Synthesis and Biological Activity Evaluation of Benzoxazinone-Pyrimidinedione Hybrids as Potent Protoporphyrinogen IX Oxidase Inhibitor

Design, synthesis, and biological evaluation of oxime ether derivatives containing 1,5-dimethyl-6-thioxo-1,3,5-triazinane-2,4-dione as protoporphyrinogen IX oxidase inhibitors

BACKGROUND

Herbicides based on protoporphyrinogen IX oxidase (PPO; EC 1.3.3.4) are widely used for weeding control in agricultural fields to safeguard food security. PPO herbicides, because of their low dosage, rapid action on weeds, slow accumulation in the environment and low toxicity to mammals, have become an important field of research in the development of new herbicides. This study presents a novel molecular scaffold with remarkably potent herbicidal activity.

RESULTS

A series of novel oxime ether derivatives containing 1,5-dimethyl-6-thioxo-1,3,5-triazinane-2,4-dione 6a-6z were designed and synthesized based on bioisosterism and substructure splicing, and characterized by 1H and 13C nuclear magnetic resonance spectroscopies, and high-resolution mass spectrometry. The configuration of compound 6u was confirmed by single-crystal X-ray diffraction. Compound 6r displayed excellent herbicidal activity of >95% against Echinochloa crus-galli, Digitaria sanguinalis, Medicago sativa and Conyza canadensis at a dosage of 37.5 g hm-2 in the glasshouse. At a dosage of 75 g hm-2, 6r was safe for application on rice and showed low toxicity (>200 μg g-1) towards Apis mellifera. Transcriptomics analysis of E. crus-galli treated by compound 6r, using oxadiazon as a positive control, revealed the compound's mode-of-action. There were eight metabolic and biosynthetic pathways of DEGs containing 'photosynthesis', 'porphyrin metabolism', 'carotenoid biosynthesis' and so on between 6r and oxadiazon as same. Scaffold94.443 (coproporphyrinogen-III oxidase) as upstream protoporphyrinogen IX changes were downregulated with quantitative reverse transcription PCR combined analysis treated 6r and oxadiazon in chlorophyll biosynthesis. Compound 6r target may be PPO and the NtPPO inhibitory effects, as represented by Ki, was 30.34 nm in vitro. Molecular docking showed that 6r could form two hydrogen bonds with Arg98.

CONCLUSION

Through bioisosterism and substructure splicing, we successfully developed compound 6r as lead compound exhibiting herbicidal activity, with no harm to rice and honeybees. Further development of herbicides based on this scaffold is warranted. © 2025 Society of Chemical Industry.

Discovery of novel benzoxazinone derivatives as promising protoporphyrinogen IX oxidase inhibitors

BACKGROUND

Protoporphyrinogen IX oxidase (PPO, EC 1.3.3.4) has emerged as a key target for developing new herbicides to protect crops from weeds. Herein, we disclose the development of two types of PPO inhibitors by modification of the benzoxazinone skeleton.

RESULTS

Two types of structurally novel benzoxazinone derivatives containing hydantoin or 1,2,3-triazole fragments were designed based on active substructure splicing and derivatization strategies. Systematic post-emergence herbicidal activity studies and crop selectivity assessments indicate that some of the compounds exhibit excellent herbicidal activity and crop safety. For instance, compound A1 shows highly effective herbicidal activity against all tested weeds at a dosage of 150 g ai/ha. Particularly, its herbicidal activity against broadleaf weeds is comparable to that of flumioxazin. Meanwhile, compound A1 exhibits superior safety for wheat and maize compared to flumioxazin within the 75-150 g ai/ha dosage range. Molecular docking studies revealed that compound A1 and flumioxazin occupy the same active cave within Nicotiana tabacum PPO (NtPPO). It is noteworthy that the carbonyl group on the oxazolone moiety of both compound A1 and flumioxazin forms beneficial interactions with Arg-98 and Phe-392.

CONCLUSION

Our research indicates that benzoxazinone derivatives containing either hydantoin or 1,2,3-triazole fragments serve as a promising chemical scaffold for the development of novel PPO-inhibiting herbicides. © 2025 Society of Chemical Industry.

