Emerging Role of Artificial Intelligence in Natural Product-Based Drug Discovery

Main Article Content

Yelfi Anwar

Abstract

Background: Natural products remain an important source of therapeutic agents, but their discovery is constrained by chemical complexity, time-consuming isolation, difficult structure elucidation, and high attrition rates. Artificial intelligence (AI), including machine learning, deep learning, graph neural networks, and generative AI, offers computational approaches to address these challenges. Method: This narrative review examines peer-reviewed, English-language literature published between 2021 and 2026, retrieved from PubMed, Scopus, ScienceDirect, and Google Scholar. The selected literature was analyzed using thematic qualitative synthesis to identify AI applications, reported contributions, and persistent limitations across the natural product discovery pipeline. Problem Identification: Despite growing interest in AI-assisted drug discovery, the extent to which current methods address the limitations of conventional approaches remains uncertain. Key concerns include data quality, model reliability, interpretability, and the need for experimental validation. Results: AI applications cover target identification, biosynthetic gene cluster mining, virtual screening, structure elucidation, network pharmacology, generative molecular design, and absorption, distribution, metabolism, excretion, and toxicity (ADMET) prediction. These methods can help prioritize candidate compounds and predict potential biological activities. However, data scarcity and bias, inconsistent evaluation practices, limited interpretability, and insufficient experimental validation remain significant barriers. Explainable AI, multi-omics integration, and self-driving laboratories represent promising developments, although their practical contributions require further validation. Conclusion: AI can support and accelerate selected stages of natural product-based drug discovery but cannot replace experimental testing or the expertise of natural product chemists and pharmacologists.

Article Details

How to Cite
Anwar, Y. (2026). Emerging Role of Artificial Intelligence in Natural Product-Based Drug Discovery. Medical : Jurnal Kesehatan Dan Kedokteran, 3(2), 376–394. https://doi.org/10.69836/medical-jkk.v3i2.985
Section
Section Policy

References

Abbas, M. K. G., Rassam, A., Karamshahi, F., Abunora, R., & Abouseada, M. "The Role of AI in Drug Discovery." ChemBioChem 25, no. 14 (2024): e202300816. https://doi.org/10.1002/cbic.202300816.

Ang, M. Y., & Choo, S. W. "The Computational Revolution in Natural Product Research: A Data-Driven Roadmap for Next-Generation Drug Development." Biology 15, no. 8 (2026): 632. https://doi.org/10.3390/BIOLOGY15080632.

Artificial intelligence for natural product drug discovery and development: Current landscape, applications, and future directions. (2025). Intelligence-Based Medicine, 12, Article 100316. https://doi.org/10.1016/j.ibmed.2025.100316

Bellini, V., Cascella, M., Cutugno, F., Russo, M., Lanza, R., Compagnone, C., & Bignami, E. "Understanding Basic Principles of Artificial Intelligence: A Practical Guide for Intensivists." Acta Biomedica 93, no. 5 (2022): e2022297. https://doi.org/10.23750/abm.v93i5.13626.

Chakraborty, C., Bhattacharya, M., Lee, S. S., Wen, Z. H., & Lo, Y. H. "The Changing Scenario of Drug Discovery Using AI to Deep Learning: Recent Advancement, Success Stories, Collaborations, and Challenges." Molecular Therapy Nucleic Acids 35, no. 3 (2024): 102295. https://doi.org/10.1016/j.omtn.2024.102295.

Ekins, S. "The Lab of the Future: Self-Driving Labs for Molecule Discovery." GEN Biotechnology 3, no. 2 (2024): 83-86.

Ferreira, F. J. N., & Carneiro, A. S. "AI-Driven Drug Discovery: A Comprehensive Review." ACS Omega 10, no. 23 (2025): 23889-23903.

