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Xu Q, Zhao Z, Liang P, Wang S, Li F, Jin S, Zhang J. Identification of novel nematode succinate dehydrogenase inhibitors: Virtual screening based on ligand-pocket interactions. Chem Biol Drug Des 2023; 101:9-23. [PMID: 34981652 DOI: 10.1111/cbdd.14019] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/10/2021] [Accepted: 12/29/2021] [Indexed: 12/15/2022]
Abstract
To discover new nematicidal succinate dehydrogenase (SDH) inhibitors with novel structures, we conducted a virtual screening of the ChemBridge library with 1.7 million compounds based on ligand-pocket interactions. The homology model of Caenorhabditis elegans SDH was established, along with a pharmacophore model based on ligand-pocket interactions. After the pharmacophore-based and docking-based screening, 19 compounds were selected for the subsequent enzymatic assays. The results showed that compound 1 (ID: 7607321) exhibited inhibitory activity against SDH with a determined IC50 value of 19.6 μM. Structural modifications and nematicidal activity studies were then carried out, which provided further evidence that compound 1 exhibited excellent nematicidal activity. Molecular dynamics simulations were then conducted to investigate the underlying molecular basis for the potency of these inhibitors against SDH. This work provides a reliable strategy and useful information for the future design of nematode SDH inhibitors.
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Affiliation(s)
- Qingbo Xu
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Zhixiang Zhao
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Peibo Liang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Simin Wang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Fang Li
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Shuhui Jin
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Jianjun Zhang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
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2
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Chen D, Yang H, Li Z, Maienfisch P, Xu X. Design, synthesis and nematicidal activities of trifluorobutene hydroxamic acid derivatives against Meloidogyne incognita. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Ye L, Wang JY, Liu XF, Guan Q, Dou NX, Li J, Zhang Q, Gao YM, Wang M, Li JS, Zhou B. Nematicidal activity of volatile organic compounds produced by Bacillus altitudinis AMCC 1040 against Meloidogyne incognita. Arch Microbiol 2022; 204:521. [PMID: 35879581 DOI: 10.1007/s00203-022-03024-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/31/2022] [Indexed: 11/30/2022]
Abstract
The application of nematicidal microorganisms and their virulence factors provides more opportunities to control root-knot nematodes. Bacillus altitudinis AMCC 1040, previously isolated from suppressive soils, showed significant nematicidal activity, and in this study, nematicidal substances produced by Bacillus altitudinis AMCC 1040 were investigated. The results of the basic properties of active substances showed that these compounds have good thermal stability and passage, are resistant to acidic environment and sensitive to alkaline conditions. Further analysis showed that it is a volatile component. Using HS-SPME-GC/MS, the volatile compounds produced by Bacillus altitudinis AMCC 1040 were identified and grouped into four major categories: ethers, alcohols, ketone, and organic acids, comprising a total of eight molecules. Six of them possess nematicidal activities, including 2,3-butanedione, acetic acid, 2-isopropoxy ethylamine, 3-methylbutyric acid, 2-methylbutyric acid and octanoic acid. Our results further our understanding of the effects of Bacillus altitudinis and its nematicidal metabolites on the management of Meloidogyne incognita and may help in finding less toxic nematicides to control root knot nematodes.
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Affiliation(s)
- Lin Ye
- Agriculture College, Ningxia University, Yinchuan, Ning'xia, China
| | - Jian-Yu Wang
- Department of Microbiology, College of Life Sciences, Shandong Agricultural University, Tai'an , 271018, China
| | - Xiao-Fang Liu
- Department of Microbiology, College of Life Sciences, Shandong Agricultural University, Tai'an , 271018, China
| | - Qi Guan
- Department of Microbiology, College of Life Sciences, Shandong Agricultural University, Tai'an , 271018, China
| | - Nong-Xiao Dou
- Department of Microbiology, College of Life Sciences, Shandong Agricultural University, Tai'an , 271018, China
| | - Jian Li
- College of Food and Bioengineering, Jimei University, Xiamen, 361021, China.
| | - Qian Zhang
- Shandong Institute of Pomology, Tai'an, 271018, China
| | - Yan-Ming Gao
- Agriculture College, Ningxia University, Yinchuan, Ning'xia, China
| | - Min Wang
- Shandong Wanhao Fertilizer Co., LTD, Jinan, 25000, China
| | - Jian-She Li
- Agriculture College, Ningxia University, Yinchuan, Ning'xia, China.
| | - Bo Zhou
- Department of Microbiology, College of Life Sciences, Shandong Agricultural University, Tai'an , 271018, China. .,National Engineering Research Center for Efficient Utilization of Soil and Fertilizer, Tai'an, 271018, China.
