Design, Synthesis, Herbicidal Evaluation, and Molecular Simulation of 2-(6-Phenylnicotinoyl)cyclohexane-1,3-dione Derivatives as Novel 4-Hydroxyphenylpyruvate Dioxygenase Inhibitors

4-Hydroxyphenylpyruvate dioxygenase (HPPD) has been an essential target enzyme in recent studies on herbicide discovery. In this study, a series of 3-hydroxy-2-(6-phenylnicotinoyl)cyclohex-2-en-1-one derivatives were rationally designed following the active substructure combination principle, yielding potent novel HPPD inhibiting herbicides. The title compounds were characterized using infrared spectroscopy (IR), ¹H and ¹³C nuclear magnetic resonance spectroscopies (NMR), and high-resolution mass spectrometry (HRMS). Among the designed compounds, IV-45 showed the highest potency against Arabidopsis thaliana HPPD (AtHPPD), with a half-maximal inhibitory concentration (IC₅₀) of 0.21 μM, exceeding that of mesotrione (0.23 μM) in vitro. Bioassay results revealed that 150 g a.i./ha of compounds IV-8 and IV-45 effectively targeted Setaria viridis and Echinochloa crus-galli, inhibiting their growth by over 80%. Crop safety tests demonstrated that compound IV-45 was safer than the commercial herbicide mesotrione for cotton and wheat. Moreover, compound IV-45 was virtually harmless to corn, rice, and peanuts. Molecular docking confirmed that compound IV-45 underwent a classical bidentate chelating interaction with Co²⁺ and a tight π-π stacking interaction with Phe381 and Phe424 in active pocket. Molecular dynamics simulations further verified that compound IV-45 stably bonded to AtHPPD, exerting a strong inhibitory effect. This work suggests the potential utility of 2-(6-phenylnicotinoyl)cyclohexane-1,3-dione as a herbicide skeleton for targeting HPPD.