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Ruszkowski M, Forlani G. Deciphering the Structure of Arabidopsis thaliana 5-enol-Pyruvyl-Shikimate-3-Phosphate Synthase: an Essential Step toward the Discovery of Novel Inhibitors to Supersede Glyphosate. Comput Struct Biotechnol J 2022; 20:1494-1505. [PMID: 35422967 PMCID: PMC8983318 DOI: 10.1016/j.csbj.2022.03.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 03/19/2022] [Accepted: 03/21/2022] [Indexed: 11/19/2022] Open
Abstract
Glyphosate interferes with plant aromatic metabolism through the inhibition of 5-enol-pyruvyl-shikimate-3-phosphate (EPSP) synthase [EPSPS, EC 2.5.1.19]. For this reason, EPSPS has been extensively studied in a vast array of organisms. This notwithstanding, up to date, the crystal structure of the protein has been solved exclusively in a few prokaryotes, while that of the plant enzyme has been only deduced in silico by similarity. This study aimed at determining the structure of EPSPS from the plant model species Arabidopsis thaliana, which has been cloned, heterologously expressed and affinity-purified. The kinetic properties of the enzyme have been determined, as well as its susceptibility to the inhibition brought about by glyphosate. The crystal structure of the protein has been resolved at high resolution (1.4 Å), showing open conformation of the enzyme, which is the state ready for substrate/inhibitor binding. This provides a framework for the structure-based design of novel EPSPS inhibitors. Surface regions near the active-site cleft entrance or at the interdomain hinge appear promising for inhibitor selectivity, while bound chloride near the active site is a potential placeholder for anionic moieties of future herbicides.
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Affiliation(s)
- Milosz Ruszkowski
- Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Synchrotron Radiation Research Section of MCL, National Cancer Institute, Argonne, IL, USA
- Corresponding author at: Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
| | - Giuseppe Forlani
- Department of Life Science and Biotechnology, University of Ferrara, Ferrara, Italy
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Howard NI, Dias MVB, Peyrot F, Chen L, Schmidt MF, Blundell TL, Abell C. Design and Structural Analysis of Aromatic Inhibitors of Type II Dehydroquinase fromMycobacterium tuberculosis. ChemMedChem 2014; 10:116-33. [DOI: 10.1002/cmdc.201402298] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Indexed: 11/09/2022]
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3
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Powell KT, Cheng C, Gudipati CS, Wooley KL. Design, synthesis, and characterization of linear fluorinated poly(benzyl ether)s: A comparison study with isomeric hyperbranched fluoropolymers. ACTA ACUST UNITED AC 2005. [DOI: 10.1039/b511555h] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Roberts CW, Roberts F, Lyons RE, Kirisits MJ, Mui EJ, Finnerty J, Johnson JJ, Ferguson DJP, Coggins JR, Krell T, Coombs GH, Milhous WK, Kyle DE, Tzipori S, Barnwell J, Dame JB, Carlton J, McLeod R. The shikimate pathway and its branches in apicomplexan parasites. J Infect Dis 2002; 185 Suppl 1:S25-36. [PMID: 11865437 DOI: 10.1086/338004] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
The shikimate pathway is essential for production of a plethora of aromatic compounds in plants, bacteria, and fungi. Seven enzymes of the shikimate pathway catalyze sequential conversion of erythrose 4-phosphate and phosphoenol pyruvate to chorismate. Chorismate is then used as a substrate for other pathways that culminate in production of folates, ubiquinone, napthoquinones, and the aromatic amino acids tryptophan, phenylalanine, and tyrosine. The shikimate pathway is absent from animals and present in the apicomplexan parasites Toxoplasma gondii, Plasmodium falciparum, and Cryptosporidium parvum. Inhibition of the pathway by glyphosate is effective in controlling growth of these parasites. These findings emphasize the potential benefits of developing additional effective inhibitors of the shikimate pathway. Such inhibitors may function as broad-spectrum antimicrobial agents that are effective against bacterial and fungal pathogens and apicomplexan parasites.
