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Mackie ERR, Barrow AS, Giel MC, Hulett MD, Gendall AR, Panjikar S, Soares da Costa TP. Repurposed inhibitor of bacterial dihydrodipicolinate reductase exhibits effective herbicidal activity. Commun Biol 2023; 6:550. [PMID: 37217566 DOI: 10.1038/s42003-023-04895-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/02/2023] [Indexed: 05/24/2023] Open
Abstract
Herbicide resistance represents one of the biggest threats to our natural environment and agricultural sector. Thus, new herbicides are urgently needed to tackle the rise in herbicide-resistant weeds. Here, we employed a novel strategy to repurpose a 'failed' antibiotic into a new and target-specific herbicidal compound. Specifically, we identified an inhibitor of bacterial dihydrodipicolinate reductase (DHDPR), an enzyme involved in lysine biosynthesis in plants and bacteria, that exhibited no antibacterial activity but severely attenuated germination of the plant Arabidopsis thaliana. We confirmed that the inhibitor targets plant DHDPR orthologues in vitro, and exhibits no toxic effects against human cell lines. A series of analogues were then synthesised with improved efficacy in germination assays and against soil-grown A. thaliana. We also showed that our lead compound is the first lysine biosynthesis inhibitor with activity against both monocotyledonous and dicotyledonous weed species, by demonstrating its effectiveness at reducing the germination and growth of Lolium rigidum (rigid ryegrass) and Raphanus raphanistrum (wild radish). These results provide proof-of-concept that DHDPR inhibition may represent a much-needed new herbicide mode of action. Furthermore, this study exemplifies the untapped potential of repurposing 'failed' antibiotic scaffolds to fast-track the development of herbicide candidates targeting the respective plant enzymes.
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Affiliation(s)
- Emily R R Mackie
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Andrew S Barrow
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Marie-Claire Giel
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Mark D Hulett
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Anthony R Gendall
- Australian Research Council Industrial Transformation Research Hub for Medicinal Agriculture, AgriBio, La Trobe University, Bundoora, VIC, 3086, Australia
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, VIC, 3168, Australia
- Department of Molecular Biology and Biochemistry, Monash University, Melbourne, VIC, 3800, Australia
| | - Tatiana P Soares da Costa
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia.
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, 3086, Australia.
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Duke SO, Dayan FE. The search for new herbicide mechanisms of action: Is there a 'holy grail'? PEST MANAGEMENT SCIENCE 2022; 78:1303-1313. [PMID: 34796620 DOI: 10.1002/ps.6726] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/18/2021] [Indexed: 05/26/2023]
Abstract
New herbicide modes of action (MOAs) are in great demand because of the burgeoning evolution of resistance of weeds to existing commercial herbicides. This need has been exacerbated by the almost complete lack of introduction of herbicides with new MOAs for almost 40 years. There are many highly phytotoxic compounds with MOAs not represented by commercial herbicides, but neither these compounds nor structural analogues have been developed as herbicides for a variety of reasons. Natural products provide knowledge of many MOAs that are not being utilized by commercial herbicides. Other means of identifying new herbicide targets are discussed, including pharmaceutical target sites and metabolomic and proteomic information, as well as the use of artificial intelligence and machine learning to predict herbicidal compounds with new MOAs. Information about several newly discovered herbicidal compounds with new MOAs is summarized. The currently increased efforts of both established companies and start-up companies are likely to result in herbicides with new MOAs that can be used in herbicide resistance management within the next decade. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Stephen O Duke
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, Oxford, MS, USA
| | - Franck E Dayan
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
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Sukhoverkov KV, Corral MG, Leroux J, Haywood J, Johnen P, Newton T, Stubbs KA, Mylne JS. Improved herbicide discovery using physico-chemical rules refined by antimalarial library screening. RSC Adv 2021; 11:8459-8467. [PMID: 35423398 PMCID: PMC8695207 DOI: 10.1039/d1ra00914a] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 02/04/2021] [Indexed: 12/13/2022] Open
Abstract
Herbicides have physico-chemical properties not unlike orally-delivered human drugs, but are known to diverge in their limits for proton donors, partition coefficients and molecular weight. To further refine rules specific for herbicides, we exploited the close evolutionary relationship between Plasmodium falciparum and plants by screening the entire Malaria Box, a chemical library of novel chemical scaffolds with activity against the blood stage of P. falciparum. Initial screening against Arabidopsis thaliana on agar media and subsequently on soil demonstrated the crucial nature of log P and formal charge are to active molecules. Using this information, a weighted scoring system was applied to a large chemical library of liver-stage effective antimalarial leads, and of the six top-scoring compounds, one had potency comparable to that of commercial herbicides. This novel compound, MMV1206386, has no close structural analogues among commercial herbicides. Physiological profiling suggested that MMV1206386 has a new mode of action and overall demonstrates how weighted rules can help during herbicide discovery programs.