In silico design of benzothiazole and phthalimide-derived hybrids as protoporphyrinogen IX oxidase inhibitors

Protoporphyrinogen IX oxidase (PPO) inhibition is a critical strategy for weed control in crop production. This study employed a computational approach integrating QSAR modelling, docking studies, and molecular dynamics to investigate the inhibitory activities of benzothiazole- and phthalimide-derived compounds against PPO. The MIA-QSAR method modelled pKi values for 52 compounds, complemented by docking and molecular dynamics to analyse ligand-enzyme interactions and identify potential agrochemical candidates. QSAR analysis yielded predictive models with r2 = 0.77, q2 = 0.55, and r2 = 0.74. MIA plots guided the design of 12 derivatives, 5 of which showed promising pKi values (7.31-8.69). Docking and molecular dynamics revealed strong binding affinity and stability for these candidates. The presence of fluorine substituents and C=O and C=S bonds in tetrahydroisoindole moieties enhanced biological activity, leading to the proposition of effective PPO inhibitors. Synthetic routes for the top candidates were outlined for future development, aiming to improve agrochemical efficacy and address resistance issues in crop protection.

Synthesis, Formation Mechanisms, and Molecular Dynamics Simulation of Novel Benzothiazole and Benzo[1,4]oxazin-3(4H)-one as Potential Acetylcholinesterase Inhibitors

A novel series of benzothiazole derivatives was synthesized using straightforward and easily implementable procedures, achieving a high yield. Among these synthesized compounds, amino acids containing the benzothiazole moiety were successfully produced through an 8-step process, with yields reaching as high as 95%. Notably, a serendipitous compound containing both benzothiazole and benzo[1,4]oxazin-3(4H)-one moieties was also synthesized using the same protocol, bypassing purification at step 7 and proceeding directly to hydrolysis. This highlights the unique role of the coupling reagent HATU (hexafluorophosphate azabenzotriazole tetramethyluronium) in the reaction, as it facilitated high yields, reaching up to 90%. The structures of the newly synthesized compounds were confirmed through spectral analysis. Density functional theory calculations suggested that energy barriers can be overcome by utilizing the energy from an exothermic reaction, enabling the thermodynamically favorable formation of this novel structure. Compounds 6d and 6f demonstrated significant inhibitory activity against the enzyme acetylcholinesterase, with IC50 values of 32.00 and 25.33 μg/mL, respectively. Molecular docking and molecular dynamics analyses indicate that compounds 6d and 6f hold potential for combating Alzheimer's disease, due to their interactions with critical amino acid residues and structural stability.

Design, Synthesis, and Herbicidal Activity of Biaryl-Pyridazinone/Phthalimide Derivatives as Novel Protoporphyrinogen Oxidase Inhibitors

In this study, a series of biaryl-pyridazinone/phthalimide derivatives were designed and synthesized as novel protoporphyrinogen IX oxidase (PPO) inhibitors. Herbicidal activity and crop safety assessments revealed that some compounds exhibited excellent herbicidal activity and crop safety profiles. For instance, at 37.5 g ai/ha, compound 7m inhibited Amaranthus retroflexus (AR), Abutilon theophrasti (AT), Medicago sativa (MS), Echinochloa crus-galli (EC), and Digitaria sanguinalis (DS) with 90% to 100% efficacy, comparable to the commercial herbicide saflufenacil (SAF). Compound 7m still showed effective weed control against the test broadleaf weeds at a lower dose of 9.375 g ai/ha. Additionally, 7m demonstrated excellent safety for wheat and corn at dosages up to 150 g ai/ha. In vitro experiments revealed that the representative compounds exhibited significant inhibitory activity against Arabidopsis thaliana PPO (AtPPO). Molecular docking of Nicotiana tabacum PPO (NtPPO) and 7m showed significant hydrogen bonding, π-π stacking, and π-alkyl interactions between 7m and residues, such as Cys-177, Thr-176, Arg-98, Phe-392, and Leu-372. Furthermore, 7m caused a notable reduction in chlorophyll (Chl) content in weeds. 7m is a promising candidate for the development of novel herbicides.

