Discovery of a Potent Thieno[2,3-<i>d</i>]pyrimidine-2,4-dione-Based Protoporphyrinogen IX Oxidase Inhibitor through an <i>In Silico</i> Structure-Guided Optimization Approach

Abstract

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 <i>in silico</i> structure-guided optimization approach of our previous lead compound <b>1</b> and designed and synthesized a new series of compounds <b>2</b>-<b>6</b>. Systematic bioassays led to the discovery of a highly potent compound <b>6g</b>, 1-methyl-3-(2,2,7-trifluoro-3-oxo-4-(prop-2-yn-1-yl)-3,4-dihydro-2<i>H</i>-benzo[<i>b</i>][1,4]oxazin-6-yl)thieno[2,3-<i>d</i>]pyrimidine-2,4(1<i>H</i>,3<i>H</i>)-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 <i>K</i>_i value of <b>6g</b> to <i>Nicotiana tabacum</i> PPO (NtPPO) was found to be 2.5 nM, showing 3-, 12-, and 18-fold higher potency relative to compound <b>1</b> (<i>K</i>_i = 7.4 nM), trifludimoxazin (<i>K</i>_i = 31 nM), and flumioxazin (<i>K</i>_i = 46 nM), respectively. Furthermore, molecular simulations further suggested that the thieno[2,3-<i>d</i>]pyrimidine-2,4-dione moiety of <b>6g</b> could form a more favorable π-π stacking interaction with the Phe392 of NtPPO than the heterocyclic moiety of compound <b>1</b>. This study provides an effective strategy to obtain enzyme inhibitors with improved performance through molecular simulation and structure-guided optimization.