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Affiliation(s)
- Kirill V Sukhoverkov
- The University of Western Australia, School of Molecular Sciences 35 Stirling Highway, Crawley Perth 6009 Australia
- The ARC Centre of Excellence in Plant Energy Biology 35 Stirling Highway, Crawley Perth 6009 Australia
| | - Maxime G Corral
- The University of Western Australia, School of Molecular Sciences 35 Stirling Highway, Crawley Perth 6009 Australia
- The ARC Centre of Excellence in Plant Energy Biology 35 Stirling Highway, Crawley Perth 6009 Australia
| | - Julie Leroux
- The University of Western Australia, School of Molecular Sciences 35 Stirling Highway, Crawley Perth 6009 Australia
- The ARC Centre of Excellence in Plant Energy Biology 35 Stirling Highway, Crawley Perth 6009 Australia
| | - Joel Haywood
- The University of Western Australia, School of Molecular Sciences 35 Stirling Highway, Crawley Perth 6009 Australia
- The ARC Centre of Excellence in Plant Energy Biology 35 Stirling Highway, Crawley Perth 6009 Australia
| | | | - Trevor Newton
- BASF SE Speyerer Straße 2 67117 Limburgerhof Germany
| | - Keith A Stubbs
- The University of Western Australia, School of Molecular Sciences 35 Stirling Highway, Crawley Perth 6009 Australia
| | - Joshua S Mylne
- The University of Western Australia, School of Molecular Sciences 35 Stirling Highway, Crawley Perth 6009 Australia
- The ARC Centre of Excellence in Plant Energy Biology 35 Stirling Highway, Crawley Perth 6009 Australia
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Hall CJ, Mackie ER, Gendall AR, Perugini MA, Soares da Costa TP. Review: amino acid biosynthesis as a target for herbicide development. PEST MANAGEMENT SCIENCE 2020; 76:3896-3904. [PMID: 32506606 DOI: 10.1002/ps.5943] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 06/03/2020] [Accepted: 06/07/2020] [Indexed: 06/11/2023]
Abstract
There are three amino acid biosynthesis pathways that are targeted by current herbicides, namely those leading to the production of aromatic amino acids, branched chain amino acids and glutamine. However, their efficacy is diminishing as a result of the increasing number of resistant weeds. Indeed, resistance to most classes of herbicides is on the rise, posing a significant threat to the utility of current herbicides to sustain effective weed management. This review provides an overview of potential herbicide targets within amino acid biosynthesis that remain unexploited commercially, and recent inhibitor discovery efforts. Despite contemporary approaches to herbicide discovery, such as chemical repurposing and the use of omics technologies, there have been no new products introduced to the market that inhibit amino acid biosynthesis over the past three decades. This highlights the chasm that exists between identifying a potent inhibitor and introducing a commercial herbicide. The unpredictability of a mode of action at the systemic level, as well as poor physicochemical properties, often contribute to a lack of progression beyond the target inhibition stage. Nevertheless, it will be important to overcome these obstacles for the development of new herbicides to protect our agricultural industry and ensure food security for an increasing world population. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Cody J Hall
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, Australia
| | - Emily Rr Mackie
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, Australia
| | - Anthony R Gendall
- Department of Animal, Plant and Soil Sciences, Australian Research Council Industrial Transformation Research Hub for Medicinal Agriculture, AgriBio, La Trobe University, Bundoora, VIC, Australia
| | - Matthew A Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, Australia
| | - Tatiana P Soares da Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, Australia
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Huang RH, Gou JY, Zhao DL, Wang D, Liu J, Ma GY, Li YQ, Zhang CS. Phytotoxicity and anti-phytopathogenic activities of marine-derived fungi and their secondary metabolites. RSC Adv 2018; 8:37573-37580. [PMID: 35558593 PMCID: PMC9089327 DOI: 10.1039/c8ra08047j] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 10/26/2018] [Indexed: 01/06/2023] Open
Abstract
