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Wu X, Yang Z, Song C, Bu M, Li W, Duan J, Yang GF, Zhang A. Hydroxamate-Containing Bisphosphonates as Fosmidomycin Analogues: Design, Synthesis, and Proherbicide Activity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:7684-7693. [PMID: 38532701 DOI: 10.1021/acs.jafc.3c07872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
Fosmidomycin (FOS) is a natural product inhibiting the DXR enzyme in the MEP pathway and has stimulated interest for finding more suitable FOS analogues. Herein, two series of FOS analogue hydroxamate-containing bisphosphonates as proherbicides were designed, with bisphosphonate replacing the phosphonic unit in FOS while retaining the hydroxamate (BPF series) or replacing it with retro-hydroxamate (BPRF series). The BPF series were synthesized through a three-step reaction sequence including Michael addition of vinylidenebisphosphonate, N-acylation, and deprotection, and the BPRF series were synthesized with a retro-Claisen condensation incorporated into the reaction sequence. Evaluation on model plants demonstrated several compounds having considerable herbicidal activities, and in particular, compound 8m exhibited multifold activity enhancement as compared to the control FOS. The proherbicide properties were comparatively validated. Furthermore, DXR enzyme assay, dimethylallyl pyrophosphate rescue, and molecular docking verified 8m to be a promising proherbicide candidate targeting the DXR enzyme. In addition, 8m also displayed good antimalarial activities.
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Affiliation(s)
- Xin Wu
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Zili Yang
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Chunlin Song
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Mengwei Bu
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Weiguo Li
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Jiang Duan
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Guang-Fu Yang
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Aidong Zhang
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan 430079, China
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Zia MP, Jain M, Muthukumaran J, Singh AK. Exploration of potential hit compounds targeting 1-deoxy-d-xylulose 5-phosphate reductoisomerase (IspC) from Acinetobacter baumannii: an in silico investigation. 3 Biotech 2024; 14:72. [PMID: 38362590 PMCID: PMC10864239 DOI: 10.1007/s13205-024-03923-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 01/07/2024] [Indexed: 02/17/2024] Open
Abstract
The emergence of carbapenem-resistant Acinetobacter baumannii, a highly concerning bacterial species designated as a Priority 1: Critical pathogen by the WHO, has become a formidable global threat. In this study, we utilised computational methods to explore the potent molecules capable of inhibiting the IspC enzyme, which plays a crucial role in the methylerythritol 4-phosphate (MEP) biosynthetic pathway. Employing high-throughput virtual screening of small molecules from the Enamine library, we focused on the highly conserved substrate binding site of the DXR target protein, resulting in the identification of 1000 potential compounds. Among these compounds, we selected the top two candidates (Z2615855584 and Z2206320703) based on Lipinski's rule of Five and ADMET filters, along with FR900098, a known IspC inhibitor, and DXP, the substrate of IspC, for molecular dynamics (MD) simulations. The MD simulation trajectories revealed remarkable structural and thermodynamic stability, as well as strong binding affinity, for all the IspC-ligand complexes. Furthermore, binding free energy calculations based on MM/PBSA (Molecular Mechanics/Poisson-Boltzmann Surface Area) methodology demonstrated significant interactions between the selected ligand molecules and IspC. Taking into consideration all the aforementioned criteria, we suggest Z2206320703 as the potent lead candidate against IspC. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-03923-w.