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4
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Yang H, Zhang R, Li Z, Maienfisch P, Xu X. Design, synthesis and nematicidal activitives of trifluorobutene amide derivatives against Meloidogyne incognita. Bioorg Med Chem Lett 2021; 40:127917. [PMID: 33705904 DOI: 10.1016/j.bmcl.2021.127917] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 11/19/2022]
Abstract
Plant parasitic nematodes have always been a pressing problem in the field of plant protection. Well-established chemical nematicides, especially organophosphorus and carbamates are the most used products for nematode control worldwide. Due to long-term overuse, they have developed serious resistance and new innovative solutions are urgently required. In this study, thirty-one novel trifluorobutene amide derivatives were designed and synthesized, and their nematicidal activities were determined. Three different synthetic methods have been developed for the final amidation reaction enabling the successfully syntheses of the target compounds independently from the nucleophilicities of the substrate amino group. Most target compounds showed good nematicidal activity in our in vitro test. Among all the compounds, compounds A8 and A23 exhibited excellent nematicidal activity against Meloidogyne incognita, their LC50 values are 2.02 mg L-1 and 0.76 mg L-1, respectively. In particular, compound A23 has found to be almost as active as the commercial nematicide fluensulfone. Furthermore, most compounds gave full control (100% inhibition) of M. incognita at 40 mg L-1 in the in vivo tests in sandy soil, the best compounds were further investigated for in vivo activity in matrix soil. Among the compound tested, compound A8 showed excellent in vivo nematicidal activity. At a concentration of 5 mg L-1 still 56% inhibition was observed. The results of our study indicate that compound A8 possesses excellent in vitro and in vivo nematicidal activity, and can be considered as promising lead molecule for further modification.
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Affiliation(s)
- Haiping Yang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Ruifeng Zhang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zhong Li
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Peter Maienfisch
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China; CreInSol MCB, CH-4118 Rodersdorf, Switzerland.
| | - Xiaoyong Xu
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China.
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Xu Q, Liang P, Lu H, Jin S, Dong Y, Zhang J. Design, Synthesis and Bioactivity of Fluopyram Derivatives Containing Diamide Moiety. CHINESE J ORG CHEM 2021. [DOI: 10.6023/cjoc202103021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Chen J, Li QX, Song B. Chemical Nematicides: Recent Research Progress and Outlook. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:12175-12188. [PMID: 33079521 DOI: 10.1021/acs.jafc.0c02871] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Plant-parasitic nematodes have caused huge economic losses to agriculture worldwide and seriously threaten the sustainable development of modern agriculture. Chemical nematicides are still the most effective means to manage nematodes. However, the long-term use of organophosphorus and carbamate nematicides has led to a lack of field control efficacy and increased nematode resistance. To meet the huge market demand and slow the growth of resistance, new nematicides are needed to enter the market. The rational design and synthesis of new chemical scaffolds to screen for new nematicides is still a difficult task. We reviewed the latest research progress of nematicidal compounds in the past decade, discussed the structure-activity relationship and mechanism of action, and recommended some nematicidal active fragments. It is hoped that this review can update the recent progress on nematicide discoveries and provide new ideas for the design and mechanism of action studies of nematicides.
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Affiliation(s)
- Jixiang Chen
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
| | - Baoan Song
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
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Xiang H, Chen Y, Zhang J, Zhang J, Pan D, Liu B, Ouyang L. Discovery of a novel sodium taurocholate cotransporting polypeptide (NTCP) inhibitor: Design, synthesis, and anti-proliferative activities. CHINESE CHEM LETT 2020. [DOI: 10.1016/j.cclet.2020.03.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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