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Molecular Docking and In Vitro Study Revealed the Inhibition Mechanism of Cutinase of Fusarium oxsyporum f.sp lycopersici by Natural Compounds of Local Turmeric in Indonesia
Abstract
Fusarium oxysporum f.sp. lycopersici (FOL) is a significant threat to tomato plants with its cutinase enzyme playing a critical role in the penetration into plant root tissue. Addressing this issue requires the gathering of essential data. Molecular docking was used to see the interaction between ligand and cutinase structure, whereas the in vitro evaluation used the rhodamine B medium to see fluorescence light expression as an indicator of cutinase activity. The results of both methods revealed turmeric’s ability can disturb cutinase enzyme and its activity. Molecular docking revealed the type and value of binding interactions between turmeric’s natural components and the cutinase enzyme. This virtual simulation attempted to hypothesize that the ligands from turmeric could obstruct the active site of the cutinase structure in order to degrade the plant cutin polymer. The selected turmeric molecules were bisdemethoxycurcumin, calebin A, curcumin, and demethoxycurcumin, which had shown the ability to bind to the active site of cutinase, namely serine (Ser-142). After docking, these four compounds showed the lowest scores (negative), which indicated an efficient binding of the active site. Experiments were continued in the petri dishes and suggested that turmeric extract successfully expressed the fade of fluorescence light expression.
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Adhikari, T. B., Gao, A., Ingram, T., & Louws, F. J. (2020). Pathogenomics characterization of an emerging fungal pathogen, Fusarium oxysporum f. sp. lycopersici in greenhouse tomato production systems. Frontiers in Microbiology, 11:1995. DOI
Afifah, L., Aena, A. C., Saputro, N. W., Kurniati, A., Maryana, R., Lestari, A., Abadi, S., & Enri, U. (2022). Maize media enhance the conidia production of entomopathogenic fungi Lecanicillium lecanii also its effective to control the weevil Cylas formicarius (Fabricius) (Coleoptera: Brentidae). AGRIVITA Journal of Agricultural Science, 44(3), 513–525. DOI
Baker, P. J., & Montclare, J. K. (2010). Biotransformations Using Cutinase. In H. N. Cheng & R. A. Gross (Eds.), ACS Symposium Series (Vol. 1043, pp. 141–158). American Chemical Society. DOI
Budiman, C., Razak, R. A., Unggit, A. R. A., Razali, R., Suzery, M., Mokhtar, R. A. M., Lee, P.-C., & Utomo, D. H. (2022). Catalytic Properties of Caseinolytic Protease Subunit of Plasmodium knowlesi and Its Inhibition by a Member of δ-Lactone, Hyptolide. Molecules, 27(12), 3787. DOI
Chen, C., Long, L., Zhang, F., Chen, Q., Chen, C., Yu, X., Liu, Q., Bao, J., & Long, Z. (2018). Antifungal activity, main active components and mechanism of Curcuma longa extract against Fusarium graminearum. PLOS ONE, 13(3), e0194284. DOI
Chen, S., Su, L., Chen, J., & Wu, J. (2013). Cutinase: Characteristics, preparation, and application. Biotechnology Advances, 31(8), 1754–1767. DOI
Chitwood-Brown, J., Vallad, G. E., Lee, T. G., & Hutton, S. F. (2021). Breeding for resistance to Fusarium wilt of tomato: A review. Genes, 12(11), 1673. DOI
