Integrated Computational Approaches for Natural Product-Based Drug Discovery: Target Prediction, Network Pharmacology, Molecular Docking, and ADMET Prediction

Authors

  • Wahyuni Agus Universitas Negeri Makassar
  • Fauziah Hasdin Universitas Negeri Makassar

DOI:

https://doi.org/10.55927/eajmr.v5i8.279

Keywords:

Natural products, Target prediction, Network pharmacology, Molecular docking, ADMET prediction

Abstract

Natural products remain an important source of drug discovery, while advances in computational approaches have accelerated early-stage candidate identification. This review aims to provide an integrated overview of target prediction, network pharmacology, molecular docking, and ADMET prediction within a unified computational workflow for natural product-based drug discovery. A narrative literature review was conducted by analyzing peer-reviewed articles published between 2015 and 2025 from major scientific databases. The reviewed studies consistently demonstrate that integrating complementary in silico approaches improves target identification, mechanism elucidation, lead compound prioritization, and pharmacokinetic assessment before experimental validation. This integrated workflow provides a practical framework to support more efficient, systematic, and evidence-based natural product-driven drug discovery.

References

Atanasov, A. G., Zotchev, S. B., Dirsch, V. M., & Supuran, C. T. (2021). Natural products in drug discovery: advances and opportunities. Nature Reviews Drug Discovery, 20(3), 200–216. https://doi.org/10.1038/s41573-020-00114-z

Chen, Y., de Bruyn Kops, C., & Kirchmair, J. (2017). Data Resources for the Computer-Guided Discovery of Bioactive Natural Products. Journal of Chemical Information and Modeling, 57(9), 2099–2111. https://doi.org/10.1021/acs.jcim.7b00341

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, 7(1), 42717. https://doi.org/10.1038/srep42717

Gfeller, D., Grosdidier, A., Wirth, M., Daina, A., Michielin, O., & Zoete, V. (2014). SwissTargetPrediction: a web server for target prediction of bioactive small molecules. Nucleic Acids Research, 42(W1), W32–W38. https://doi.org/10.1093/nar/gku293

Hollingsworth, S. A., & Dror, R. O. (2018). Molecular Dynamics Simulation for All. Neuron, 99(6), 1129–1143. https://doi.org/10.1016/j.neuron.2018.08.011

Hopkins, A. L. (2008). Network pharmacology: the next paradigm in drug discovery. Nature Chemical Biology, 4(11), 682–690. https://doi.org/10.1038/nchembio.118

Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., Bridgland, A., Meyer, C., Kohl, S. A. A., Ballard, A. J., Cowie, A., Romera-Paredes, B., Nikolov, S., Jain, R., Adler, J., … Hassabis, D. (2021). Highly accurate protein structure prediction with AlphaFold. Nature, 596(7873), 583–589. https://doi.org/10.1038/s41586-021-03819-2

Liu, Z., Guo, F., Wang, Y., Li, C., Zhang, X., Li, H., Diao, L., Gu, J., Wang, W., Li, D., & He, F. (2016). BATMAN-TCM: a Bioinformatics Analysis Tool for Molecular mechanism of Traditional Chinese Medicine. Scientific Reports, 6(1), 21146. https://doi.org/10.1038/srep21146

Meng, X.-Y., Zhang, H.-X., Mezei, M., & Cui, M. (2011). Molecular Docking: A Powerful Approach for Structure-Based Drug Discovery. Current Computer Aided-Drug Design, 7(2), 146–157. https://doi.org/10.2174/157340911795677602

Newman, D. J., & Cragg, G. M. (2020). Natural Products as Sources of New Drugs over the Nearly Four Decades from 01/1981 to 09/2019. Journal of Natural Products, 83(3), 770–803. https://doi.org/10.1021/acs.jnatprod.9b01285

Nogales, C., Mamdouh, Z. M., List, M., Kiel, C., Casas, A. I., & Schmidt, H. H. H. W. (2022). Network pharmacology: curing causal mechanisms instead of treating symptoms. Trends in Pharmacological Sciences, 43(2), 136–150. https://doi.org/10.1016/j.tips.2021.11.004

