An In silico Approach to Identify a Potential Phyto-Herbicide Candidate against 5- Enolpyruvyl Shikimate-3-Phosphate (EPSP) Synthase
Article Sidebar
Main Article Content
Abstract
Crop contamination with chemical herbicide residues is one of the major problems on a global scale. Bioherbicides have been accepted as a promising material to be used in weed control. This study aims to find a potential phyto-herbicide candidate using an in silico approach. A 2D similarity search was used to find the natural compounds having a chemical structure similar to that of glyphosate against natural compound databases. Then, phyto-herbicide candidates were confirmed via molecular docking and property screening. 2-Phosphoglycerate, C00000123, was selected as the potential phyto-herbicide candidate based on the lowest binding energy (-6.45 kcal/mol) similar to that of the reference glyphosate (-7.42 kcal/mol), and it was not a substrate of EPSP synthase. The binding pattern between 2-Phosphoglycerate and EPSP synthase was similar to that of glyphosate binding via Lys22, Lys411, Gly96, Arg124, Arg344, and Arg386. Moreover, 2-Phosphoglycerate had a herbicide-likeness property and was an enzyme inhibitor. It was produced in Oryza sativa L. Therefore, 2-Phosphoglycerate displayed an effective inhibition. However, further wet-lab experiments must be performed to validate the herbicide effectiveness of 2-Phosphoglycerate, and its role as an effective phyto-herbicide inhibitor.
Article Details
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
References
Paola Balderrama-Carmona A, Patricia Silva-Beltrán N, Alberto Zamora Alvarez L, Patricia Adan Bante N, Felipe Moran Palacio E. Consequences of herbicide use in rural environments and their effect on agricultural workers. IntechOpen 2020.
Ferrante M, Rapisarda P, Grasso A, Favara C, Conti GO. Glyphosate and environmental toxicity with “One Health” approach, a review. Environ Res 2023;235:116678.
Tall T, Puigbó P. The Glyphosate Target Enzyme5-Enolpyruvyl Shikimate 3-Phosphate Synthase (EPSPS) Contains Several EPSPS Associated Domains in Fungi. Proceedings 2021;76:6.
Zulet-González A, Barco-Antoñanzas M, Gil-Monreal M, Royuela M, Zabalza A. Increased Glyphosate-Induced Gene Expression in the Shikimate Pathway Is Abolished in the Presence of Aromatic Amino Acids and Mimicked by Shikimate. Front Plant Sci 2020;11:459.
Averesch NJH, Krömer JO. Metabolic engineering of the shikimate pathway for production of aromatics and derived compounds present and future strain construction strategies. Front Bioeng Biotechnol 2018;6(32):1-32.
Bailey KL. The bioherbicide approach to weed control using plant pathogens. In: Abrol DP, editor. Integrated Pest Management. Academic Press, San Diego. 2014;245-66.
Cordeau S, Triolet M, Wayman S, Steinberg C, Guillemin JP. Bioherbicides: Dead in the water? A review of the existing products for integrated weed management. Crop Prot 2016;87:44-9.
Dayan FE, Duke SO. Discovery for new herbicide sites of action by quantification of plant primary metabolite and enzyme pools. Engineering 2020;6(5):509-14.
Permatasari GW, Putranto RA, Widiastuti H. Structure-based virtual screening of bioherbicide candidates for weeds in sugarcane plantation using in silico approaches. Menara Perkebunan 2020; 88(2):100-10.
Antony A, Karuppasamy R. Searching of novel herbicides for paddy field weed management-A case study with Acetyl-CoA Carboxylase. Agronomy 2022;12:1635.
Kumar N, Rani P, Agarwal S, Singh DV. 6-Ethoxy-4- N-(2-morpholin-4-ylethyl) -2-Npropan-2-yl-1,3, 5-triazine-2, 4-diamine endows herbicidal activity against Phalaris minor a weed of wheat crop field: An insilico and experimental approaches of herbicide discovery. J Mol Model 2022; 28(4):77.
Szilágyi K, Flachner B, Hajdú I, Szaszkó M, Dobi K, L˝orincz Z, Cseh S, Dormán G. Rapid identification of potential drug candidates from multi-million compounds’ repositories. combination of 2D similarity search with 3D ligand/structure based methods and in vitro screening. Molecules 2021;26:5593.
Skinnider MA, Dejong CA, Franczak BC. et al. Comparative analysis of chemical similarity methods for modular natural products with a hypothetical structure enumeration algorithm. J Cheminform 2017;9:46.
Kumar A. Chemical similarity methods: A tutorial review. The Chem. educator, 2011;16:46-50.
Almalki FA, Shawky AM, Abdalla AN, Gouda AM. Icotinib, Almonertinib and Olmutinib. A 2D Similarity/Docking-based study to predict the potential binding modes and interactions into EGFR, Molecules 2021;26(21):6423.