Dallakyan, S., & Olson, A. J. (2015). Small-Molecule Library Screening by Docking with PyRx. In J. E. Hempel, C. H. Williams, & C. C. Hong (Eds.), Chemical Biology (Vol. 1263, pp. 243–250). Springer New York. DOI
Dao, T. T., Sehgal, P., Tung, T. T., Møller, J. V., Nielsen, J., Palmgren, M., Christensen, S. B., & Fuglsang, A. T. (2016). Demethoxycurcumin Is A Potent Inhibitor of P-Type ATPases from Diverse Kingdoms of Life. PLOS ONE, 11(9), e0163260. DOI
Dar, A. M., & Mir, S. (2017). Molecular Docking: Approaches, Types, Applications and Basic Challenges. Journal of Analytical & Bioanalytical Techniques, 08(02). DOI
Degani, O. (2015). Production and Purification of Cutinase from Fusarium oxysporum Using Modified Growth Media and a Specific Cutinase Substrate. Advances in Bioscience and Biotechnology, 6(4), 245–258. DOI
Fourie, G., Steenkamp, E. T., Ploetz, R. C., Gordon, T. R., & Viljoen, A. (2011). Current status of the taxonomic position of Fusarium oxysporum formae specialis cubense within the Fusarium oxysporum complex. Infection, Genetics and Evolution, 11(3), 533–542. DOI
Güler Güney, İ., & Güldür, E. (2018). Inoculation Techniques for Assessing Pathogenicity of Rhizoctonia solani, Macrophomina phaseolina, Fusarium oxysporum and Fusarium solani on Pepper Seedlings. Türkiye Tarımsal Araştırmalar Dergisi, 5(1), 1–8. DOI
Hafizi, R., Salleh, B., & Latiffah, Z. (2013). Morphological and molecular characterization of Fusarium. solani and F. oxysporum associated with crown disease of oil palm. Brazilian Journal of Microbiology, 44(3), 959–968. DOI
Li, Y., Wei, J., Yang, H., Dai, J., & Ge, X. (2021). Molecular dynamics investigation of the interaction between Colletotrichum capsici cutinase and berberine suggested a mechanism for reduced enzyme activity. PLoS ONE, 16(2), e0163260. DOI
Mangat, H. K., Rani, M., Pathak, R. K., Yadav, I. S., Utreja, D., Chhuneja, P. K., & Chhuneja, P. (2022). Virtual screening, molecular dynamics and binding energy-MM-PBSA studies of natural compounds to identify potential EcR inhibitors against Bemisia tabaci Gennadius. PLoS ONE, 17(1), e0261545. DOI
Manikandan, R., Harish, S., Karthikeyan, G., & Raguchander, T. (2018). Comparative proteomic analysis of different isolates of Fusarium oxysporum f.sp. Lycopersici to exploit the differentially expressed proteins responsible for virulence on tomato plants. Frontiers in Microbiology, 9, 420. DOI
McGovern, R. J. (2015). Management of tomato diseases caused by Fusarium oxysporum. Crop Protection, 73, 78–92. DOI
Misas-Villamil, J. C., & van der Hoorn, R. AL. (2008). Enzyme-inhibitor interactions at the plant-pathogen interface. Current Opinion in Plant Biology, 11(4), 380–388. DOI
Mueller, A.-L., Brockmueller, A., Kunnumakkara, A. B., & Shakibaei, M. (2022). Calebin A, a Compound of Turmeric, Down-Regulates Inflammation in Tenocytes by NF-κB/Scleraxis Signaling. International Journal of Molecular Sciences, 23(3), 1695. DOI
Nurhalimah, Muhibuddin, A., & Syib’li, M. A. (2022). Screening of yeast isolates for the biocontrol of Sclerotium rolfsii. Biodiversitas Journal of Biological Diversity, 23(7), 3820–3826. DOI
Oza, K., Khumji, J., & Maitreya, B. (2021). Antifungal Activity of Turmeric (Curcuma longa) Rhizome against Different Fungi. Journal of Natural Sciences and Mathematics, 11(64), 29014–29017.
