Binding Affinity of Potato, Cassava, and Purple Yam Phytochemicals to Fusarium Proteins: Insights from Molecular Docking

Gilang Vaza Benatar; Abdul Hakim; Siti Nur Anisah; Roni Maulan Sidiq; Rafif Naufal Assadel Tarigan

doi:10.29303/jbt.v25i4.10096

Binding Affinity of Potato, Cassava, and Purple Yam Phytochemicals to Fusarium Proteins: Insights from Molecular Docking

Authors

Gilang Vaza Benatar , Abdul Hakim , Siti Nur Anisah , Roni Maulan Sidiq , Rafif Naufal Assadel Tarigan

DOI:

10.29303/jbt.v25i4.10096

Published:

2025-10-09

Issue:

Vol. 25 No. 4 (2025): in Progress

Keywords:

Anthocyanins, Bioinformatics, Phytopathogens, Phytochemistry, Secondary metabolites

Articles

Downloads

pdf

How to Cite

Benatar, G. V., Hakim, A., Anisah, S. N., Sidiq, R. M., & Tarigan, R. N. A. (2025). Binding Affinity of Potato, Cassava, and Purple Yam Phytochemicals to Fusarium Proteins: Insights from Molecular Docking. Jurnal Biologi Tropis, 25(4), 5325–5338. https://doi.org/10.29303/jbt.v25i4.10096

Download Citation

Downloads

Download data is not yet available.

Metrics

Metrics Loading ...

Abstract

Fusarium species are destructive plant pathogens responsible for severe crop losses thereby posing a critical threat to global food security. Sustainable strategies to control Fusarium-induced diseases are urgently needed due to limitations of synthetic fungicides. This study investigated the interaction of phytochemicals from potato (Solanum tuberosum), cassava (Manihot esculenta), and purple yam (Dioscorea alata) with three Fusarium proteins: LaeA, Pep2, and VeA. Protein structures were modeled and validated using stereochemical analyses, followed by molecular docking with representative metabolites, including pyrogallol, cyclogallipharaol, scopoletin, linamarin, cyanidin-3-glucoside, and peonidin-3-glucoside. Docking results showed that potato metabolites exhibited moderate binding activity, cassava metabolites displayed broader inhibitory potential, and purple yam anthocyanins demonstrated the strongest affinities (–6.7 to –7.4 kcal/mol) through multiple hydrogen bonds, hydrophobic contacts, and electrostatic interactions. Among the targets, Pep2 showed consistently stable interactions, while LaeA and VeA exhibited greater flexibility but remained responsive to anthocyanins. These findings highlight the potential of edible crop-derived phytochemicals, particularly anthocyanins and scopoletin, as eco-friendly antifungal agents. The structural basis provided here supports future experimental validation and the development of sustainable crop protection strategies.

References

Atkovska, K., Samsonov, S. A., Paszkowski-Rogacz, M., & Pisabarro, M. T. (2014). Multipose binding in molecular docking. International Journal of Molecular Sciences, 15(2), 2622–2645. https://doi.org/10.3390/ijms15022622

Bisen, K., Pal, R. K., & Silas, V. J. (2023). Biofortified Vermicompost Mediated Induced Resistance Response in Tomato against Fusarium oxysporum f. sp. lycopersici. International Journal of Environment and Climate Change, 13(12), 735–751. https://doi.org/10.9734/ijecc/2023/v13i123736

Bolia, A., Gerek, Z. N., & Ozkan, S. B. (2014). BP-dock: A flexible docking scheme for exploring protein-ligand interactions based on unbound structures. Journal of Chemical Information and Modeling, 54(3), 913–925. https://doi.org/10.1021/ci4004927

Dhar, A., Sisk, T. R., & Robustelli, P. (2025). Ensemble Docking for Intrinsically Disordered Proteins. Journal of Chemical Information and Modeling, 65(13), 6847–6860. https://doi.org/10.1021/acs.jcim.5c00370

Ekwomadu, T. I., & Mwanza, M. (2023). Fusarium Fungi Pathogens, Identification, Adverse Effects, Disease Management, and Global Food Security: A Review of the Latest Research. Agriculture (Switzerland), 13(9). https://doi.org/10.3390/agriculture13091810

Fan, J., Fu, A., & Zhang, L. (2019). Progress in molecular docking. Quantitative Biology, 7(2), 83–89. https://doi.org/10.1007/s40484-019-0172-y

Fraser-Smith, S., Czislowski, E., Meldrum, R. A., Zander, M., O’Neill, W., Balali, G. R., & Aitken, E. A. B. (2014). Sequence variation in the putative effector gene SIX8 facilitates molecular differentiation of Fusarium oxysporum f. sp. cubense. Plant Pathology, 63(5), 1044–1052. https://doi.org/10.1111/ppa.12184

