In Silico Determination of The Antifungal Effect of Plant Active Molecules Against Botrytis Cinerea by Molecular Docking

Year 2024, Volume: 34 Issue: 2, 323 - 334, 30.06.2024

Vildan Atalay Beyza Yılmaz Mehmet Emin Uras

https://doi.org/10.29133/yyutbd.1377395

Abstract

Botrytis cinerea, which has developed many strategies to infect plants, can survive in harsh environmental conditions, and has a wide host range, has become an important problem both economically and ecologically by causing tons of crop losses for many years. The residues in soil and crops caused by chemical pesticides used to get rid of agricultural pests pose serious threats to human and environmental health, such as hormonal abnormalities and acute respiratory poisoning, especially in children. The most critical step to avoid these hazards will be to replace chemical pesticides with plant-active molecules. At the same time, these studies primarily in silico will provide a return in terms of both time and cost. Inhibition of pectin methyl esterase, an important virulence factor of B. cinerea, will ensure the organism is controlled. In order to determine candidate biofungicide effector molecules, QSAR parameter values of 409 plant active molecules were calculated. Firstly, conformer distribution and geometry optimizations were performed with Spartan 14’ software. Docking studies of the optimized molecules were carried out through Autodock Vina software, while visualization studies to make sense of the interactions between the target receptor structure and effector molecules were used by BIOVIA Discovery Studio software. As a result of all the analyses, the molecules that are alternatives to chemical pesticides as biofungicides were determined to be the following molecules: Podolactone B, Repin, Sandaracopimaradienediol, 6-Hydrogenistein, Artemisinin, Lycoricidine, 6-Methoxygossypol, Viscidulin, Ciprofloxacin, and 7,4’-Dihydroxyflavan.