Panno, S., Davino, S., Caruso, A. G., Bertacca, S., Crnogorac, A., Mandić, A., Noris, E., & Matić, S. (2021). A review of the most common and economically important diseases that undermine the cultivation of tomato crop in the mediterranean basin. Agronomy, 11(11), 2188. DOI
Panuthai, T., Sihanonth, P., Piapukiew, J., Sooksai, S., Sangvanich, P., & Karnchanatat, A. (2012). An extracellular lipase from the endophytic fungi Fusarium oxysporum isolated from the Thai medicinal plant. Croton oblongifolius Roxb. African Journal of Microbiology Research, 6(11), 2622-2638. DOI
Rocha, A. L. M., Di Pietro, A., Ruiz-Roldán, C., & Roncero, M. I. G. (2008). Ctf1, a transcriptional activator of cutinase and lipase genes in Fusarium oxysporum is dispensable for virulence. Molecular Plant Pathology, 9(3), 293–304. DOI
Roy, A., Kucukural, A., & Zhang, Y. (2010). I-TASSER: A unified platform for automated protein structure and function prediction. Nature Protocols, 5(4), 725–738. DOI
Rueda-Rueda, H., Prieto-Correa, E., & Jiménez-Junca, C. (2020). Cutinases obtained from filamentous fungi: A comparison of screening methods. DYNA, 87(214), 183–190. DOI
Salmaso, V., & Moro, S. (2018). Bridging Molecular Docking to Molecular Dynamics in Exploring Ligand-Protein Recognition Process: An Overview. Frontiers in Pharmacology, 9, 923. DOI
Sandur, S. K., Pandey, M. K., Sung, B., Ahn, K. S., Murakami, A., Sethi, G., Limtrakul, P., Badmaev, V., & Aggarwal, B. B. (2007). Curcumin, demethoxycurcumin, bisdemethoxycurcumin, tetrahydrocurcumin and turmerones differentially regulate anti-inflammatory and anti-proliferative responses through a ROS-independent mechanism. Carcinogenesis, 28(8), 1765–1773. DOI
Serrano, M., Coluccia, F., Torres, M., L’Haridon, F., & Métraux, J. P. (2014). The cuticle and plant defense to pathogens. Frontiers in Plant Science, 5(274), 1–8. DOI
Singh, V. K., Singh, H. B., & Upadhyay, R. S. (2017). Role of fusaric acid in the development of ‘Fusarium wilt’ symptoms in tomato: Physiological, biochemical and proteomic perspectives. Plant Physiology and Biochemistry, 118, 320–332. DOI
Srinivas, C., Nirmala Devi, D., Narasimha Murthy, K., Mohan, C. D., Lakshmeesha, T. R., Singh, B., Kalagatur, N. K., Niranjana, S. R., Hashem, A., Alqarawi, A. A., Tabassum, B., Abd_Allah, E. F., Chandra Nayaka, S., & Srivastava, R. K. (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. DOI
Stierand, K., & Rarey, M. (2010). Drawing the PDB: Protein-ligand complexes in two dimensions. ACS Medicinal Chemistry Letters, 1(9), 540–545. DOI
Suprihatin, T., Rahayu, S., Rifa, M., & Widyarti, S. (2020). Senyawa pada Serbuk Rimpang Kunyit (Curcuma longa L.) yang Berpotensi sebagai Antioksidan. Buletin Anatomi dan Fisiologi 5(1), 35–42. DOI
Tan, W. J., Thanh, T. A. V., Rafael, E. S., Chen, Y. S., & Yeo, F. K. S. (2021). Morphological and molecular characterization of Fusarium spp. associated with Fusarium wilt disease of Piper nigrum L. in Northwestern region of Sarawak. Malaysian Journal of Microbiology, 17(2), 165–177. DOI
Therasme, O., Volk, T. A., Cabrera, A. M., Eisenbies, M. H., & Amidon, T. E. (2018). Hot water extraction improves the characteristics of willow and sugar maple biomass with different amount of bark. Frontiers in Energy Research, 6, 93. DOI
Wargasetia, T. L., Ratnawati, H., Widodo, N., & Widyananda, M. H. (2021). Bioinformatics Study of Sea Cucumber Peptides as Antibreast Cancer Through Inhibiting the Activity of Overexpressed Protein (EGFR, PI3K, AKT1, and CDK4). Cancer Informatics, 20, 117693512110318. DOI
Yang, D., Wang, T., Long, M., & Li, P. (2020). Quercetin: Its Main Pharmacological Activity and Potential Application in Clinical Medicine. Oxidative Medicine and Cellular Longevity, 2020, 1–13 DOI
Yang, J., & Zhang, Y. (2015). Protein Structure and Function Prediction Using I‐TASSER. Current Protocols in Bioinformatics, 52(1). DOI
DOI: http://doi.org/10.17503/agrivita.v45i3.3966
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