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Affiliation(s)
- Mahrukh Parveez Zia
- Department of Biotechnology, School of Engineering and Technology, Sharda University, P.C. 201310, Greater Noida, Uttar Pradesh India
| | - Monika Jain
- Department of Biotechnology, School of Engineering and Technology, Sharda University, P.C. 201310, Greater Noida, Uttar Pradesh India
| | - Jayaraman Muthukumaran
- Department of Biotechnology, School of Engineering and Technology, Sharda University, P.C. 201310, Greater Noida, Uttar Pradesh India
| | - Amit Kumar Singh
- Department of Biotechnology, School of Engineering and Technology, Sharda University, P.C. 201310, Greater Noida, Uttar Pradesh India
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Wu X, Bu M, Yang Z, Ping H, Song C, Duan J, Zhang A. Design and synthesis of fosmidomycin analogs containing aza-linkers and their biological activity evaluation. PEST MANAGEMENT SCIENCE 2024; 80:846-856. [PMID: 37794283 DOI: 10.1002/ps.7810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/02/2023] [Accepted: 10/05/2023] [Indexed: 10/06/2023]
Abstract
BACKGROUND The enzymes involved in the 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway are attractive targets of a new mode of action for developing anti-infective drugs and herbicides, and inhibitors against 1-deoxy-d-xylulose 5-phosphate reductoisomerase (IspC), the second key enzyme in the pathway, have been intensively investigated; however, few works are reported regarding IspC inhibitors designed for new herbicide discovery. RESULTS A series of fosmidomycin (FOS) analogs were designed with nitrogen-containing linkers replacing the trimethylene linker between the two active substructures of FOS, phosphonic acid and hydroxamic acid. Synthesis followed a facile three-step route of sequential aza-Michael addition of α-amino acids to dibenzyl vinylphosphonate, amidation of the amino acid carboxyl with O-benzyl hydroxylamine, and simultaneous removal of the benzyl protective groups. Biological activity evaluation of IspC and model plants revealed that some compounds had moderate enzyme and model plant growth inhibition effects. In particular, compound 10g, which has a N-(4-fluorophenylethyl) nitrogen-containing linker, exhibited the best plant inhibition activities, superior to the control FOS against the model plants Arabidopsis thaliana, Brassica napus L., Amaranthus retroflexus and Echinochloa crus-galli. A dimethylallyl pyrophosphate rescue assay on A. thaliana confirmed that both 10g and FOS exert their herbicidal activity by blocking the MEP pathway. This result consistent with molecular docking, which confirmed 10g and FOS binding to the IspC active site in a similar way. CONCLUSION Compound 10g has excellent herbicidal activity and represents the first herbicide lead structure of a new mode of action that targets IspC enzyme in the MEP pathway. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Xin Wu
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan, China
| | - Mengwei Bu
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan, China
| | - Zili Yang
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan, China
| | - Hongrui Ping
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan, China
| | - Chunlin Song
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan, China
| | - Jiang Duan
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan, China
| | - Aidong Zhang
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan, China
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Wu X, Yang Z, Bu M, Duan J, Zhang A. Design, Synthesis and Bioactivity Evaluation of Heterocycle-Containing Mono- and Bisphosphonic Acid Compounds. Molecules 2023; 28:7509. [PMID: 38005231 PMCID: PMC10673511 DOI: 10.3390/molecules28227509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Fosmidomycin (FOS) is a naturally occurring compound active against the 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) enzyme in the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway, and using it as a template for lead structure design is an effective strategy to develop new active compounds. In this work, by replacing the hydroxamate unit of FOS with pyrazole, isoxazole and the related heterocycles that also have metal ion binding affinity, while retaining the monophosphonic acid in FOS or replacing it with a bisphosphonic acid group, heterocycle-containing mono- and bisphosphonic acid compounds as FOS analogs were designed. The key steps involved in the facile synthesis of these FOS analogs included the Michael addition of diethyl vinylphosphonate or tetraethyl vinylidenebisphosphonate to β-dicarbonyl compounds and the subsequent cyclic condensation with hydrazine or hydroxylamine. Two additional isoxazolinone-bearing FOS analogs were synthesized via the Michaelis-Becker reaction with diethyl phosphite as a key step. The bioactivity evaluation on model plants demonstrated that several compounds have better herbicidal activities compared to FOS, with the most active compound showing a 3.7-fold inhibitory activity on Arabidopsis thaliana, while on the roots and stalks of Brassica napus L. and Echinochloa crus-galli in a pre-emergence inhibitory activity test, the activities of this compound were found to be 3.2- and 14.3-fold and 5.4- and 9.4-fold, respectively, and in a post-emergency activity test on Amaranthus retroflexus and Echinochloa crus-galli, 2.2- and 2.0-fold inhibition activities were displayed. Despite the significant herbicidal activity, this compound exhibited a DXR inhibitory activity lower than that of FOS but comparable to that of other non-hydroxamate DXR inhibitors, and the dimethylallyl pyrophosphate rescue assay gave no statistical significance, suggesting that a different target might be involved in the inhibiting process. This work demonstrates that using bioisosteric replacement can be considered as a valuable strategy to discover new FOS analogs that may have high herbicidal activities.