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Affiliation(s)
- Craig W Roberts
- Department of Immunology, University of Strathclyde, Glasgow, United Kingdom
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5
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Sikorski JA, Peterson ML, Corey SD, Font JL, Walker MC. New 4-(α-Hetero-Phosphonomethyl) Pyrrole 2-Carboxylates are EPSP Synthase Inhibitors. PHOSPHORUS SULFUR 1999. [DOI: 10.1080/10426509908546320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- James A. Sikorski
- a Monsanto Company , St. Louis, Missouri 63198, USA
- b Monsanto Company , St. Louis, Missouri 63198, USA
- c Monsanto Company , St. Louis, Missouri 63198, USA
- d Monsanto Company , St. Louis, Missouri 63198, USA
- e Monsanto Company , St. Louis, Missouri 63198, USA
| | - Mark L. Peterson
- a Monsanto Company , St. Louis, Missouri 63198, USA
- b Monsanto Company , St. Louis, Missouri 63198, USA
- c Monsanto Company , St. Louis, Missouri 63198, USA
- d Monsanto Company , St. Louis, Missouri 63198, USA
- e Monsanto Company , St. Louis, Missouri 63198, USA
| | - Susan D. Corey
- a Monsanto Company , St. Louis, Missouri 63198, USA
- b Monsanto Company , St. Louis, Missouri 63198, USA
- c Monsanto Company , St. Louis, Missouri 63198, USA
- d Monsanto Company , St. Louis, Missouri 63198, USA
- e Monsanto Company , St. Louis, Missouri 63198, USA
| | - Jose L. Font
- a Monsanto Company , St. Louis, Missouri 63198, USA
- b Monsanto Company , St. Louis, Missouri 63198, USA
- c Monsanto Company , St. Louis, Missouri 63198, USA
- d Monsanto Company , St. Louis, Missouri 63198, USA
- e Monsanto Company , St. Louis, Missouri 63198, USA
| | - Mark C. Walker
- a Monsanto Company , St. Louis, Missouri 63198, USA
- b Monsanto Company , St. Louis, Missouri 63198, USA
- c Monsanto Company , St. Louis, Missouri 63198, USA
- d Monsanto Company , St. Louis, Missouri 63198, USA
- e Monsanto Company , St. Louis, Missouri 63198, USA
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Parmar VS, Kumar A, Bisht KS, Mukherjee S, Prasad AK, Sharma SK, Wengel J, Olsen CE. Novel chemoselective de-esterification of esters of polyacetoxy aromatic acids by lipases. Tetrahedron 1997. [DOI: 10.1016/s0040-4020(96)01118-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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7
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Shah A, Font JL, Miller MJ, Ream JE, Walker MC, Sikorski JA. New aromatic inhibitors of EPSP synthase incorporating hydroxymalonates as novel 3-phosphate replacements. Bioorg Med Chem 1997; 5:323-34. [PMID: 9061197 DOI: 10.1016/s0968-0896(96)00239-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A new, aromatic analogue of the EPSP synthase enzyme reaction intermediate 1 has been identified, which contains a 3-hydroxymalonate moiety in place of the usual 3-phosphate group. This simplified inhibitor was readily prepared in five steps from ethyl 3,4-dihydroxybenzoate. The resulting tetrahedral intermediate mimic 9 is an effective, competitive inhibitor versus S3P with an apparent Ki of 0.57 +/- 0.06 microM. This result demonstrates that 3-hydroxymalonates exhibit potencies comparable to aromatic inhibitors containing the previously identified 3-malonate ether replacements and can thus function as suitable 3-phosphate mimics in this system. These new compounds provide another example in which a simple benzene ring can be used effectively in place of the more complex shikimate ring in the design of EPSP synthase inhibitors. Furthermore, the greater potency of 9 versus the glycolate derivative 10 and the 5-deoxy-analog 11, again confirms the requirement for multiple anionic charges at the dihydroxybenzoate 5-position in order to attain effective inhibition of this enzyme.
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Affiliation(s)
- A Shah
- Ceregen Corporate Research, Unit of Monsanto Company, St. Louis, MO 63198, USA
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8
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Peterson ML, Corey SD, Font JL, Walker MC, Sikorski JA. New simplified inhibitors of EPSP synthase: The importance of ring size for recognition at the shikimate 3-phosphate site. Bioorg Med Chem Lett 1996. [DOI: 10.1016/s0960-894x(96)00527-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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9
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Miller MJ, Cleary DG, Ream JE, Snyder KR, Sikorski JA. New EPSP synthase inhibitors: synthesis and evaluation of an aromatic tetrahedral intermediate mimic containing a 3-malonate ether as a 3-phosphate surrogate. Bioorg Med Chem 1995; 3:1685-92. [PMID: 8770393 DOI: 10.1016/0968-0896(95)00156-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A new analog of the EPSP synthase enzyme reaction intermediate 1, containing a 3-malonate ether moiety in place of the usual 3-phosphate group, was synthesized from 3,5-dihydroxybenzoic acid. This simple, synthetically accessible aromatic compound (5) is an effective competitive inhibitor versus S3P with an apparent Ki of 1.3 +/- 0.22 microM. This result demonstrates that a simple benzene ring can be a suitable achiral substitute for the more complex shikimate ring in the design of EPSP synthase inhibitors. Furthermore, the greater potency of 5 versus the phenol 6, glycolate 7 and the gallic acid analog 8 demonstrates the requirement for multiple anionic charges at the dihydroxybenzoate 5-position in order to attain effective inhibition of this enzyme. However, this 3-malonate ether substituted compound was at least 10-fold less effective as a bisubstrate inhibitor than the corresponding 3-phosphate. This suggests that tetrahedral intermediate mimics possessing a 3-malonate ether moiety are less effective than their corresponding 3-phosphates in accessing the optimal enzyme conformation stabilizing 1.
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Affiliation(s)
- M J Miller
- Ceregen Corporate Research, Units of Monsanto Company, St Louis, MO 63198, USA
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