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Cai ZM, Huang GY, Dong J, Chen LJ, Ye BQ, Lin HY, Wang DW, Yang GF. Discovery of Tetrazolamide- benzimidazol-2-ones as Novel 4-Hydroxyphenylpyruvate Dioxygenase Inhibitors. J Agric Food Chem 2024; 72:3884-3893. [PMID: 38375801 DOI: 10.1021/acs.jafc.3c06798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
4-Hydroxyphenylpyruvate dioxygenase (HPPD, EC 1.13.11.27) is one of the most valuable herbicide targets due to its unique biological functions. In search of HPPD inhibitors with promising biological performance, we designed and synthesized a series of novel tetrazolamide-benzimidazol-2-ones using a structure-based drug design strategy. Among the synthesized compounds, 1-(2-chlorobenzyl)-3-methyl-N-(1-methyl-1H-tetrazol-5-yl)-2-oxo-2,3-dihydro-1H-benzo[d]imidazole-4-carboxamide, 25, IC50 = 10 nM, was identified to be the most outstanding HPPD inhibitor, which showed more than 36-fold increased Arabidopsis thaliana HPPD (AtHPPD) inhibition potency than mesotrione (IC50 = 363 nM). Our AtHPPD-25 complex indicated that one nitrogen atom on the tetrazole ring and the oxygen atom on the amide group formed a classical bidentate chelation interaction with the metal ion, the benzimidazol-2-one ring created a tight π-π stacking interaction with Phe381 and Phe424, and some hydrophobic interactions were also found between the ortho-Cl-benzyl group and surrounding residues. Compound 32 showed more than 80% inhibition against all four tested weeds at 150 g ai/ha by the postemergence application. Our results indicated that the tetrazolamide-benzimidazol-2-one scaffold may be a new lead structure for herbicide discovery.
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Affiliation(s)
- Zhuo-Mei Cai
- National Key Laboratory of Green Pesticide, Central China Normal University, Wuhan 430079, P. R. China
- International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Guang-Yi Huang
- National Key Laboratory of Green Pesticide, Central China Normal University, Wuhan 430079, P. R. China
- International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Jin Dong
- National Key Laboratory of Green Pesticide, Central China Normal University, Wuhan 430079, P. R. China
- International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Li-Jun Chen
- National Key Laboratory of Green Pesticide, Central China Normal University, Wuhan 430079, P. R. China
- International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Bao-Qing Ye
- National Key Laboratory of Green Pesticide, Central China Normal University, Wuhan 430079, P. R. China
- International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Hong-Yan Lin
- National Key Laboratory of Green Pesticide, Central China Normal University, Wuhan 430079, P. R. China
- International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Da-Wei Wang
- National Key Laboratory of Green Pesticide, Central China Normal University, Wuhan 430079, P. R. China
- International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Guang-Fu Yang
- National Key Laboratory of Green Pesticide, Central China Normal University, Wuhan 430079, P. R. China
- International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
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Saber A, Srhir M, Hökelek T, Mague JT, Hamou Ahabchane N, Sebbar NK, Essassi EM. Crystal structure, Hirshfeld surface analysis and inter-action energy and DFT studies of 1-methyl-3-(prop-2-yn-1-yl)-2,3-di-hydro-1 H-1,3-benzo-diazol-2-one. Acta Crystallogr E Crystallogr Commun 2019; 75:1940-1946. [PMID: 31871762 PMCID: PMC6895944 DOI: 10.1107/s2056989019015779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 11/21/2019] [Indexed: 11/20/2022]
Abstract
In the title mol-ecule, C11H10N2O, the di-hydro-benzimidazol-2-one moiety is essentially planar, with the prop-2-yn-1-yl substituent rotated well out of this plane. In the crystal, C-HMthy⋯π(ring) inter-actions and C-HProp⋯ODhyr (Mthy = methyl, Prop = prop-2-yn-1-yl and Dhyr = di-hydro) hydrogen bonds form corrugated layers parallel to (10), which are associated through additional C-HBnz⋯ODhyr (Bnz = benzene) hydrogen bonds and head-to-tail, slipped, π-stacking [centroid-to-centroid distance = 3.7712 (7) Å] inter-actions between di-hydro-benzimidazol-2-one moieties. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions to the crystal packing are from H⋯H (44.1%), H⋯C/C⋯H (33.5%) and O⋯H/H⋯O (13.4%) inter-actions. Hydrogen-bonding and van der Waals inter-actions are the dominant inter-actions in the crystal packing. Computational chemistry calculations indicate that in the crystal, C-H⋯O hydrogen-bond energies are 46.8 and 32.5 (for C-HProp⋯ODhyr) and 20.2 (for C-HBnz⋯ODhyr) kJ mol-1. Density functional theory (DFT) optimized structures at the B3LYP/6-311 G(d,p) level are compared with the experimentally determined mol-ecular structure in the solid state. The HOMO-LUMO behaviour was elucidated to determine the energy gap.