To find new pesticides for agricultural use, 133 fungal strains were isolated from coastal marine habitats, from which 37 independent isolates were identified, belonging to 20 genera in nine orders, and the diversity of the isolated fungi were discussed. The phytotoxicity and anti-phytopathogenic fungal and bacterial activities of these 37 extracts, and two previously isolated fungal extracts were evaluated, displaying different levels of bioactivity. Based on the bioactive and chemical screening, an Alternaria sp. (P8) strain, which showed prominent bioactivity and contained abundant secondary metabolites was selected for further chemical investigation; one new compound, a benzopyranone (1), and seven known compounds (2-8) were obtained. Their structures were determined by analysing extensive NMR spectroscopic data and ECD comparisons. Compounds 1, 2, and 6-8 showed obvious phytotoxicity, especially against amaranth, and compound 1 also showed potent antifungal activity toward Alternaria brassicicola. To the best of our knowledge, this is the first report of the phytotoxicity of marine-derived fungi and their secondary metabolites. These studies should provide the foundation for future research into the use of such fungal extracts to combat weeds and diseases in agriculture.
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Affiliation(s)
- Rui-Huan Huang
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences Qingdao 266101 China +86-532-8870-2115
| | - Jian-Yu Gou
- Zunyi Branch, Guizhou Tobacco Company Zunyi 563000 China
| | - Dong-Lin Zhao
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences Qingdao 266101 China +86-532-8870-2115
| | - Dan Wang
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences Qingdao 266101 China +86-532-8870-2115
| | - Jing Liu
- Zunyi Branch, Guizhou Tobacco Company Zunyi 563000 China
| | - Guo-Yong Ma
- Zunyi Branch, Guizhou Tobacco Company Zunyi 563000 China
| | - Yi-Qiang Li
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences Qingdao 266101 China +86-532-8870-2115
| | - Cheng-Sheng Zhang
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences Qingdao 266101 China +86-532-8870-2115
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Corral MG, Haywood J, Stehl LH, Stubbs KA, Murcha MW, Mylne JS. Targeting plant DIHYDROFOLATE REDUCTASE with antifolates and mechanisms for genetic resistance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:727-742. [PMID: 29876984 DOI: 10.1111/tpj.13983] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/16/2018] [Accepted: 05/21/2018] [Indexed: 06/08/2023]
Abstract
The folate biosynthetic pathway and its key enzyme dihydrofolate reductase (DHFR) is a popular target for drug development due to its essential role in the synthesis of DNA precursors and some amino acids. Despite its importance, little is known about plant DHFRs, which, like the enzymes from the malarial parasite Plasmodium, are bifunctional, possessing DHFR and thymidylate synthase (TS) domains. Here using genetic knockout lines we confirmed that either DHFR-TS1 or DHFR-TS2 (but not DHFR-TS3) was essential for seed development. Screening mutated Arabidopsis thaliana seeds for resistance to antimalarial DHFR-inhibitor drugs pyrimethamine and cycloguanil identified causal lesions in DHFR-TS1 and DHFR-TS2, respectively, near the predicted substrate-binding site. The different drug resistance profiles for the plants, enabled by the G137D mutation in DHFR-TS1 and the A71V mutation in DHFR-TS2, were consistent with biochemical studies using recombinant proteins and could be explained by structural models. These findings provide a great improvement in our understanding of plant DHFR-TS and suggest how plant-specific inhibitors might be developed, as DHFR is not currently targeted by commercial herbicides.
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Affiliation(s)
- Maxime G Corral
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Joel Haywood
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Luca H Stehl
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
- Faculty of Biology, The University of Freiburg, Schaenzlestrasse 1, Freiburg, 79104, Germany
| | - Keith A Stubbs
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Monika W Murcha
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Joshua S Mylne
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
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