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Affiliation(s)
| | | | | | - Jiang Duan
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan 430079, China; (X.W.); (Z.Y.); (M.B.)
| | - Aidong Zhang
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan 430079, China; (X.W.); (Z.Y.); (M.B.)
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Wu X, Ping H, Song C, Duan J, Zhang A. Optimization synthesis of phosphorous-containing natural products fosmidomycin and FR900098. PHOSPHORUS SULFUR 2023. [DOI: 10.1080/10426507.2023.2173756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Xin Wu
- Key Laboratory of Pesticides & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei, China
| | - Hongrui Ping
- Key Laboratory of Pesticides & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei, China
| | - Chunlin Song
- Key Laboratory of Pesticides & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei, China
| | - Jiang Duan
- Key Laboratory of Pesticides & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei, China
| | - Aidong Zhang
- Key Laboratory of Pesticides & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei, China
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Gierse RM, Oerlemans R, Reddem ER, Gawriljuk VO, Alhayek A, Baitinger D, Jakobi H, Laber B, Lange G, Hirsch AKH, Groves MR. First crystal structures of 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Mycobacterium tuberculosis indicate a distinct mechanism of intermediate stabilization. Sci Rep 2022; 12:7221. [PMID: 35508530 PMCID: PMC9068908 DOI: 10.1038/s41598-022-11205-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 04/15/2022] [Indexed: 11/18/2022] Open
Abstract
The development of drug resistance by Mycobacterium tuberculosis and other pathogenic bacteria emphasizes the need for new antibiotics. Unlike animals, most bacteria synthesize isoprenoid precursors through the MEP pathway. 1-Deoxy-d-xylulose 5-phosphate synthase (DXPS) catalyzes the first reaction of the MEP pathway and is an attractive target for the development of new antibiotics. We report here the successful use of a loop truncation to crystallize and solve the first DXPS structures of a pathogen, namely M. tuberculosis (MtDXPS). The main difference found to other DXPS structures is in the active site where a highly coordinated water was found, showing a new mechanism for the enamine-intermediate stabilization. Unlike other DXPS structures, a “fork-like” motif could be identified in the enamine structure, using a different residue for the interaction with the cofactor, potentially leading to a decrease in the stability of the intermediate. In addition, electron density suggesting a phosphate group could be found close to the active site, provides new evidence for the D-GAP binding site. These results provide the opportunity to improve or develop new inhibitors specific for MtDXPS through structure-based drug design.
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Affiliation(s)
- Robin M Gierse
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Campus Building E 8.1, 66123, Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany.,Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Rick Oerlemans
- Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AV, Groningen, The Netherlands
| | - Eswar R Reddem
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.,Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AV, Groningen, The Netherlands
| | - Victor O Gawriljuk
- Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AV, Groningen, The Netherlands.,São Carlos Institute of Physics, University of São Paulo, Av. João Dagnone, 1100-Santa Angelina, São Carlos, SP, 13563-120, Brazil
| | - Alaa Alhayek
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Campus Building E 8.1, 66123, Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Dominik Baitinger
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Campus Building E 8.1, 66123, Saarbrücken, Germany
| | - Harald Jakobi
- Research & Development Crop Science, Bayer AG, Industriepark Höchst, 65926, Frankfurt, Germany
| | - Bernd Laber
- Research & Development Crop Science, Bayer AG, Industriepark Höchst, 65926, Frankfurt, Germany
| | - Gudrun Lange
- Research & Development Crop Science, Bayer AG, Industriepark Höchst, 65926, Frankfurt, Germany
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Campus Building E 8.1, 66123, Saarbrücken, Germany. .,Department of Pharmacy, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany. .,Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
| | - Matthew R Groves
- Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AV, Groningen, The Netherlands.