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Affiliation(s)
- Asmaa Saber
- Laboratoire de Chimie Organique Hétérocyclique URAC 21, Pôle de Compétence Pharmacochimie, Av. Ibn Battouta, BP 1014, Faculté des Sciences, Université Mohammed V, Rabat, Morocco
| | - Mohamed Srhir
- Laboratoire de Chimie Organique Hétérocyclique URAC 21, Pôle de Compétence Pharmacochimie, Av. Ibn Battouta, BP 1014, Faculté des Sciences, Université Mohammed V, Rabat, Morocco
| | - Tuncer Hökelek
- Department of Physics, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Joel T. Mague
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA
| | - Noureddine Hamou Ahabchane
- Laboratoire de Chimie Organique Hétérocyclique URAC 21, Pôle de Compétence Pharmacochimie, Av. Ibn Battouta, BP 1014, Faculté des Sciences, Université Mohammed V, Rabat, Morocco
| | - Nada Kheira Sebbar
- Laboratoire de Chimie Organique Hétérocyclique URAC 21, Pôle de Compétence Pharmacochimie, Av. Ibn Battouta, BP 1014, Faculté des Sciences, Université Mohammed V, Rabat, Morocco
- Laboratoire de Chimie Appliquée et Environnement, Equipe de Chimie Bioorganique Appliquée, Faculté des Sciences, Université Ibn Zohr, Agadir, Morocco
| | - El Mokhtar Essassi
- Laboratoire de Chimie Organique Hétérocyclique URAC 21, Pôle de Compétence Pharmacochimie, Av. Ibn Battouta, BP 1014, Faculté des Sciences, Université Mohammed V, Rabat, Morocco
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Mostarda S, Gür Maz T, Piccinno A, Cerra B, Banoglu E. Optimisation by Design of Experiment of Benzimidazol-2-One Synthesis under Flow Conditions. Molecules 2019; 24:molecules24132447. [PMID: 31277341 PMCID: PMC6651037 DOI: 10.3390/molecules24132447] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 06/27/2019] [Accepted: 06/28/2019] [Indexed: 01/19/2023] Open
Abstract
A novel flow-based approach for the preparation of benzimidazol-2-one (1) scaffold by the 1,1′-carbonyldiimidazole (CDI)-promoted cyclocarbonylation of o-phenylenediamine (2) is reported. Starting from a preliminary batch screening, the model reaction was successfully translated under flow conditions and optimised by means of design of experiment (DoE). The method allowed the efficient preparation of this privileged scaffold and to set up a general protocol for the multigram-scale preparation in high yield, purity, and productivity, and was successfully applied for the multigram flow synthesis of N-(2-chlorobenzyl)-5-cyano-benzimidazol-2-one, which is a key synthon for hit-to-lead explorations in our anti-inflammatory drug discovery program.
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Affiliation(s)
- Serena Mostarda
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
- Current affiliation: Novartis Pharma AG, CH-4002 Basel, Switzerland
| | - Tugçe Gür Maz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, Etiler, 06560 Ankara, Turkey
| | - Alessandro Piccinno
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Bruno Cerra
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy.
| | - Erden Banoglu
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, Etiler, 06560 Ankara, Turkey.
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