Structure-Guided Discovery of Silicon-Containing Subnanomolar Inhibitor of Hydroxyphenylpyruvate Dioxygenase as a Potential Herbicide

Abstract

4-Hydroxyphenylpyruvate dioxygenase (HPPD, EC 1.13.11.27) has been recognized as one of the most promising targets in the field of herbicide innovation considering the severity of weed resistance currently. In a persistent effort to develop effective HPPD-inhibiting herbicides, a structure-guided strategy was carried out to perform the structural optimization for triketone-quinazoline-2,4-diones, a novel HPPD inhibitor scaffold first discovered in our lab. Herein, starting from the crystal structure of Arabidopsis thaliana (At)­HPPD complexed with 6-(2-hydroxy-6-oxocyclohex-1-ene-1-carbonyl)-1,5-dimethyl-3-(o-tolyl)­quinazoline-2,4­(1H,3H)-dione (MBQ), three subseries of quinazoline-2,4-dione derivatives were designed and prepared by optimizing the hydrophobic interactions between the side chain of the core structure at the R1 position and the hydrophobic pocket at the active site entrance of AtHPPD. 6-(2-Hydroxy-6-oxocyclohex-1-ene-1-carbonyl)-1,5-dimethyl-3-(3-(trimethylsilyl)­prop-2-yn-1-yl)­quinazoline-2,4­(1H,3H)-dione (60) with the best inhibitory activity against AtHPPD was identified to be the first subnanomolar-range AtHPPD inhibitor (K i = 0.86 nM), which significantly outperformed that of the lead compound MBQ (K i = 8.2 nM). Further determination of the crystal structure of AtHPPD in complex with compound 60 (1.85 Å) and the binding energy calculation provided a molecular basis for the understanding of its high efficiency. Additionally, the greenhouse assay indicated that 6-(2-hydroxy-6-oxocyclohex-1-ene-1-carbonyl)-1,5-dimethyl-3-propylquinazoline-2,4­(1H,3H)-dione (28) and compound 60 showed acceptable crop safety against peanut and good herbicidal activity with a broad spectrum. Moreover, compound 28 also showed superior selectivity for wheat at the dosage of 120 g ai/ha and favorable herbicidal efficacy toward the gramineous weeds at the dosage of as low as 30 g ai/ha. We believe that compounds 28 and 60 have promising prospects as new herbicide candidates for wheat and peanut fields.

Synthesis and Herbicidal Activity of Triketone-Aminopyridines as Potent p-Hydroxyphenylpyruvate Dioxygenase Inhibitors

“…A coupled enzyme assay was utilized to quantitatively analyze the inhibitory rate of HPPD inhibitors as previously reported. ,− All the synthesized samples were dissolved in DMSO as a stock solution that could be diluted to various concentrations before use. On the basis of the above information, the evaluation of the activity of HPPD inhibitors was accomplished in vitro with purified At HPPD in hand through an ultraviolet/visible plate reader to monitor the maleylacetoacetate at 318 nm.…”

“…All the tested inhibitors were configured as standby concentrates using Tween-80 as an emulsifying agent and DMF as a solvent along with a concentration of 1% (mass fraction) . These solutions were further diluted to the required concentration with distilled water just before use (150, 120, 60, and 30 g ai/ha) and then applied to pot-grown experiments in the greenhouse. − The diluted formulation solutions contained inhibitors or not sprayed evenly to the tested broadleaf weeds and gramineous weeds growing in the four-leaf stage, along with performing three repetitions per assay. The herbicidal responses of all samples were counted visually after 30 days via a visual observation method.…”

In vivo fluorescent screening for HPPD‐targeted herbicide discovery

“…Of note, inhibitor‐based probes usually demonstrate the advantage of binding with the enzyme cavities instead of rapidly diffusing away, 43–47 enabling the in situ real‐time fluorescence imaging of enzyme of interest. Previously, we obtained a comprehensive understanding of the HPPD catalytic mechanism, as well as the detailed structural basis of HPPD interacting with the inhibitors 48,49 . We herein designed two fluorescent probes conjugating the HPPD inhibitors as pharmacophores to Nile blue as a fluorophore with a suitable linker.…”

Design, Synthesis, and Herbicidal Activity of Naphthalimide–Aroyl Hybrids as Potent Transketolase Inhibitors

“…5 There are currently about 26 herbicide sites of action, including acetohydroxyacid synthase, 6 acetyl-coenzyme A carboxylase, 7 protoporphyrinogen IX oxidase, 8 and 4-hydroxyphenylpyruvatedioxygenase (HPPD)-inhibiting herbicides, 9 and so on. 10 However, due to the frequent and long-term overuse of limited types of herbicides in the fields, the weed resistance to these pesticides has become increasingly severe. 11−13 Thus, it is urgent to discover potential targets and develop new herbicides based on them, which was recognized as the most effective way to solve weed resistance.…”

“…20 Structure-based virtual screening is an effective way used in TBDD, which screen large collections of compounds via molecular docking to confirm molecular structures that are most likely to bind into a specific target protein. 5,21,22 In our previous report, a series of potential hit compounds interacting with TK were virtually filtered out from the SPECS database using homology modeling and virtual screening. 23 Among them, compound 1n (Figure 1) with higher binding affinities (ΔG cal = 8.91 kcal/mol) was selected as the lead compound for further structure optimization in this study.…”