Hussain, M. A., Li, L., Kalu, A., Wu, X., & Naumovski, N. (2025). Sustainable Food Security and Nutritional Challenges. Sustainability (Switzerland), 17(3), 1–14. https://doi.org/10.3390/su17030874

Hussein, B. R. M., Moustafa, A. H., Abdou, A., Drar, A. M., & Abdel-Raheem, S. A. A. (2024). Preparation, Agricultural Bioactivity Evaluation, Structure–Activity Relationships Estimation, and Molecular Docking of Some Quinazoline Compounds. Journal of Agricultural and Food Chemistry, 72(16), 8973–8982. https://doi.org/10.1021/acs.jafc.3c08840

Ikyenge, B. A., Samoh, F. T., Agbidye, I. G., & Asogwa, N. (2024). Antifungal Activity of Ethanolic Extract of Potato Peels on Fungi Causing Rot in Mango Fruits. Journal of Chemical Society of Nigeria, 49(6), 885–895. https://doi.org/10.46602/jcsn.v49i6.1016

Kingsley, L. J., Wilson, G. L., Essex, M. E., & Lill, M. A. (2015). Combining structure- and ligand-based approaches to improve site of metabolism prediction in CYP2C9 substrates. Pharmaceutical Research, 32(3), 986–1001. https://doi.org/10.1007/s11095-014-1511-3

Kurnianingsih, N., Ratnawati, R., Nazwar, T. A., Ali, M., & Fatchiyah, F. (2021). Purple Sweet Potatoes from East Java of Indonesia Revealed the Macronutrient, Anthocyanin Compound and Antidepressant Activity Candidate. Medical Archives, 75(2), 94–100. https://doi.org/10.5455/medarh.2021.75.94-100

Kusch, S., Qian, J., Loos, A., Kümmel, F., Spanu, P. D., & Panstruga, R. (2023). Long- term and rapid evolution in powdery mildew fungi. Molecular Ecology, 33. https://doi.org/10.1111/mec.16909

Madhushan, A., Weerasingha, D. B., Ilyukhin, E., Taylor, P. W. J., Ratnayake, A. S., Liu, J. K., & Maharachchikumbura, S. S. N. (2025). From Natural Hosts to Agricultural Threats: The Evolutionary Journey of Phytopathogenic Fungi. Journal of Fungi, 11(1), 1–29. https://doi.org/10.3390/jof11010025

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

Merhej, J., Urban, M., Dufresne, M., Hammond-Kosack, K. E., Richard-Forget, F., & Barreau, C. (2012). The velvet gene, FgVe1, affects fungal development and positively regulates trichothecene biosynthesis and pathogenicity in Fusarium graminearum. Molecular Plant Pathology, 13(4), 363–374. https://doi.org/10.1111/j.1364-3703.2011.00755.x

Mohidin, S. R. N. S. P., Moshawih, S., Hermansyah, A., Asmuni, M. I., Shafqat, N., & Ming, L. C. (2023). Cassava (Manihot esculenta Crantz): A Systematic Review for the Pharmacological Activities, Traditional Uses, Nutritional Values, and Phytochemistry. Journal of Evidence-Based Integrative Medicine, 28, 2515690X231206227. https://doi.org/10.1177/2515690X231206227

Nasr, B. N., Guillemain, H., Lagarde, N., Zagury, J. F., & Montes, M. (2013). Multiple structures for virtual ligand screening: Defining binding site properties-based criteria to optimize the selection of the query. Journal of Chemical Information and Modeling, 53(2), 293–311. https://doi.org/10.1021/ci3004557

Pan, K., Chen, J., Li, H., Xu, S., Wang, J., Yan, X., Zhao, Y., Jiang, H., Khan, A., Tahir Khan, M., Powell, C. A., Wen, R., & Zhang, M. (2025). Genomic and metabolomic insights into the biocontrol potential of Bacillus velezensis ZHR0 against sugarcane smut. Frontiers in Microbiology, 16(May), 1–17. https://doi.org/10.3389/fmicb.2025.1582763

Pfordt, A., Romero, L. R., Schiwek, S., Karlovsky, P., & von Tiedemann, A. (2020). Impact of environmental conditions and agronomic practices on the prevalence of fusarium species associated with ear-and stalk rot in maize. Pathogens, 9(3), 1–17. https://doi.org/10.3390/pathogens9030236

Resiani, N. M. D., Suryathi, N. W., & Iswara, P. G. A. R. (2025). Management of Major Pests and Diseases of Shallots by Utilizing Local - Natural Resources Towards a Sustainable Environment. IOP Conference Series: Earth and Environmental Science, 1452(1). https://doi.org/10.1088/1755-1315/1452/1/012026

