1
|
Christoff RM, Al Bayer M, Soares da Costa TP, Perugini MA, Abbott BM. Enhancing allosteric inhibition of dihydrodipicolinate synthase through the design and synthesis of novel dimeric compounds. RSC Med Chem 2023; 14:1698-1703. [PMID: 37731698 PMCID: PMC10507794 DOI: 10.1039/d3md00044c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 07/01/2023] [Indexed: 09/22/2023] Open
Abstract
The synthesis of the first dimeric inhibitor of E. coli dihydrodipicolinate synthase (DHDPS) is reported herein. Inspired by 2,4-thiazolidinedione based ligands previously shown to inhibit DHDPS, a series of dimeric inhibitors were designed and synthesised, incorporating various alkyl chain bridges between two 2,4-thiazolidinedione moieties. Aiming to exploit the multimeric nature of this enzyme and enhance potency, a dimeric compound with a single methylene bridge achieved the desired outcome with low micromolar inhibition of E. coli DHDPS observed. This work highlights the continued importance of investigation into DHDPS as an antibacterial target. Furthermore, we demonstrate the design of dimeric ligands can provide a promising strategy to improve potency in the search for novel bioactive compounds.
Collapse
Affiliation(s)
- Rebecca M Christoff
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University Melbourne Victoria 3086 Australia
| | - Mohammad Al Bayer
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University Melbourne Victoria 3086 Australia
| | - Tatiana P Soares da Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University Melbourne Victoria 3086 Australia
| | - Matthew A Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University Melbourne Victoria 3086 Australia
| | - Belinda M Abbott
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University Melbourne Victoria 3086 Australia
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
CRISPR/Cas Genome Editing Technologies for Plant Improvement against Biotic and Abiotic Stresses: Advances, Limitations, and Future Perspectives. Cells 2022; 11:cells11233928. [PMID: 36497186 PMCID: PMC9736268 DOI: 10.3390/cells11233928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Crossbreeding, mutation breeding, and traditional transgenic breeding take much time to improve desirable characters/traits. CRISPR/Cas-mediated genome editing (GE) is a game-changing tool that can create variation in desired traits, such as biotic and abiotic resistance, increase quality and yield in less time with easy applications, high efficiency, and low cost in producing the targeted edits for rapid improvement of crop plants. Plant pathogens and the severe environment cause considerable crop losses worldwide. GE approaches have emerged and opened new doors for breeding multiple-resistance crop varieties. Here, we have summarized recent advances in CRISPR/Cas-mediated GE for resistance against biotic and abiotic stresses in a crop molecular breeding program that includes the modification and improvement of genes response to biotic stresses induced by fungus, virus, and bacterial pathogens. We also discussed in depth the application of CRISPR/Cas for abiotic stresses (herbicide, drought, heat, and cold) in plants. In addition, we discussed the limitations and future challenges faced by breeders using GE tools for crop improvement and suggested directions for future improvements in GE for agricultural applications, providing novel ideas to create super cultivars with broad resistance to biotic and abiotic stress.
Collapse
|
4
|
Mather JC, Wyllie JA, Hamilton A, Soares da Costa TP, Barnard PJ. Antibacterial silver and gold complexes of imidazole and 1,2,4-triazole derived N-heterocyclic carbenes. Dalton Trans 2022; 51:12056-12070. [PMID: 35876319 DOI: 10.1039/d2dt01657e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of gold(I) (4a-4h, 5a-5b) and silver(I) (3a-3h) complexes of 1,2,4-triazolylidene and imidazolylidene based N-heterocyclic carbene ligands were prepared and the antibacterial activities of these complexes have been evaluated. The complexes were characterised using 1H-NMR, 13C-NMR, HRMS and in the cases of 3a, 3c, 4b and 5b by X-ray crystallography. The gold(I) complexes with phenyl substituents (4a-4d) were found to have potent antibacterial activity against Gram-positive bacteria, with the complexes of the 1,2,4-triazolylidene ligands being more active (4c, MIC = 4-8 μg mL-1 against Enterococcus faecium and 2 μg mL-1 against Staphylococcus aureus) than the analogous imidazolylidene complexes 4a and 4b (4a, MIC = 64 μg mL-1 against E. faecium and 2-4 μg mL-1 against S. aureus). Two of the silver(I) complexes have promising antibacterial activity against Acinetobacter baumannii (3f, MIC = 2-4 μg mL-1 and 3g, MIC = 2 μg mL-1). Silver(I) complex 3f and gold(I) complex 4c were tested against multi-drug resistant bacterial strains and high levels of antibacterial activity were observed. The potential for antibacterial resistance to develop against these metal containing complexes was investigated and significantly, no resistance was observed upon continuous treatment, whilst resistance was developed against the widely used broad-spectrum antibiotic ciprofloxacin in the same bacterial strains, under the conditions tested. The solution and gas phase stabilities of the complexes have been investigated using a combination of 1H-NMR, HRMS and detailed computational mechanistic studies were undertaken to gain insights into the possible decomposition reactions for silver complexes in aqueous solution.