Design, Synthesis, and Biological Activity Evaluation of Novel Phenoxypyridine Derivatives Containing Acylthiourea Fragments as Protoporphyrinogen Oxidase Inhibitor Herbicides

Protoporphyrinogen oxidase (PPO, EC 1.3.3.4) plays a crucial role in the biosynthesis of chlorophyll in plants. PPO inhibitor herbicides are noted for their broad-spectrum activity, high efficiency, low toxicity, and minimal environmental impact, positioning them as effective targets for the discovery of environmentally friendly herbicides. In this research, utilizing the principles of bioisosterism and substructure activity splicing, 42 phenoxypyridine derivatives containing acylthiourea fragments were synthesized. Among them, the compound g13 exhibited superior inhibitory efficacy against six target weed species in greenhouse herbicidal trials. In vitro enzyme activity assays indicated that g13 significantly inhibited Echinochloa crus-galli PPO (EcPPO), with an IC50 value of 0.109 ± 0.018 μM, demonstrating superior inhibitory activity compared to oxyfluorfen. Furthermore, compound g13 exhibited superior crop safety compared to oxyfluorfen and holds potential application prospects for weed management in wheat and cotton. Molecular docking and dynamics simulations were employed to elucidate the binding mode and molecular mechanism of g13 with NtPPO. Potential metabolic pathways for g13 in plant systems were also analyzed. These experimental and theoretical results indicate that g13 is a promising lead candidate for PPO inhibitor herbicides.

Design, Synthesis, and Herbicidal Evaluation of Novel Synthetic Auxin Herbicides Containing 6-Indolylpyridine Oxime Ester/Amine

In this study, a series of 6-indolylpyridine oxime ester/amide derivatives were synthesized as novel synthetic auxin herbicides (SAHs) for postemergence herbicidal applications. At 30 g ai/ha, compounds 9q, 9u, 9v and 9w demonstrated inhibition rates of 90 to 100% against weeds Echinochloa crus-galli (EC) and Digitaria sanguinalis (DS). Even at a reduced 7.5 g ai/ha, these compounds maintained over 90% inhibition against four broadleaf weeds, with effects comparable to those of commercial herbicides halauxifen-methyl (HAM), indolauxipyr (IND) and indolauxipyr-cyanomethyl (INC). Crop sensitivity tests confirmed the suitability of compounds 9w and 9u for application in wheat and rice fields at 30 g ai/ha. Molecular docking analysis revealed that compound 9w formed significant hydrogen bonding and π-π stacking interactions with key amino acid residues. Additionally, half maximal inhibitory concentration (IC50) values of compounds 9u and 9w for IAA in vitro inhibition activity were 6.153 and 4.389 μM, respectively, outperforming HAM (9.061 μM). Compounds 9u and 9w show promising potential as lead candidates for novel SAHs.

Novel N-Phenyltriazinone Carboxylic Acid Derivatives as Promising Protoporphyrinogen IX Oxidase Inhibitors

Protoporphyrinogen IX oxidase (PPO) is a critical target for new herbicide development. We used a scaffold hopping strategy to develop 49 novel N-phenyltriazinone carboxylic acid derivatives and assessed their function as PPO inhibitors. Bioassay revealed that compound D5 exhibited excellent inhibitory activity against Nicotiana tabacum PPO (NtPPO) with a Ki of 33.7 nM, comparable to that of trifludimoxazin (Ki = 31.1 nM). Compound D5 also exhibited remarkable postemergence herbicidal activity against five weed species (Setaria faberii, Echinochloa crusgalli, Amaranthus retroflexus, Abutilon juncea, and Portulaca oleracea) at an ultralow concentration (9.375 g a.i./ha), and it showed broad-spectrum herbicidal activity and relatively high safety in wheat, rice, and peanut at 150 and 75 g a.i./ha, respectively. In molecular simulations, compound D5 stably binds NtPPO via π-π stacking with Phe392 and a sandwiched π-alkyl interaction with the key amino acids Leu356 and Leu372. This study shows that the novel N-phenyltriazinone carboxylic acid derivative D5 is a promising PPO inhibitor for agricultural weed control.