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Li Y, Li X, Zhang J, Li D, Yan L, You M, Zhang J, Lei X, Chang D, Ji X, An J, Li M, Bai S, Yan J. Physiological and Proteomic Responses of Contrasting Alfalfa ( Medicago sativa L.) Varieties to High Temperature Stress. FRONTIERS IN PLANT SCIENCE 2021; 12:753011. [PMID: 34956258 PMCID: PMC8695758 DOI: 10.3389/fpls.2021.753011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/11/2021] [Indexed: 06/14/2023]
Abstract
High temperature (HT) is an important factor for limiting global plant distribution and agricultural production. As the global temperature continues to rise, it is essential to clarify the physiological and molecular mechanisms of alfalfa responding the high temperature, which will contribute to the improvement of heat resistance in leguminous crops. In this study, the physiological and proteomic responses of two alfalfa (Medicago sativa L.) varieties contrasting in heat tolerance, MS30 (heat-tolerant) and MS37 (heat-sensitive), were comparatively analyzed under the treatments of continuously rising temperatures for 42 days. The results showed that under the HT stress, the chlorophyll content and the chlorophyll fluorescence parameter (Fv/Fm) of alfalfa were significant reduced and some key photosynthesis-related proteins showed a down-regulated trend. Moreover, the content of Malondialdehyde (MDA) and the electrolyte leakage (EL) of alfalfa showed an upward trend, which indicates both alfalfa varieties were damaged under HT stress. However, because the antioxidation-reduction and osmotic adjustment ability of MS30 were significantly stronger than MS37, the damage degree of the photosynthetic system and membrane system of MS30 is significantly lower than that of MS37. On this basis, the global proteomics analysis was undertaken by tandem mass tags (TMT) technique, a total of 6,704 proteins were identified and quantified. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that a series of key pathways including photosynthesis, metabolism, adjustment and repair were affected by HT stress. Through analyzing Venn diagrams of two alfalfa varieties, 160 and 213 differentially expressed proteins (DEPs) that had dynamic changes under HT stress were identified from MS30 and MS37, respectively. Among these DEPs, we screened out some key DEPs, such as ATP-dependent zinc metalloprotease FTSH protein, vitamin K epoxide reductase family protein, ClpB3, etc., which plays important functions in response to HT stress. In conclusion, the stronger heat-tolerance of MS30 was attributed to its higher adjustment and repair ability, which could cause the metabolic process of MS30 is more conducive to maintaining its survival and growth than MS37, especially at the later period of HT stress. This study provides a useful catalog of the Medicago sativa L. proteomes with the insight into its future genetic improvement of heat-resistance.
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Affiliation(s)
- Yingzhu Li
- Institute of Herbaceous Plants, Sichuan Academy of Grassland Science, Chengdu, China
| | - Xinrui Li
- Institute of Herbaceous Plants, Sichuan Academy of Grassland Science, Chengdu, China
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jin Zhang
- Institute of Herbaceous Plants, Sichuan Academy of Grassland Science, Chengdu, China
| | - Daxu Li
- Institute of Herbaceous Plants, Sichuan Academy of Grassland Science, Chengdu, China
| | - Lijun Yan
- Institute of Herbaceous Plants, Sichuan Academy of Grassland Science, Chengdu, China
| | - Minghong You
- Institute of Herbaceous Plants, Sichuan Academy of Grassland Science, Chengdu, China
| | - Jianbo Zhang
- Institute of Herbaceous Plants, Sichuan Academy of Grassland Science, Chengdu, China
| | - Xiong Lei
- Institute of Herbaceous Plants, Sichuan Academy of Grassland Science, Chengdu, China
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Dan Chang
- Institute of Herbaceous Plants, Sichuan Academy of Grassland Science, Chengdu, China
| | - Xiaofei Ji
- Institute of Herbaceous Plants, Sichuan Academy of Grassland Science, Chengdu, China
| | - Jinchan An
- Institute of Herbaceous Plants, Sichuan Academy of Grassland Science, Chengdu, China
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Mingfeng Li
- Institute of Herbaceous Plants, Sichuan Academy of Grassland Science, Chengdu, China
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Shiqie Bai
- Institute of Herbaceous Plants, Sichuan Academy of Grassland Science, Chengdu, China
| | - Jiajun Yan
- Institute of Herbaceous Plants, Sichuan Academy of Grassland Science, Chengdu, China
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