Collapse
Affiliation(s)
- Joel C Mather
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Victoria, 3086, Australia.
| | - Jessica A Wyllie
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Victoria, 3086, Australia.
| | - Alex Hamilton
- Biomolecular Sciences Research Centre (BMRC) and Department of Biosciences and Chemistry, Sheffield Hallam University, Sheffield, S1 1WB, UK
| | - Tatiana P Soares da Costa
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Victoria, 3086, Australia.
| | - Peter J Barnard
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Victoria, 3086, Australia.
| |
Collapse
|
5
|
Mackie ERR, Barrow AS, Christoff RM, Abbott BM, Gendall AR, Soares da Costa TP. A dual-target herbicidal inhibitor of lysine biosynthesis. eLife 2022; 11:78235. [PMID: 35723913 PMCID: PMC9208756 DOI: 10.7554/elife.78235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/10/2022] [Indexed: 11/29/2022] Open
Abstract
Herbicides with novel modes of action are urgently needed to safeguard global agricultural industries against the damaging effects of herbicide-resistant weeds. We recently developed the first herbicidal inhibitors of lysine biosynthesis, which provided proof-of-concept for a promising novel herbicide target. In this study, we expanded upon our understanding of the mode of action of herbicidal lysine biosynthesis inhibitors. We previously postulated that these inhibitors may act as proherbicides. Here, we show this is not the case. We report an additional mode of action of these inhibitors, through their inhibition of a second lysine biosynthesis enzyme, and investigate the molecular determinants of inhibition. Furthermore, we extend our herbicidal activity analyses to include a weed species of global significance.
Collapse
Affiliation(s)
- Emily R R Mackie
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia.,School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Waite Campus, Glen Osmond, Australia
| | - Andrew S Barrow
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Rebecca M Christoff
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Belinda M Abbott
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Anthony R Gendall
- Australian Research Council Industrial Transformation Research Hub for Medicinal Agriculture, AgriBio, La Trobe University, Bundoora, Australia.,Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Australia
| | - Tatiana P Soares da Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia.,School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Waite Campus, Glen Osmond, Australia
| |
Collapse
|
6
|
Braga ÍDO, Carvalho da Silva TL, Belo Silva VN, Rodrigues Neto JC, Ribeiro JADA, Abdelnur PV, de Sousa CAF, Souza MT. Deep Untargeted Metabolomics Analysis to Further Characterize the Adaptation Response of Gliricidia sepium (Jacq.) Walp. to Very High Salinity Stress. FRONTIERS IN PLANT SCIENCE 2022; 13:869105. [PMID: 35665181 PMCID: PMC9161747 DOI: 10.3389/fpls.2022.869105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/28/2022] [Indexed: 06/15/2023]
Abstract
The multipurpose tree Gliricidia sepium (Jacq.) Walp. adapts to a very high level of salt stress (≥20 dS m-1) and resumes the production of new leaves around 2 weeks after losing all leaves due to abrupt salinity stress. The integration of metabolome and transcriptome profiles from gliricidia leaves points to a central role of the phenylpropanoid biosynthesis pathway in the short-term response to salinity stress. In this study, a deeper untargeted metabolomics analysis of the leaves and roots of young gliricidia plants was conducted to characterize the mechanism(s) behind this adaptation response. The polar and lipidic fractions from leaf and root samples were extracted and analyzed on a UHPLC.ESI.Q-TOF.HRMS system. Acquired data were analyzed using the XCMS Online, and MetaboAnalyst platforms, via three distinct and complementary strategies. Together, the results obtained first led us to postulate that these plants are salt-excluding plants, which adapted to high salinity stress via two salt-excluding mechanisms, starting in the canopy-severe defoliation-and concluding in the roots-limited entry of Na. Besides that, it was possible to show that the phenylpropanoid biosynthesis pathway plays a role throughout the entire adaptation response, starting in the short term and continuing in the long one. The roots metabolome analysis revealed 11 distinct metabolic pathways affected by salt stress, and the initial analysis of the two most affected ones-steroid biosynthesis and lysine biosynthesis-led us also to postulate that the accumulation of lignin and some phytosterols, as well as lysine biosynthesis-but not degradation, play a role in promoting the adaptation response. However, additional studies are necessary to investigate these hypotheses.
