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Ma T, Gao S, Zhao LX, Ye F, Fu Y. 4-Hydroxyphenylpyruvate Dioxygenase Inhibitors: From Molecular Design to Synthesis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 39047218 DOI: 10.1021/acs.jafc.4c01171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Weed resistance is a critical issue in crop production. Among the known herbicides, 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitors are crucial for addressing weed resistance. HPPD inhibitors constitute a pivotal aspect of contemporary crop protection strategies. The advantages of these herbicides are their broad weed spectrum, flexible application, and excellent compatibility with other herbicides. They also exhibit satisfactory crop selectivity and low toxicity and are environmentally friendly. An increasing number of new HPPD inhibitors have been designed by combining computer-aided drug design with conventional design approaches. Herein, the molecular design and structural features of innovative HPPD inhibitors are reviewed to guide the development of new HPPD inhibitors possessing an enhanced biological efficacy.
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Affiliation(s)
- Tengfei Ma
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Shuang Gao
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
- Key Laboratory of Agricultural Functional Molecule Design and Utilization of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Li-Xia Zhao
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
- Key Laboratory of Agricultural Functional Molecule Design and Utilization of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Fei Ye
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
- Key Laboratory of Agricultural Functional Molecule Design and Utilization of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Ying Fu
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
- Key Laboratory of Agricultural Functional Molecule Design and Utilization of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
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Shi J, Gao S, Zhang PX, Zhang FH, Zhao LX, Ye F, Fu Y. Identification of novel dual-target 4-hydroxyphenylpyruvate dioxygenase & phytoene dehydrogenase inhibitors via multiple virtual screening. Int J Biol Macromol 2024; 276:133892. [PMID: 39019355 DOI: 10.1016/j.ijbiomac.2024.133892] [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: 03/27/2024] [Revised: 07/12/2024] [Accepted: 07/13/2024] [Indexed: 07/19/2024]
Abstract
Two important plant enzymes are 4-hydroxyphenylpyruvate dioxygenase (HPPD; EC 1.13.11.27), which is necessary for biosynthesis of plastoquinone and tocopherols, and phytoene dehydrogenase (PDS; EC 1.3.99.26), which plays an important role in colour rendering. Dual-target proteins that inhibit pigment synthesis will prevent resistant weeds and improve the spectral characteristics of herbicides. This study introduces virtual screening of pharmacophores based on the complex structure of the two targets. A three-dimensional database was established by screening 1,492,858 compounds based on the Lipinski principle. HPPD&PDS dual-target receptor-ligand pharmacophore models were then constructed, and nine potential dual-target inhibitors were obtained through pharmacophore modeling, molecular docking, and molecular dynamics simulations. Ultimately, ADMET prediction software yielded three compounds with high potential as dual-target herbicides. The obtained nine inhibitors were stable when combined with both HPPD and PDS proteins. This study offers guidance for the development of HPPD&PDS dual-target inhibitors with novel skeletons.
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Affiliation(s)
- Juan Shi
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, PR China
| | - Shuang Gao
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, PR China; Key Laboratory of Agricultural Functional Molecule Design and Utilization of Heilongjiang Province, PR China
| | - Pan-Xiu Zhang
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, PR China
| | - Fang-Hao Zhang
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, PR China
| | - Li-Xia Zhao
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, PR China; Key Laboratory of Agricultural Functional Molecule Design and Utilization of Heilongjiang Province, PR China
| | - Fei Ye
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, PR China; Key Laboratory of Agricultural Functional Molecule Design and Utilization of Heilongjiang Province, PR China.
| | - Ying Fu
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, PR China; Key Laboratory of Agricultural Functional Molecule Design and Utilization of Heilongjiang Province, PR China.
