Discovery of a Potent Thieno[2,3-d]pyrimidine-2,4-dione-Based Protoporphyrinogen IX Oxidase Inhibitor through an In Silico Structure-Guided Optimization Approach,Journal of Agricultural and Food Chemistry

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Discovery of a Potent Thieno[2,3-d]pyrimidine-2,4-dione-Based Protoporphyrinogen IX Oxidase Inhibitor through an In Silico Structure-Guided Optimization Approach
Journal of Agricultural and Food Chemistry ( IF 5.7 ) Pub Date : 2021-11-19 , DOI: 10.1021/acs.jafc.1c05665
Da-Wei Wang ₁ , Hang Zhang ₁ , Shu-Yi Yu ₁ , Rui-Bo Zhang ₁ , Lu Liang ₁ , Xia Wang ₁ , Huang-Ze Yang ₁ , Zhen Xi ₁

Affiliation

A key objective for herbicide research is to develop new compounds with improved bioactivity. Protoporphyrinogen IX oxidase (PPO) is an essential target for herbicide discovery. Here, we report using an in silico structure-guided optimization approach of our previous lead compound 1 and designed and synthesized a new series of compounds 2–6. Systematic bioassays led to the discovery of a highly potent compound 6g, 1-methyl-3-(2,2,7-trifluoro-3-oxo-4-(prop-2-yn-1-yl)-3,4-dihydro-2H-benzo[b][1,4]oxazin-6-yl)thieno[2,3-d]pyrimidine-2,4(1H,3H)-dione, which exhibited an excellent and wide spectrum of weed control at the rates of 30–75 g ai/ha by the postemergence application and is relatively safe on maize at 75 g ai/ha. Additionally, the K_i value of 6g to Nicotiana tabacum PPO (NtPPO) was found to be 2.5 nM, showing 3-, 12-, and 18-fold higher potency relative to compound 1 (K_i = 7.4 nM), trifludimoxazin (K_i = 31 nM), and flumioxazin (K_i = 46 nM), respectively. Furthermore, molecular simulations further suggested that the thieno[2,3-d]pyrimidine-2,4-dione moiety of 6g could form a more favorable π–π stacking interaction with the Phe392 of NtPPO than the heterocyclic moiety of compound 1. This study provides an effective strategy to obtain enzyme inhibitors with improved performance through molecular simulation and structure-guided optimization.

中文翻译：

通过计算机结构引导优化方法发现有效的噻吩并[2,3-d]嘧啶-2,4-二酮基原卟啉原 IX 氧化酶抑制剂

除草剂研究的一个关键目标是开发具有改进生物活性的新化合物。原卟啉原 IX 氧化酶 (PPO) 是发现除草剂的重要目标。在这里，我们报告了使用我们之前的先导化合物1的计算机结构引导优化方法，并设计和合成了一系列新的化合物2-6。系统的生物测定发现了一种高效的化合物6g , 1-methyl-3-(2,2,7-trifluoro-3-oxo-4-(prop-2-yn-1-yl)-3,4- dihydro-2 H -benzo[ b ][1,4]oxazin-6-yl)thieno[2,3- d ]pyrimidine-2,4(1 H ,3 H)-二酮，通过出苗后施用以 30-75 g ai/ha 的比率表现出优异且广谱的杂草控制，并且在 75 g ai/ha 的玉米上相对安全。此外，发现6g对烟草PPO (NtPPO)的K _i值为2.5 nM，显示出相对于化合物1 ( K _i = 7.4 nM)、trifludimoxazin ( K _i = 31 nM) 和氟咪嗪 ( K _i = 46 nM)。此外，分子模拟进一步表明6g的噻吩并[2,3- d ]嘧啶-2,4-二酮部分与化合物1的杂环部分相比，NtPPO 的 Phe392 可以形成更有利的 π-π 堆积相互作用。本研究提供了一种有效的策略，通过分子模拟和结构引导优化来获得具有改进性能的酶抑制剂。

更新日期：2021-12-01

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