. T., Nguyen, H. T., Ho, D. V., Do, T. T., Tran, M. H., Nguyen, T. K., & Pham, P. T. V. (2022). In silico and in Vitro Evaluation of Alkaloids from Goniothalamus elegans Ast. for Breast cancer Treatment. Natural Product Communications, 17(3). https://doi.org/10.1177/1934578X221088110
- Vernanda, G. A., & Sari, I. W. W. (2024). Studi Komparatif: Manajemen Diri pada Pasien Diabetes Mellitus Tipe II di Wilayah Perkotaan dan Pedesaan. Jurnal Ilmu Medis Indonesia, 3(2), 47-57. doi:10.35912/jimi.v3i2.2996
- Widyananda, M. H., Fatchiyah, F., Muflikhah, L., Ulfa, S. M., & Widodo, N. (2023). Computational examination to reveal Kaempferol as the most potent active compound from Euphorbia hirta against breast cancer by targeting AKT1 and ER?. Egyptian Journal of Basic and Applied Sciences, 10(1), 753-767. doi:http://dx.doi.org/10.1080/2314808X.2023.2272385
- Yeni, Y. T. N., Wardana, F. A., & Pawana, I. P. A. (2025). Pengaruh Circuit Training terhadap Peningkatan Agility pada Pemain Futsal. Jurnal Ilmu Medis Indonesia, 4(1), 9-20. doi:10.35912/jimi.v4i1.4393
Most read articles by the same author(s)
- Saeful Amin, Zulfan Alfairuz Zabbady Hurry, Tri Adi Sumantri, Rifqi Ahmad Fauzi, Studi Komputasional Senyawa Flavonoid Tanaman Obat sebagai Kandidat Agen Antidiabetik , Jurnal Ilmu Medis Indonesia: Vol. 4 No. 1 (2024): September
- Saeful Amin, Nenden Laila Nurafifah Muhtar, Dhiyaa Kaamilah Sumardiawan, Tipani Sri Yulianingsih Yulianingsih, Studi In Silico Senyawa Daun Salam Sebagai Antidiabetes Melalui Mekanisme Inhibitor SGLT-2 , Jurnal Ilmu Medis Indonesia: Vol. 4 No. 1 (2024): September
- Saeful Amin, Imelda Wihdatunnisa, Rohmah Aisyah, Yoga Sugama Kurniawan, Potensi Senyawa Kuersetin sebagai Antikanker Payudara melalui Pendekatan Molecular Docking , Jurnal Ilmu Medis Indonesia: Vol. 4 No. 1 (2024): September
- Saeful Amin, Popih Heryanto, Rahil Athaya, Nabila Ainul Fitri, Perkembangan Terkini dalam Desain Obat Berbasis Kimia Medisinal , Jurnal Ilmu Medis Indonesia: Vol. 4 No. 1 (2024): September
- Saeful Amin, Delya Pujiyani, Nisrina Putri Rusiyana, Shafa Meyliana Azzahra, Evaluasi Potensi Antikanker Senyawa Daun Kelor melalui Kimia Medisinal , Jurnal Ilmu Medis Indonesia: Vol. 4 No. 1 (2024): September
- Saeful Amin, Syifa Mustafidah, Nazelia Saila Nabila, Cici Maharani, Review Artikel: Pendekatan in Silico dalam Kimia Medisinal tentang Resistensi Antibiotik , Jurnal Ilmu Medis Indonesia: Vol. 4 No. 1 (2024): September
- Saeful Amin, Galuh Taruna Supriatna, Mohamad Idwar Ardian, Muhammad Iqmal Abdurrahman, Potensi Senyawa Turunan Terpenoid sebagai Agen Anti-Kanker , Jurnal Ilmu Medis Indonesia: Vol. 4 No. 1 (2024): September