Synthesis and Evaluation of Herbicidal Ureidopyrimidine Compounds: Focus on Sulfonamide Modifications

In this study, 32 novel ureidopyrimidine compounds containing sulfonamide fragments were strategically designed and synthesized through active substructure combination. Postemergence herbicidal activity assays demonstrated that compounds 13a, 14d, and 15c exhibited superior efficacy against broadleaf weeds, including Zinnia elegans and Abutilon theophrasti, with compound 15c achieving a remarkable 95% control rate at 9.375 g a.i./ha, comparable to that of the commercial herbicide saflufenacil. Molecular docking simulations revealed that these compounds, along with saflufenacil, establish hydrogen bonds with protoporphyrinogen oxidase, particularly involving important amino acid residues, including ARG-98, GLY-175, and ASN-67. Structure-activity relationship analysis, supported by density functional theory calculations and molecular electrostatic potential studies, highlighted the importance of negatively charged regions in herbicidal activity. This comprehensive research provides valuable insights into the design and development of potent herbicides, establishing a strong foundation for future advancements in agricultural chemistry.

Recent Progress in the Synthesis of Benzoxazin-4-Ones, Applications in N-Directed Ortho-Functionalizations, and Biological Significance

The development of efficient synthetic procedures to access fused N, O-heterocyclic skeletons has been a pivotal research topic in organic synthesis for several years. Owing to the applications of N, O-fused heterocycles in organic synthesis, material sciences, and medicinal chemistry, significant efforts have been dedicated to design novel methods for their construction. To this end, 1,3-benzoxazin-4-ones are privileged candidates for N, O-heterocyclic molecules often found in natural products, agrochemicals, and materials science applications. In this review, we aim to summarize the existing literature on the synthesis of 1,3-benzoxazin-4-ones from 2010 onwards. Moreover, 1,3-benzoxazin-4-ones have also been identified as an excellent native directing group for the ortho-functionalization via C-H activation, which is often a strenuous task requiring pre-functionalized substrates. In the latter part of this report, we compiled several interesting examples of N-directed functionalizations of 1,3-benzoxazin-4-ones. Additionally, to emphasize biological importance, recent developments on the anticancer evaluations of benzoxazine-4-one core are included. We believe that by harnessing the methodologies discussed herein, new possibilities could be unlocked for the synthesis of fused N, O-heterocycles, leading to the development of novel biologically active compounds and functional materials.

Application of Difluoromethyl Isosteres in the Design of Pesticide Active Molecules

Difluoromethyl (CF2H) groups have been found in many listed pesticides due to their unique physical and chemical properties and outstanding biological activity. In pesticide molecules, compared with the drastic changes brought by trifluoromethyl, difluoromethyl usually moderately regulates the metabolic stability, lipophilicity, bioavailability, and binding affinity of compounds. Therefore, difluoromethylation has become an effective means to modify the biological activity of pesticide molecules. This paper reviews the representative literatures and patents containing difluoromethyl groups in the past 10 years, and introduces the research progress. The aim is to provide an effective reference value for the study of difluoromethyl in pesticides.

Design, Synthesis, and Herbicidal Activity of Novel Tetrahydrophthalimide Derivatives Containing Oxadiazole/Thiadiazole Moieties

Protoporphyrinogen oxidase (PPO, EC 1.3.3.4) has a high status in the development of new inhibitors. To develop novel and highly effective PPO inhibitors, active substructure linking and bioisosterism replacement strategies were used to design and synthesize novel tetrahydrophthalimide derivatives containing oxadiazole/thiadiazole moieties, and their inhibitory effects on Nicotiana tobacco PPO (NtPPO) and herbicidal activity were evaluated. Among them, compounds B11 (Ki = 9.05 nM) and B20 (Ki = 10.23 nM) showed significantly better inhibitory activity against NtPPO than that against flumiclorac-pentyl (Ki = 46.02 nM). Meanwhile, compounds A20 and B20 were 100% effective against three weeds (Abutilon theophrasti, Amaranthus retroflexus, and Portulaca oleracea) at 37.5 g a.i./ha. It was worth observing that compound B11 was more than 90% effective against three weeds (Abutilon theophrasti, Amaranthus retroflexus, and Portulaca oleracea) at 18.75 and 9.375 g a.i./ha. It was also safer to rice, maize, and wheat than flumiclorac-pentyl at 150 g a.i./ha. In addition, the molecular docking results showed that compound B11 could stably bind to NtPPO and it had a stronger hydrogen bond with Arg98 (2.9 Å) than that of flumiclorac-pentyl (3.2 Å). This research suggests that compound B11 could be used as a new PPO inhibitor, and it could help control weeds in agricultural production.