Leng XY, Gao S, Ma YF, Zhao LX, Wang M, Ye F, Fu Y. Discovery of novel HPPD inhibitors: Virtual screening, molecular design, structure modification and biological evaluation. Pestic Biochem Physiol 2023;192:105390.
Molinspiration Cheminformatics free web services, https://www.molinspiration.com, Slovensky Grob, Slovakia Republic
Avram S, Funar-Timofei S, Borota A, Chennamaneni SR, Manchala AK, Muresan S. Quantitative estimation of pesticidelikeness for agrochemical discovery. J Cheminform 2014; 6(42).
Kim S, Chen J, Cheng T, Gindulyte A, He J, He S, Li Q, Shoemaker BA, Thiessen PA, Yu B, Zaslavsky L, Zhang J, Bolton EE. PubChem 2023 update. Nucleic Acids Res 2023;51(D1):D1373-80.
Hattori M, Tanaka N, Kanehisa M, Goto S. SIMCOMP/SUBCOMP: Chemical structure search servers for network analyses. Nucleic Acids Res 2010;38:W652-6.
Kanehisa M, Goto S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 2000;28:27-30.
Afendi FM, Okada T, Yamazaki M, Hirai-Morita A, Nakamura Y, Nakamura K, Ikeda S, Takahashi H, Md. Altaf-Ul-Amin Darusman LK, Saito K, Kanaya S. KNApSAcK family databases: Integrated metabolite-plant species databases for multifaceted plant research. Plant Cell Physiol 2012;53:e1(1-12).
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000;28:235-42.
Schönbrunn E, Eschenburg S, Shuttleworth WA, Schloss JV, Amrhein N, Evans JNS, Kabsch W. Interaction of the herbicide glyphosate with its target enzyme 5-enolpyruvylshikimate 3-phosphate synthase in atomic detail. Proc Natl Acad Sci USA 2001;98(4):1376-80.
Funke T, Han H, Healy-Fried ML, Fischer M, Schönbrunn E. Molecular basis for the herbicide resistance of Roundup ready crops. PNAS 2006;103(35):13010-5.
Pratama MRF, Poerwono H, Siswodihardjo S. Introducing a two‐dimensional graph of docking score difference vs. similarity of ligand‐receptor interactions. IJBiotech 2021;26(1):54‐60.
Morris GM, Huey R, Lindstorm W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTool4: Automated docking with selective flexible. J Comput Chem 2009;30(16):2785-91.
Atilgan E, Hu J. Improving protein docking using sustainable genetic algorithms. IJCISIM, 2011;3;248-55.
Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ. Automated Docking Using a Lamarckian Genetic Algorithm and Empirical Binding Free Energy Function. J Comput Chem, 1998;19;1639-62.
D.S. Biovia, “Discovery Studio Visualizer, 19.1”, San Diego: Dassault Systèmes. 2019.
IBM Corp. Released 2017. IBM SPSS statistics for Windows, version 25.0. Armonk, NY: IBM Corp.
Xu X, Zou X. Dissimilar ligands bind in a similar fashion: A guide to ligand bindingmode prediction with application to CELPP Studies. Int J Mol Sci 2021;22,12320.
Krämer U. The natural history of model organisms: Planting molecular functions in an ecological context with Arabidopsis thaliana. eLife 2015;4:e06100.
Jain AS, Sushma P, Dharmashekar C, Beelagi MS, Prasad SK, Shivamallu C, Prasad A, Syed A, Marraiki N, Prasad KS, In silico evaluation of flavonoids as effective antiviral agents on the spike glycoprotein of SARS-CoV-2. Saudi J Biol Sci 2021;28(1):1040-51.
Rahaman F, Shukor Juraimi A, Rafii MY, Uddin K, Hassan L, Chowdhury AK, Karim SMR, Yusuf Rini B, Yusuff O, Bashar HMK, Hossain A. Allelopathic potential in rice - a biochemical tool for plant defense against weeds. Front Plant Sci 2022;13: 1072723.
Chung IM, Ahn JK, Yun SJ. Identification of allelopathic compounds from rice (Oryza sativa L.) straw and their biological activity. Can J Plant Sci 2001;81:815-9.
Gu CZ, Xia XM, Lv J, Tan JW, Baerson SR, Pan ZQ, Song YY, Zeng RS. Diterpenoids with herbicidal and antifungal activities from hulls of rice (Oryza sativa). Fitoterapia 2019;136:104183.
Yang X, Xing X, Liu Y, Zheng Y. Screening of potential inhibitors targeting the main protease structure of SARS-CoV-2 via molecular docking. Front Pharmacol 2022;13(6):962863.