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Luo D, Bai Z, Bai H, Liu N, Han J, Ma C, Wu D, Bai L, Li Z. A first-in-class dimethyl 2-acetamido terephthalate inhibitor targeting Conyza canadensis SHMT1 with a novel herbicidal mode-of-action. J Adv Res 2023:S2090-1232(23)00295-3. [PMID: 37820886 DOI: 10.1016/j.jare.2023.10.003] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/26/2023] [Accepted: 10/04/2023] [Indexed: 10/13/2023] Open
Abstract
INTRODUCTION Herbicide application is a highly efficiency method of weed control that boots agricultural output and assures food security. The development of novel herbicides focuses on improved bioactivity and new modes of action. The amino acid biosynthesis was validated as a promising novel mode of action for herbicidal compounds. However, the amino acid biosynthesis enzyme remains largely unexplored for herbicidal targets. OBJECTIVES Serine hydroxymethyl transferase (SHMT) is an essentialenzyme in the photorespiratory cycle. The study aims to explore Conyza canadensis SHMT1 (CcSHMT1) as a promising target for herbicide discovery. METHODS Structure determination of CcSHMT1 was resolved by X-ray crystallography. Virtual screening docking experiments were performed with Glide version 5.5. Novel derivatives of dimethyl 2-acetamido terephthalate were further designed, synthesized, and bioassay. The druggability of the inhibitor was evidenced by ultrastructural changes in mitochondria, in vivo and vitro enzyme activity assays, and genetics analysis. RESULTS CcSHMT1 has a typical PLP-dependent enzyme 3D structure. The dimethyl 2-acetamido terephthalate-containing compounds had herbicidal activity. Dimethyl 2-(2-(4-(2-(4-bromo-2-chlorophenoxy) acetyl)piperazin-1-yl)acetamido) terephthalate (Compound 9ay, EC50 = 193.8 g a.i./ ha) exhibited the highest herbicidal activity on tested weed among the synthesized compounds. Compound 9ay had no obvious adverse effect on the growth of maize and honeybees. Compound 9ay was verified to target CcSHMT1 as an herbicide candidate. CONCLUSION A first-in-class CcSHMT1 inhibitor that could be developed as a potent herbicide with a new mode of action and provide an avenue for discovering novel inhibitors of pyridoxal-5-phosphate-dependent enzymes.
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Affiliation(s)
- Dingfeng Luo
- Hunan Provincial Key Laboratory for Biology and Control of Weeds, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Longping Branch, College of Biology, Hunan University, Changsha 410125, China
| | - Zhendong Bai
- Hunan Provincial Key Laboratory for Biology and Control of Weeds, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Haodong Bai
- Hunan Provincial Key Laboratory for Biology and Control of Weeds, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Na Liu
- Hunan Provincial Key Laboratory for Biology and Control of Weeds, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Longping Branch, College of Biology, Hunan University, Changsha 410125, China
| | - Jincai Han
- Hunan Provincial Key Laboratory for Biology and Control of Weeds, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Longping Branch, College of Biology, Hunan University, Changsha 410125, China
| | - Changsheng Ma
- Hunan Provincial Key Laboratory for Biology and Control of Weeds, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Longping Branch, College of Biology, Hunan University, Changsha 410125, China
| | - Di Wu
- Hunan Provincial Key Laboratory for Biology and Control of Weeds, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Lianyang Bai
- Hunan Provincial Key Laboratory for Biology and Control of Weeds, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Longping Branch, College of Biology, Hunan University, Changsha 410125, China.
| | - Zuren Li
- Hunan Provincial Key Laboratory for Biology and Control of Weeds, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Longping Branch, College of Biology, Hunan University, Changsha 410125, China.
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Honarmand Ebrahimi K, Ciofi-baffoni S, Hagedoorn P, Nicolet Y, Le Brun NE, Hagen WR, Armstrong FA. Iron–sulfur clusters as inhibitors and catalysts of viral replication. Nat Chem. [DOI: 10.1038/s41557-021-00882-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 12/15/2021] [Indexed: 12/11/2022]
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Liu HJ, Yang ZL, Ren LL, Wang YM, Wang X, Qian TT. Functional Divergence of the Glutamine Phosphoribosyl Pyrophosphate Amidotransferase (ASE) Gene Family in Arabidopsis. J EVOL BIOCHEM PHYS+ 2021. [DOI: 10.1134/s0022093021060119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Li C, Chen S, Huang T, Zhang F, Yuan J, Chang H, Li W, Han W. Conformational Changes of Glutamine 5'-Phosphoribosylpyrophosphate Amidotransferase for Two Substrates Analogue Binding: Insight from Conventional Molecular Dynamics and Accelerated Molecular Dynamics Simulations. Front Chem 2021; 9:640994. [PMID: 33718330 PMCID: PMC7953260 DOI: 10.3389/fchem.2021.640994] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 12/13/2020] [Accepted: 01/19/2021] [Indexed: 12/31/2022] Open
Abstract
Glutamine 5′-phosphoribosylpyrophosphate amidotransferase (GPATase) catalyzes the synthesis of phosphoribosylamine, pyrophosphate, and glutamate from phosphoribosylpyrophosphate, as well as glutamine at two sites (i.e., glutaminase and phosphoribosylpyrophosphate sites), through a 20 Å NH3 channel. In this study, conventional molecular dynamics (cMD) simulations and enhanced sampling accelerated molecular dynamics (aMD) simulations were integrated to characterize the mechanism for coordination catalysis at two separate active sites in the enzyme. Results of cMD simulations illustrated the mechanism by which two substrate analogues, namely, DON and cPRPP, affect the structural stability of GPATase from the perspective of dynamic behavior. aMD simulations obtained several key findings. First, a comparison of protein conformational changes in the complexes of GPATase–DON and GPATase–DON–cPRPP showed that binding cPRPP to the PRTase flexible loop (K326 to L350) substantially effected the formation of the R73-DON salt bridge. Moreover, only the PRTase flexible loop in the GPATase–DON–cPRPP complex could remain closed and had sufficient space for cPRPP binding, indicating that binding of DON to the glutamine loop had an impact on the PRTase flexible loop. Finally, both DON and cPRPP tightly bonded to the two domains, thereby inducing the glutamine loop and the PRTase flexible loop to move close to each other. This movement facilitated the transfer of NH3 via the NH3 channel. These theoretical results are useful to the ongoing research on efficient inhibitors related to GPATase.
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Affiliation(s)
- Congcong Li
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun, China
| | - Siao Chen
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun, China
| | - Tianci Huang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun, China
| | - Fangning Zhang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun, China
| | - Jiawei Yuan
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun, China
| | - Hao Chang
- Jilin Province TeyiFood Biotechnology Company Limited, Changchun, China
| | - Wannan Li
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun, China
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun, China
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