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.