Collapse
Affiliation(s)
| | | | | | | | | | - Patrícia Verardi Abdelnur
- Institute of Chemistry, Federal University of Goiás, Campus Samambaia, Goiânia, Brazil
- Brazilian Agricultural Research Corporation, Embrapa Agroenergy, Brasília, Brazil
| | | | - Manoel Teixeira Souza
- Graduate Program of Plant Biotechnology, Federal University of Lavras, Lavras, Brazil
- Brazilian Agricultural Research Corporation, Embrapa Agroenergy, Brasília, Brazil
| |
Collapse
|
7
|
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: 28] [Impact Index Per Article: 14.0] [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.
Collapse
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
| |
Collapse
|
8
|
Wong ACS, Massel K, Lam Y, Hintzsche J, Chauhan BS. Biotechnological Road Map for Innovative Weed Management. FRONTIERS IN PLANT SCIENCE 2022; 13:887723. [PMID: 35548307 PMCID: PMC9082642 DOI: 10.3389/fpls.2022.887723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/07/2022] [Indexed: 05/07/2023]
Abstract
In most agriculture farmlands, weed management is predominantly reliant on integrated weed management (IWM) strategies, such as herbicide application. However, the overuse and misuse of herbicides, coupled with the lack of novel active ingredients, has resulted in the uptrend of herbicide-resistant weeds globally. Moreover, weedy traits that contribute to weed seed bank persistence further exacerbate the challenges in weed management. Despite ongoing efforts in identifying and improving current weed management processes, the pressing need for novel control techniques in agricultural weed management should not be overlooked. The advent of CRISPR/Cas9 gene-editing systems, coupled with the recent advances in "omics" and cheaper sequencing technologies, has brought into focus the potential of managing weeds in farmlands through direct genetic control approaches, but could be achieved stably or transiently. These approaches encompass a range of technologies that could potentially manipulate expression of key genes in weeds to reduce its fitness and competitiveness, or, by altering the crop to improve its competitiveness or herbicide tolerance. The push for reducing or circumventing the use of chemicals in farmlands has provided an added incentive to develop practical and feasible molecular approaches for weed management, although there are significant technical, practical, and regulatory challenges for utilizing these prospective molecular technologies in weed management.
Collapse
Affiliation(s)
- Albert Chern Sun Wong
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
- *Correspondence: Albert Chern Sun Wong,
| | - Karen Massel
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Yasmine Lam
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Jessica Hintzsche
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Bhagirath Singh Chauhan
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Gatton, QLD, Australia
- School of Agriculture and Food Sciences, The University of Queensland, Gatton, QLD, Australia
| |
Collapse
|
9
|
Christoff RM, Soares da Costa TP, Bayat S, Holien JK, Perugini MA, Abbott BM. Synthesis and structure-activity relationship studies of 2,4-thiazolidinediones and analogous heterocycles as inhibitors of dihydrodipicolinate synthase. Bioorg Med Chem 2021; 52:116518. [PMID: 34826680 DOI: 10.1016/j.bmc.2021.116518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/03/2021] [Accepted: 11/05/2021] [Indexed: 10/19/2022]
Abstract
Dihydrodipicolinate synthase (DHDPS), responsible for the first committed step of the diaminopimelate pathway for lysine biosynthesis, has become an attractive target for the development of new antibacterial and herbicidal agents. Herein, we report the discovery and exploration of the first inhibitors of E. coli DHDPS which have been identified from screening lead and are not based on substrates from the lysine biosynthesis pathway. Over 50 thiazolidinediones and related analogues have been prepared in order to thoroughly evaluate the structure-activity relationships against this enzyme of significant interest.
Collapse
Affiliation(s)
- Rebecca M Christoff
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Tatiana P Soares da Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Saadi Bayat
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Jessica K Holien
- School of Science, STEM College, RMIT University, Melbourne, Victoria 3000, Australia
| | - Matthew A Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Belinda M Abbott
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia.
| |
Collapse
|