Ribeiro, J. A., Albuquerque, A., Materatski, P., Patanita, M., Varanda, C. M. R., Félix, M. D. R., & Campos, M. D. (2022). Tomato Response to Fusarium spp. Infection under Field Conditions: Study of Potential Genes Involved. Horticulturae, 8(5), 1–13. https://doi.org/10.3390/horticulturae8050433

Samoh, F., Aloo, B., Isaac, A., & Nguemo, T. (2025). GC-MS Profile and Antibacterial Evaluation of the Ethanolic Extracts of Banana and Sweet Potato Peels. ChemClass Journal, 9, 660–671. https://doi.org/10.33003/chemclass-2025-0902/187

Savary, S., Willocquet, L., Pethybridge, S. J., Esker, P., McRoberts, N., & Nelson, A. (2019). The global burden of pathogens and pests on major food crops. Nature Ecology and Evolution, 3(3), 430–439. https://doi.org/10.1038/s41559-018-0793-y

Srinivas, C., Nirmala Devi, D., Narasimha Murthy, K., Mohan, C. D., Lakshmeesha, T. R., Singh, B. P., Kalagatur, N. K., Niranjana, S. R., Hashem, A., Alqarawi, A. A., Tabassum, B., Abd_Allah, E. F., & Chandra Nayaka, S. (2019). Fusarium oxysporum f. sp. lycopersici causal agent of vascular wilt disease of tomato: Biology to diversity– A review. Saudi Journal of Biological Sciences, 26(7), 1315–1324. https://doi.org/10.1016/j.sjbs.2019.06.002

Srivastav, V. K., Singh, V., & Tiwari, M. (2016). Recent Advancements in Docking Methodologies. https://doi.org/10.4018/978-1-5225-0115-2

Suarez, P. E. G., Siciliano, A., Spampinato, M., Maione, A., Guida, M., Libralato, G., & Galdiero, E. (2024). Ecotoxicity and Mutagenicity Assessment of Novel Antifungal Agents VT-1161 and T-2307. Molecules, 29(19), 1–10. https://doi.org/10.3390/molecules29194739

Uwineza, P. A., Kwiatkowska, M., Gwiazdowski, R., Stępień, Ł., Bryła, M., & Waśkiewicz, A. (2024). Field Assessment of Lamium album in Reducing Mycotoxin Biosynthesis in Winter Wheat Infected by Fusarium culmorum. Agriculture (Switzerland), 14(5), 1–13. https://doi.org/10.3390/agriculture14050647

Verma, A. K., Majid, A., Hossain, S., Ahmed, S. F., Ashid, M., Bhojiya, A. A., Ameta, S., Upadhyay, S. K., K.Srivastava, A., Kumar, N., Vishvakarma, Yadav, V. K., Teli, P. K., Harina, & Alam, M. (2021). Identification of 1 , 2 , 4-triazine and its derivatives against Lanosterol 14 - demethylase ( CYP51 ) property of Candida albicans : Influence on the development of new antifungal therapeutic strategies. August. https://doi.org/10.20944/preprints202108.0359.v1

Wang, G., Zhang, H., Wang, Y., Liu, F., Li, E., Ma, J., Yang, B., Zhang, C., Li, L., & Liu, Y. (2019). Requirement of LaeA, VeA, and VelB on Asexual Development, Ochratoxin A Biosynthesis, and Fungal Virulence in Aspergillus ochraceus. Frontiers in Microbiology, 10(November), 1–10. https://doi.org/10.3389/fmicb.2019.02759

Wang, J., Li, C., Qiu, R., Li, X., Zhao, J., Bai, J., Chen, Y., & Li, S. (2021). Complete genome sequence of a novel mitovirus from the phytopathogenic fungus Fusarium oxysporum. Archives of Virology, 166(11), 3211–3216. https://doi.org/10.1007/s00705-021-05210-y

License

This work is licensed under a Creative Commons Attribution 4.0 International License.

Jurnal Biologi Tropis is licensed under a Creative Commons Attribution 4.0 International License.

The copyright of the received article shall be assigned to the author as the owner of the paper. The intended copyright includes the right to publish the article in various forms (including reprints). The journal maintains the publishing rights to the published articles.

Authors are permitted to disseminate published articles by sharing the link/DOI of the article at the journal. Authors are allowed to use their articles for any legal purposes deemed necessary without written permission from the journal with an acknowledgment of initial publication to this journal.

Binding Affinity of Potato, Cassava, and Purple Yam Phytochemicals to Fusarium Proteins: Insights from Molecular Docking

Authors

DOI:

Published:

Issue:

Keywords:

Articles

Downloads

How to Cite

Downloads

Metrics

Abstract

References

License

Most read articles by the same author(s)

Similar Articles

Menu

Manuscript Template

visitor

Keywords

Mitra Kerja sama

Open Access Journals

Contact Us

Information

Share & Follow