Fontanella, F., D'Alessandro, T., Nardone, E., De Stefano, C., Vicidomini, C., & Roviello, G. N. "Artificial Intelligence for Natural Products Drug Discovery in Neurodegenerative Therapies: A Review." Biomolecules 16, no. 1 (2026): 129. https://doi.org/10.3390/biom16010129.

Gangwal, A., & Lavecchia, A. "Artificial Intelligence in Natural Product Drug Discovery: Current Applications and Future Perspectives." Journal of Medicinal Chemistry 68, no. 4 (2025): 3948-3969.

Hasselgren, C., & Oprea, T. I. (2024). Artificial intelligence for drug discovery: Are we there yet? Annual Review of Pharmacology and Toxicology, 64, 527–550. https://doi.org/10.1146/annurev-pharmtox-040323-040828

Lavecchia, A. "Explainable Artificial Intelligence in Drug Discovery: Bridging Predictive Power and Mechanistic Insight." Wiley Interdisciplinary Reviews: Computational Molecular Science 15, no. 5 (2025): e70049. https://doi.org/10.1002/wcms.70049.

Lavecchia, A. (2026). Artificial intelligence-driven natural product drug discovery: From computational genome mining to clinical translation. Medicinal Research Reviews. https://doi.org/10.1002/med.70098

Mullowney, M. W., Duncan, K. R., Elsayed, S. S., Garg, N., van der Hooft, J. J. J., Martin, N. I., Meijer, D., et al. "Artificial Intelligence for Natural Product Drug Discovery." Nature Reviews Drug Discovery 22, no. 11 (2023): 895-916. https://doi.org/10.1038/s41573-023-00774-7.

Qadri, Y. A., Shaikh, S., Ahmad, K., Choi, I., Kim, S. W., & Vasilakos, A. V. (2025). Explainable artificial intelligence: A perspective on drug discovery. Pharmaceutics, 17(9), Article 1119. https://doi.org/10.3390/pharmaceutics17091119

Saldívar-González, F. I., Aldas-Bulos, V. D., Medina-Franco, J. L., & Plisson, F. (2022). Natural product drug discovery in the artificial intelligence era. Chemical Science, 13(6), 1526–1546. https://doi.org/10.1039/D1SC04471K

Santana, K., do Nascimento, L. D., Lima e Lima, A., Damasceno, V., Nahum, C., Braga, R. C., & Lameira, J. "Applications of Virtual Screening in Bioprospecting: Facts, Shifts, and Perspectives to Explore the Chemo-Structural Diversity of Natural Products." Frontiers in Chemistry 9 (2021): 662688. https://doi.org/10.3389/fchem.2021.662688.

Sourlos, N., Vliegenthart, R., Santinha, J., Klontzas, M. E., Cuocolo, R., Huisman, M., & van Ooijen, P. "Recommendations for the Creation of Benchmark Datasets for Reproducible Artificial Intelligence in Radiology." Insights into Imaging 15, no. 1 (2024): 248. https://doi.org/10.1186/s13244-024-01833-2.

Tang, X., Dai, H., Knight, E., Wu, F., Li, Y., Li, T., & Gerstein, M. "A Survey of Generative AI for De Novo Drug Design: New Frontiers in Molecule and Protein Generation." Briefings in Bioinformatics 25, no. 4 (2024): bbae338. https://doi.org/10.1093/bib/bbae338.

Yuan, X., Yang, X., Pan, Q., Luo, C., Luan, X., & Zhang, H. "Artificial Intelligence in Natural Products Research." Chinese Journal of Natural Medicines 23, no. 11 (2025): 1342-1357. https://doi.org/10.1016/S1875-5364(25)60902-2.

Zhang, O., Lin, H., Zhang, X., Wang, X., Wu, Z., Ye, Q., Zhao, W., et al. "Graph Neural Networks in Modern AI-Aided Drug Discovery." Chemical Reviews 125, no. 20 (2025): 10001-10103. https://doi.org/10.1021/acs.chemrev.5c00461.