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Zhang CQ, Gao S, Bo L, Song HM, Liu LM, Zheng MX, Fu Y, Ye F. Design, Synthesis, and Biological Activity of Novel Triketone-Containing Phenoxy Nicotinyl Inhibitors of HPPD. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:11321-11330. [PMID: 38714361 DOI: 10.1021/acs.jafc.3c08705] [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: 05/09/2024]
Abstract
4-Hydroxyphenylpyruvate dioxygenase (HPPD) is a crucial target enzyme in albino herbicides. The inhibition of HPPD activity interferes with the synthesis of carotenoids, blocking photosynthesis and resulting in bleaching and necrosis. To develop herbicides with excellent activity, a series of 3-hydroxy-2-(6-substituted phenoxynicotinoyl)-2-cyclohexen-1-one derivatives were designed via active substructure combination. The title compounds were characterized via infrared spectroscopy, 1H and 13C nuclear magnetic resonance spectroscopies, and high-resolution mass spectrometry. The structure of compound III-17 was confirmed via single-crystal X-ray diffraction. Preliminary tests demonstrated that some compounds had good herbicidal activity. Crop safety tests revealed that compound III-29 was safer than the commercial herbicide mesotrione in wheat and peanuts. Moreover, the compound exhibited the highest inhibitory activity against Arabidopsis thaliana HPPD (AtHPPD), with a half-maximal inhibitory concentration of 0.19 μM, demonstrating superior activity compared with mesotrione (0.28 μM) in vitro. A three-dimensional quantitative structure-activity relationship study revealed that the introduction of smaller groups to the 5-position of cyclohexanedione and negative charges to the 3-position of the benzene ring enhanced the herbicidal activity. A molecular structure comparison demonstrated that compound III-29 was beneficial to plant absorption and conduction. Molecular docking and molecular dynamics simulations further verified the stability of the complex formed by compound III-29 and AtHPPD. Thus, this study may provide insights into the development of green and efficient herbicides.
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Affiliation(s)
- Chen-Qing Zhang
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Shuang Gao
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Lin Bo
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Hao-Min Song
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Li-Ming Liu
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Mei-Xin Zheng
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Ying Fu
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Fei Ye
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
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Xu QX, Guo L, Li Y, Wang ZW, Hu P, Yang GM, Pan Y. In silico screening-based discovery of benzamide derivatives as inhibitors of Rho-associated kinase-1 (ROCK1). J Biomol Struct Dyn 2023:1-18. [PMID: 37668086 DOI: 10.1080/07391102.2023.2253918] [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: 02/09/2023] [Accepted: 07/17/2023] [Indexed: 09/06/2023]
Abstract
As a pivotal node in modulating various cell behaviors, Rho-associated kinase-1 (ROCK1) has attracted significant attention as a promising therapeutic target in a variety of diseases. Benzamide has been widely reported as a ROCK1 inhibitors in recent years. To better understand its pharmacological properties and to explore its potential inhibitors, a series of ROCK1 inhibitors derived from N-methyl-4-(4-pyrazolidinyl) benzamides (MPBs) were investigated by using three-dimensional quantitative structure-activity relationship (3D-QSAR) models, pharmacophore models, molecular docking, and molecular dynamics (MD) simulation. The comparative Molecular Field Analysis (CoMFA) model (q2 = 0.616, R2 = 0.972, ONC = 4, and r2pred = 0.983) and the best Comparative Molecular Similarity Indices Analysis (CoMSIA) model (q2= 0.740, R2 = 0.982, ONC = 6, and r2pred = 0.824) exhibited reliable predictability with satisfactory validation parameters. In the subsequent virtual screening, VS03 and VS05 were identified to have superior predicted activities and higher docking scores, meanwhile they demonstrated to be reasonably stable in the binding pocket through MD simulations. These results provide a significant theoretical direction for the rational design and development of novel ROCK1 inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Qi-Xuan Xu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Liang Guo
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yuan Li
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhao-Wei Wang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Po Hu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Guang-Ming Yang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yang Pan
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