Noor, F., Tahir ul Qamar, M., Ashfaq, U. A., Albutti, A., Alwashmi, A. S. S., & Aljasir, M. A. (2022). Network Pharmacology Approach for Medicinal Plants: Review and Assessment. Pharmaceuticals, 15(5), 572. https://doi.org/10.3390/ph15050572

Pagadala, N. S., Syed, K., & Tuszynski, J. (2017). Software for molecular docking: a review. Biophysical Reviews, 9(2), 91–102. https://doi.org/10.1007/s12551-016-0247-1

Paul, D., Sanap, G., Shenoy, S., Kalyane, D., Kalia, K., & Tekade, R. K. (2021). Artificial intelligence in drug discovery and development. Drug Discovery Today, 26(1), 80–93. https://doi.org/10.1016/j.drudis.2020.10.010

Pinzi, L., & Rastelli, G. (2019). Molecular Docking: Shifting Paradigms in Drug Discovery. International Journal of Molecular Sciences, 20(18), 4331. https://doi.org/10.3390/ijms20184331

Pires, D. E. V., Blundell, T. L., & Ascher, D. B. (2015). pkCSM: Predicting Small-Molecule Pharmacokinetic and Toxicity Properties Using Graph-Based Signatures. Journal of Medicinal Chemistry, 58(9), 4066–4072. https://doi.org /10.1021/acs.jmedchem.5b00104

Romano, J. D., & Tatonetti, N. P. (2019). Informatics and Computational Methods in Natural Product Drug Discovery: A Review and Perspectives. Frontiers in Genetics, 10. https://doi.org/10.3389/fgene.2019.00368

Ru, J., Li, P., Wang, J., Zhou, W., Li, B., Huang, C., Li, P., Guo, Z., Tao, W., Yang, Y., Xu, X., Li, Y., Wang, Y., & Yang, L. (2014). TCMSP: a database of systems pharmacology for drug discovery from herbal medicines. Journal of Cheminformatics, 6(1), 13. https://doi.org/10.1186/1758-2946-6-13

Sadybekov, A. V., & Katritch, V. (2023). Computational approaches streamlining drug discovery. Nature, 616(7958), 673–685.https://doi.org/10.1038/s41586-023-05905-z

Simoben, C. V., Babiaka, S. B., Moumbock, A. F. A., Namba-Nzanguim, C. T., Eni, D. B., Medina-Franco, J. L., Günther, S., Ntie-Kang, F., & Sippl, W. (2023). Challenges in natural product-based drug discovery assisted with in silico - based methods. RSC Advances, 13(45), 31578–31594. https://doi.org/10.1039/D3RA06831E

Szklarczyk, D., Kirsch, R., Koutrouli, M., Nastou, K., Mehryary, F., Hachilif, R., Gable, A. L., Fang, T., Doncheva, N. T., Pyysalo, S., Bork, P., Jensen, L. J., & von Mering, C. (2023). The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Research, 51(D1), D638–D646. https://doi.org/10.1093/nar/gkac100

Varadi, M., Anyango, S., Deshpande, M., Nair, S., Natassia, C., Yordanova, G., Yuan, D., Stroe, O., Wood, G., Laydon, A., Žídek, A., Green, T., Tunyasuvunakool, K., Petersen, S., Jumper, J., Clancy, E., Green, R., Vora, A., Lutfi, M., … Velankar, S. (2022). AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. Nucleic Acids Research, 50(D1), D439–D444. https://doi.org/10.1093/nar/gkab1061

Yang, H., Lou, C., Sun, L., Li, J., Cai, Y., Wang, Z., Li, W., Liu, G., & Tang, Y. (2019). admetSAR 2.0: web-service for prediction and optimization of chemical ADMET properties. Bioinformatics, 35(6), 1067–1069. https://doi.org/10.1093/ bioinformatics/bty707

Published

2026-08-29

Issue

Section

Articles