Discovery of Novel N-Phenyltriazinone Derivatives Containing Oxime Ether or Oxime Ester Moieties as Promising Protoporphyrinogen IX Oxidase Inhibitors

Protoporphyrinogen IX oxidase (PPO, EC 1.3.3.4) is one of the most important targets for the discovery of green herbicides. In order to find novel PPO inhibitors with a higher herbicidal activity, a series of novel N-phenyltriazinone derivatives containing oxime ether and oxime ester groups were designed and synthesized based on the strategy of pharmacophore and scaffold hopping. Bioassay results revealed that some compounds showed herbicidal activities; especially, compound B16 exhibited broad-spectrum and excellent 100% herbicidal effects to Echinochloa crusgalli, Digitaria sanguinalis, Setaria faberii, Abutilon juncea, Amaranthus retroflexus, and Portulaca oleracea at a concentration of 37.5 g a.i./ha, which were comparable to trifludimoxazin. Nicotiana tabacum PPO (NtPPO) enzyme inhibitory assay indicated that B16 showed an excellent enzyme inhibitory activity with a value of 32.14 nM, which was similar to that of trifludimoxazin (31.33 nM). Meanwhile, compound B16 revealed more safety for crops (rice, maize, wheat, peanut, soybean, and cotton) than trifludimoxazin at a dose of 150 g a.i./ha. Moreover, molecular docking and molecular dynamics simulation further showed that B16 has a very strong and stable binding to NtPPO. It indicated that B16 can be used as a potential PPO inhibitor and herbicide candidate for application in the field.

Design, Synthesis, and Biological Evaluation of Pyridazinone-Containing Derivatives As Novel Protoporphyrinogen IX Oxidase Inhibitor

Protoporphyrinogen IX oxidase (PPO, E.C. 1.3.3.4) plays a pivotal role in chlorophyll biosynthesis in plants, making it a prime target for herbicide development. In this study, we conducted an investigation aimed at discovering PPO-inhibiting herbicides. Through this endeavor, we successfully identified a series of novel compounds based on the pyridazinone scaffold. Following structural optimization and biological assessment, compound 10ae, known as ethyl 3-((6-fluoro-5-(6-oxo-4-(trifluoromethyl)pyridazin-1(6H)-yl)benzo[d]thiazol-2-yl)thio)propanoate, emerged as a standout performer. It exhibited robust activity against Nicotiana tabacum PPO (NtPPO) with an inhibition constant (Ki) value of 0.0338 μM. Concurrently, we employed molecular simulations to obtain further insight into the binding mechanism with NtPPO. Additionally, another compound, namely, ethyl 2-((6-fluoro-5-(5-methyl-6-oxo-4-(trifluoromethyl)pyridazin-1(6H)-yl)benzo[d]thiazol-2-yl)thio)propanoate (10bh), demonstrated broad-spectrum and highly effective herbicidal properties against all six tested weeds (Leaf mustard, Chickweed, Chenopodium serotinum, Alopecurus aequalis, Poa annua, and Polypogon fugax) at the dosage of 150 g a.i./ha through postemergence application in a greenhouse. This work identified a novel lead compound (10bh) that showed good activity in vitro and excellent herbicidal activity in vivo and had promising prospects as a new PPO-inhibiting herbicide lead.

Design, Synthesis, and Herbicidal Evaluation of Pyrrolidinone-Containing 2-Phenylpyridine Derivatives as Novel Protoporphyrinogen Oxidase Inhibitors