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Islam M, Khan A, Khan M, Halim SA, Ullah S, Hussain J, Al-Harrasi A, Shafiq Z, Tasleem M, El-Gokha A. Synthesis and biological evaluation of 2-nitrocinnamaldehyde derived thiosemicarbazones as urease inhibitors. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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Ding Y, Zhao DM, Kang T, Shi J, Ye F, Fu Y. Design, Synthesis, and Structure-Activity Relationship of Novel Aryl-Substituted Formyl Oxazolidine Derivatives as Herbicide Safeners. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:7654-7668. [PMID: 37191232 DOI: 10.1021/acs.jafc.3c00467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Nicosulfuron is the leading herbicide in the global sulfonylurea (SU) herbicide market; it was jointly developed by DuPont and Ishihara. Recently, the widespread use of nicosulfuron has led to increasingly prominent agricultural production hazards, such as environmental harm and influence on subsequent crops. The use of herbicide safeners can significantly alleviate herbicide injury to protect crop plants and expand the application scope of existing herbicides. A series of novel aryl-substituted formyl oxazolidine derivatives were designed using the active group combination method. Title compounds were synthesized using an efficient one-pot method and characterized by infrared (IR) spectrometry, 1H and 13C nuclear magnetic resonance (NMR), and high-resolution mass spectrometry (HRMS). The chemical structure of compound V-25 was further identified by X-ray single crystallography. The bioactivity assay and structure-activity relationship proved that nicosulfuron phytotoxicity to maize could be reduced by most title compounds. The glutathione S-transferase (GST) activity and acetolactate synthase (ALS) in vivo were determined, and compound V-12 showed inspiring activity comparable to that of the commercial safener isoxadifen-ethyl. The molecular docking model indicated that compound V-12 competed with nicosulfuron for the acetolactate synthase active site and that this is the protective mechanism of safeners. Absorption, distribution, metabolism, excretion, and toxicity (ADMET) predictions demonstrated that compound V-12 exhibited superior pharmacokinetic properties to the commercialized safener isoxadifen-ethyl. The target compound V-12 shows strong herbicide safener activity in maize; thus, it may be a potential candidate compound that can help further protect maize from herbicide damage.
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Affiliation(s)
- Yu Ding
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
| | - Dong-Mei Zhao
- School of Food Engineering, East University of Heilongjiang, Harbin, Heilongjiang 150076, People's Republic of China
| | - Tao Kang
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
| | - Juan Shi
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
| | - Fei Ye
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
- School of Food Engineering, East University of Heilongjiang, Harbin, Heilongjiang 150076, People's Republic of China
| | - Ying Fu
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
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Yang D, Wang YE, Chen M, Liu H, Huo J, Zhang J. Discovery of Bis-5-cyclopropylisoxazole-4-carboxamides as Novel Potential 4-Hydroxyphenylpyruvate Dioxygenase Inhibitors. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:5136-5142. [PMID: 36972477 DOI: 10.1021/acs.jafc.2c08912] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
4-Hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27; HPPD) represents a potential target for novel herbicide development. To discover the more promising HPPD inhibitor, we designed and synthesized a series of bis-5-cyclopropylisoxazole-4-carboxamides with different linkers using a multitarget pesticide design strategy. Among them, compounds b9 and b10 displayed excellent herbicidal activities versus Digitaria sanguinalis (DS) and Amaranthus retroflexus (AR) with the inhibition of about 90% at the concentration of 100 mg/L in vitro, which was better than that of isoxaflutole (IFT). Furthermore, compounds b9 and b10 displayed the best inhibitory effect versus DS and AR with the inhibition of about 90 and 85% at 90 g (ai)/ha in the greenhouse, respectively. The structure-activity relationship study showed that the flexible linker (6 carbon atoms) is responsible for increasing their herbicidal activity. The molecular docking analyses showed that compounds b9 and b10 could more closely bind to the active site of HPPD and thus exhibited a better inhibitory effect. Altogether, these results indicated that compounds b9 and b10 could be used as potential herbicide candidates targeting HPPD.
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Affiliation(s)
- Dongchen Yang
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, P. R. China
| | - Yan-En Wang
- College of Science, Hebei Agricultural University, Baoding 071001, P. R. China
| | - Miaomiao Chen
- Scientific Rescearch Academy, Hebei Agricultural University, Baoding 071001, P. R. China
| | - Haiyan Liu
- College of Science, Hebei Agricultural University, Baoding 071001, P. R. China
| | - Jingqian Huo
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, P. R. China
| | - Jinlin Zhang
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, P. R. China
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