Keywords

Botrytis cinerea, Molecular Docking, QSAR parameters, Biopesticides

References

• Abbey, J. A., Percival, D., Abbey, L., Asiedu, S. K., Prithiviraj, B., & Schilder, A. (2019). Biofungicides as alternative to synthetic fungicide control of grey mould (Botrytis cinerea)–prospects and challenges. Biocontrol science and technology, 29(3), 207-228.
• Atalay, V. E., & Asar, S. (2024). Determination of the inhibition effect of hesperetin and its derivatives on Candida glabrata by molecular docking method. The European Chemistry and Biotechnology Journal, (1), 27-38
• BIOVIA, D. S. (2021). Discovery Studio Visualizer; v21. 1.0. 20298 Dassault Systèmes: San Diego. CA, USA.
• Bock, C. H., Barbedo, J. G., Del Ponte, E. M., Bohnenkamp, D., & Mahlein, A. K. (2020). From visual estimates to fully automated sensor-based measurements of plant disease severity: status and challenges for improving accuracy. Phytopathology Research, 2, 1-30.
• Boukaew, S., Prasertsan, P., Troulet, C., & Bardin, M. (2017). Biological control of tomato gray mold caused by Botrytis cinerea by using Streptomyces spp. BioControl, 62, 793-803.
• Chilvers, M. I., & du Toit, L. J. (2006). Detection and identification of Botrytis species associated with neck rot, scape blight, and umbel blight of onion. Plant Health Progress, 7(1), 38.
• Chun, S. W., Song, D. J., Lee, K. H., Kim, M. J., Kim, M. S., Kim, K. S., & Mo, C. (2024). Deep learning algorithm development for early detection of Botrytis cinerea infected strawberry fruit using hyperspectral fluorescence imaging. Postharvest Biology and Technology, 214, 112918.
• 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.
• Dean, R., Van Kan, J. A., Pretorius, Z. A., Hammond‐Kosack, K. E., Di Pietro, A., Spanu, P. D., ... & Foster, G. D. (2012). The Top 10 fungal pathogens in molecular plant pathology. Molecular plant pathology, 13(4), 414-430.
• Demirel, S., Usta, M., & Güller, A. (2022). In silico analysis of ribosome-inactivating protein (tritin) from common wheat plants (Triticum aestivum L.). Avrupa Bilim Ve Teknoloji Dergisi(33), 79-87.
• Diab, M. K., Mead, H. M., Khedr, M. A., Nafie, M. S., Abu-Elsaoud, A. M., & El-Shatoury, S. A. (2024). Metabolite profiling and in-silico studies show multiple effects of insecticidal actinobacterium on Spodoptera littoralis. Scientific Reports, 14(1), 3057.
• Duke, J. A. (2020). Database of biologically active phytochemicals & their activity. CRC Press.
• Eberhardt, J., Santos-Martins, D., Tillack, A. F., & Forli, S. (2021). AutoDock Vina 1.2. 0: New docking methods, expanded force field, and python bindings. Journal of chemical information and modeling, 61(8), 3891-3898.
• Elad, Y., Williamson, B., Tudzynski, P., & Delen, N. (Eds.). (2004). Botrytis: biology, pathology and control. Springer Science & Business Media.
• Ez-Zoubi, A., Ez Zoubi, Y., Bentata, F., El-Mrabet, A., Ben Tahir, C., Labhilili, M., & Farah, A. (2023). Preparation and characterization of a biopesticide based on artemisia herba-alba essential oil encapsulated with succinic acid‐modified beta‐cyclodextrin. Journal of Chemistry, 2023(1), 3830819.
• Hawthorne, B. T. (1988). Fungi causing storage rots on fruit of Cucurbita spp. New Zealand journal of experimental agriculture, 16(2), 151-157.
• Hehre, W. J. (2003). A guide to molecular mechanics and quantum chemical calculations (Vol. 2). Irvine, CA: Wavefunction.
• Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., ... & Hassabis, D. (2021). Highly accurate protein structure prediction with AlphaFold. Nature, 596(7873), 583-589.
• Karakaya, A., & Bayraktar, H. (2009). Botrytis disease of kiwifruit in Turkey. Australasian Plant Disease Notes, 4(1), 87-88.
• Kurbetli, İ., Aydoğdu, M., Sülü, G., & Polat, İ. (2016). First report of pre-harvest rot of pear fruit caused by Botrytis cinerea in Turkey. New Disease Reports, 34(1), 16-16.
• Latorre, B., Elfar Aedo, K., & Ferrada, E. E. (2015). Gray mold caused by Botrytis cinerea limits grape production in Chile. Ciencia e Investigacion Agraria, 42(3), 305-330.
• Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (1997). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced drug delivery reviews, 23(1-3), 3-25.
• Mathew, D., Kumar, C. S., & Cherian, K. A. (2021). Foliar fungal disease classification in banana plants using elliptical local binary pattern on multiresolution dual tree complex wavelet transform domain. Information processing in Agriculture, 8(4), 581-592.
• Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of computational chemistry, 30(16), 2785-2791.
• Nakajima, M., & Akutsu, K. (2014). Virulence factors of Botrytis cinerea. Journal of General Plant Pathology, 80(1), 15-23.
• Petrasch, S., Knapp, S. J., Van Kan, J. A., & Blanco‐Ulate, B. (2019). Grey mould of strawberry, a devastating disease caused by the ubiquitous necrotrophic fungal pathogen Botrytis cinerea. Molecular plant pathology, 20(6), 877-892.
• Pimentel, D., Krummel, J., Gallahan, D., Hough, J., Merrill, A., Schreiner, I., ... & Fiance, S. (1978). Benefits and costs of pesticide use in US food production. BioScience, 28(12), 772-784.
• Pimentel, D., McLaughlin, L., Zepp, A., Lakitan, B., Kraus, T., Kleinman, P., ... & Selig, G. (1991). Environmental and economic effects of reducing pesticide use. BioScience, 41(6), 402-409.
• Prusky, D., & Lichter, A. (2007). Activation of quiescent infections by postharvest pathogens during transition from the biotrophic to the necrotrophic stage. FEMS microbiology letters, 268(1), 1-8.
• Rojas, D. S., & Gilbert, G. S. (2024). The response of botrytis cinerea to fire in a coast redwood forest. International Journal of Plant Biology, 15(1), 94-101.
• Sadek, M. E., Shabana, Y. M., Sayed-Ahmed, K., & Abou Tabl, A. H. (2022). Antifungal activities of sulfur and copper nanoparticles against cucumber postharvest diseases caused by Botrytis cinerea and Sclerotinia sclerotiorum. Journal of Fungi, 8(4), 412.
• Stahl, M., & Rarey, M. (2001). Detailed analysis of scoring functions for virtual screening. Journal of medicinal chemistry, 44(7), 1035-1042.
• Stahr, M. N., & Quesada-Ocampo, L. M. (2019). Black rot of sweetpotato: A comprehensive diagnostic guide. Plant health progress, 20(4), 255-260.
• Sun, K., van Tuinen, A., van Kan, J. A., Wolters, A. M. A., Jacobsen, E., Visser, R. G., & Bai, Y. (2017). Silencing of DND1 in potato and tomato impedes conidial germination, attachment and hyphal growth of Botrytis cinerea. BMC plant biology, 17, 1-12.
• Sunil, C. K., Jaidhar, C. D., & Patil, N. (2023). Systematic study on deep learning-based plant disease detection or classification. Artificial Intelligence Review, 56(12), 14955-15052.
• TOB. (2023). Tarım ve Orman Bakanlığı Bitki Koruma Ürünleri Daire Başkanlığı. Retrieved 10.10.2023 from https://bku.tarimorman.gov.tr/Zararli/Details/1252
• Usta, Mustafa & Güller, Abdullah & Demirel, Serap & Korkmaz, Gülüstan & Kurt, Zeynelabidin. (2023). New insights into tomato spotted wilt orthotospovirus (TSWV) infections in Türkiye: Molecular detection, phylogenetic analysis, and in silico docking study. Notulae Botanicae Horti Agrobotanici Cluj-Napoca, 51(3), 13245-13245.
• Valette-Collet, O., Cimerman, A., Reignault, P., Levis, C., & Boccara, M. (2003). Disruption of Botrytis cinerea pectin methylesterase gene Bcpme1 reduces virulence on several host plants. Molecular Plant-Microbe Interactions, 16(4), 360-367.
• Viret, O., Keller, M., Jaudzems, V. G., & Cole, F. M. (2004). Botrytis cinerea infection of grape flowers: light and electron microscopical studies of infection sites. Phytopathology, 94(8), 850-857.
• Vivekanandhan, P., Alharbi, S. A., & Ansari, M. J. (2024). Toxicity, biochemical and molecular docking studies of Acacia nilotica L., essential oils against insect pests. Toxicon, 243, 107737.
• Wang, L., Hu, J., Li, D., Reymick, O. O., Tan, X., & Tao, N. (2022). Isolation and control of Botrytis cinerea in postharvest green pepper fruit. Scientia Horticulturae, 302, 111159.
• Williamson, B., Tudzynski, B., Tudzynski, P., & Van Kan, J. A. (2007). Botrytis cinerea: the cause of grey mould disease. Molecular plant pathology, 8(5), 561-580.
• Wyss, P. C., Gerber, P., Hartman, P. G., Hubschwerlen, C., Locher, H., Marty, H. P., & Stahl, M. (2003). Novel dihydrofolate reductase inhibitors. Structure-based versus diversity-based library design and high-throughput synthesis and screening. Journal of medicinal chemistry, 46(12), 2304-2312.
• Xiao, C. L. (2006). Postharvest fruit rots in d'Anjou pears caused by Botrytis cinerea, Potebniamyces pyri, and Sphaeropsis pyriputrescens. Plant health progress, 7(1), 40.
• Youssef, K., de Oliveira, A. G., Tischer, C. A., Hussain, I., & Roberto, S. R. (2019). Synergistic effect of a novel chitosan/silica nanocomposites-based formulation against gray mold of table grapes and its possible mode of action. International journal of biological macromolecules, 141, 247-258.