In this work, a series of pyrrolidinone-containing 2-phenylpyridine derivatives were synthesized and evaluated as novel protoporphyrinogen IX oxidase (PPO, EC 1.3.3.4) inhibitors for herbicide development. At 150 g ai/ha, compounds 4d, 4f, and 4l can inhibit the grassy weeds of Echinochloa crus-galli (EC), Digitaria sanguinalis (DS), and Lolium perenne (LP) with a range of 60 to 90%. Remarkably, at 9.375 g ai/ha, these compounds showed 100% inhibition effects against broadleaf weeds of Amaranthus retroflexus (AR) and Abutilon theophrasti (AT), which were comparable to the performance of the commercial herbicides flumioxazin (FLU) and saflufenacil (SAF) and better than that of acifluorfen (ACI). Molecular docking analyses revealed significant hydrogen bonding and π-π stacking interactions between compounds 4d and 4l with Arg98, Asn67, and Phe392, respectively. Additionally, representative compounds were chosen for in vivo assessment of PPO inhibitory activity, with compounds 4d, 4f, and 4l demonstrating excellent inhibitory effects. Notably, compounds 4d and 4l induced the accumulation of reactive oxygen species (ROS) and a reduction in the chlorophyll (Chl) content. Consequently, compounds 4d, 4f, and 4l are promising lead candidates for the development of novel PPO herbicides.

Discovery of Pyridyl-Benzothiazol Hybrids as Novel Protoporphyrinogen Oxidase Inhibitors via Scaffold Hopping

In order to discover novel protoporphyrinogen oxidase (PPO) inhibitors with excellent herbicidal activity, a series of structurally novel 6-(pyridin-2-yl) benzothiazole derivatives were designed based on the scaffold hopping strategy. The in vitro experiments demonstrated that the newly synthesized compounds exhibited noteworthy inhibitory activity against Arabidopsis thaliana PPO (AtPPO), with IC50 values ranging from 0.06 to 1.36 μM. Preliminary postemergence herbicidal activity tests and crop safety studies indicated that some of our compounds exhibited excellent herbicidal activity and crop safety. For instance, compound (rac)-7as exhibited superior herbicidal activities to commercially available flumioxazin (FLU) and saflufenacil (SAF) at all the tested concentrations and showed effective herbicidal activities even at a dosage as low as 18.75 g ai/ha. Meanwhile, compound (rac)-7as showed good crop safety for wheat at a dosage as high as 150 g of ai/ha. Although the absolute configuration of compound 7as has no obvious effect on its herbicidal activity, compound (R)-7as showed a slightly higher crop safety than compound (S)-7as. Molecular simulation studies of Nicotiana tabacum PPO (NtPPO) and our candidate compounds showed that the benzothiazole moiety of compounds (R)-7as or (S)-7as formed multiple π-π stacking interactions with FAD, and the pyridine ring generated π-π stacking with Phe-392. Our finding proved that the pyridyl-benzothiazol hybrids are promising scaffolds for the development of PPO-inhibiting herbicides.

Synthesis of Benzoxazines by Heterogeneous Multicomponent Biochemo Multienzymes Cascade Reaction

This work describes the possibility to combine multicomponent chemistry and multienzymes cascade transformations in a unique reactive framework to yield highly functionalized 1,4-benzoxazines under favorable heterogeneous conditions. The synthetic scheme involved the generation in situ of electrophilic reactive quinone intermediates of tyrosol esters catalyzed by lipase M and tyrosinase followed by nucleophilic 1,6-Michael addition of selected α-amino acid methyl esters, and successive intramolecular lactonization and aromatization processes. The immobilization of the multienzymes cascade on electroactive lignin nanoparticles improved the sustainability and recyclability of the overall system.

Design, Synthesis, and Herbicidal Activity of Substituted 3-(Pyridin-2-yl)Phenylamino Derivatives

To discover protoporphyrinogen oxidase (PPO) inhibitors with robust herbicidal activity and crop safety, three types of substituted 3-(pyridin-2-yl)phenylamino derivatives bearing amide, urea, or thiourea as side chain were designed via structure splicing strategy. Postemergence herbicidal activity assessment of 33 newly prepared compounds revealed that many of our compounds such as 6a, 7b, and 8d exhibited superior herbicidal activities against broadleaf and monocotyledon weeds to commercial acifluorfen. In particular, compound 8d exhibited excellent herbicidal activities and high crop safety at a dosage range of 37.5-150 g ai/ha. PPO inhibitory studies supported our compounds as typical PPO inhibitors. Molecular docking studies revealed that compound 8d provided effective interactions with Nicotiana tabacum PPO (NtPPO) via diverse interaction models, such as π-π stacking and hydrogen bonds. Molecular dynamics (MD) simulation studies and degradation studies were also conducted to gain insight into the inhibitory mechanism. Our study indicates that compound 8d may be a candidate molecule for the development of novel herbicides.