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

Discovery of a Class of Novel Succinate Dehydrogenase Inhibitors Containing a Coumarin Structure

Succinate dehydrogenase (SDH) has emerged as a highly promising target in modern agricultural research, playing a crucial role in developing environmentally friendly and efficient fungicides for combating agricultural pathogens. This study presents the discovery of a novel class of SDH inhibitors (I-III) incorporating coumarin segments achieved through an active fragment swapping and linking strategy. Fungicidal activity assays revealed that several compounds within this series demonstrate significant inhibitory effects against the tested fungal strains. Through comprehensive structure-activity relationship studies, compound N-(1-((3-butyl-4-methyl-2-oxo-2H-chromen-7-yl)oxy)propan-2-yl)-3-(difluoromethyl)-N-methoxy-1-methyl-1H-pyrazole-4-carboxamide (IIk) exhibited potent inhibitory activity against various fungal species. Notably, it demonstrated superior efficacy against S. sclerotiorum with an EC50 value of 1.14 μg/mL, outperforming the commercial control agent thifluzamide (EC50 = 4.90 μg/mL). Molecular docking simulations indicated that hydrophobic interactions serve as the primary binding mechanism between the ligand and SDH. Intriguingly, compound IIk displayed dual functionality, not only acting as an effective fungicide but also promoting the growth of wheat seedlings and Arabidopsis thaliana, resulting in increased plant biomass. Preliminary investigations into its growth-promoting mechanism suggest that IIk enhances the nitrate reductase activity, thereby facilitating plant growth.

The first example of white-light emission based on pyrimido[4',5':4,5]thieno[2,3-d]pyrimidine moiety: Synthesis, photophysical, and antimicrobial studies

A series of new AIE systems based on the pyrimidothienopyrimidine skeleton were efficiently synthesized and fully characterized. These compounds exhibited weak emission in solution but strong solid-state fluorescence with a red shift. Notably, compound 16 displayed unique white-light emission from a single-component system and tunable emission colors in DMF/water mixtures. This dual emission behavior, arising from AIE and excimer formation, is unprecedented for pyrimidothienopyrimidine derivatives. Although compounds 9a and 9b exhibited AIEE behavior, compounds 15c and 18 demonstrated AIE behavior, with significantly enhanced fluorescence intensity upon water addition. Moreover, most synthesized compounds exhibited moderate to strong antimicrobial activity against various bacterial and fungal strains, suggesting their potential for biological applications.

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.

Design, Synthesis, and Herbicidal Activity of Novel 5-Acylbarbituric Acid Derivatives Containing Maleimide Moieties and Evaluation of Their Mode of Action

In continuation of our search for herbicide lead compounds with novel structures and enhanced activities, a total of thirty 5-acylbarbituric acid derivatives containing maleimide moieties were designed and synthesized, and their herbicidal activities were evaluated in the greenhouse. The bioassay results showed that some of the newly synthesized target compounds had good herbicidal activity, of which BT-IV-1 displayed an excellent inhibitory effect on Brassia campestris, Amaranthus retroflexus, Amaranthus blitum, Chenopodium album, Portulaca oleracea, and Abutilon theophrasti, with inhibition rate > 80% at the dosage of 37.5 g ha-1, and it was determined to be safe for Oryza sativa, Zea mays, and Panicum miliaceum at the dosage of 75 g ha-1. Studying the molecular mechanism by phenotypic observation, membrane permeability evaluation, molecular docking, and in vitro maize protoporphyrinogen oxidase (PPO) activity evaluation reveals that BT-IV-1 is a PPO inhibitor. The present work indicates that BT-IV-1 can serve as a potential lead compound for the further development of novel PPO-inhibiting herbicides.

Discovery of N-Phenylphthalimides Containing Ether Moiety as Potential Protoporphyrinogen IX Oxidase Inhibitors

The discovery of novel protoporphyrinogen IX oxidase (PPO) inhibitors has become a key focus in herbicide development. To explore new PPO inhibitors, a series of N-phenylphthalimide derivatives with ether moieties were designed and successfully synthesized. Among these, compound B18 (Ki = 10.3 nM) exhibited a strong inhibitory effect on NtPPO, outperforming flumiclorac-pentyl (Ki = 46.3 nM) and flumioxazin (Ki = 52.0 nM). It is noted that compounds A3, B18, B19, and B20 showed broad-spectrum herbicidal activity against the tested weeds at 75 g a.i./ha. In addition, results of molecular simulation and density functional theory (DFT) calculations indicated that compound B18 possessed not only a robust hydrogen bond with Arg98 of NtPPO but also superior chemical reactivity, electrostatic field, and strong polarity. Therefore, compound B18 may be regarded as a promising lead compound for the development of high-efficiency PPO inhibitors.

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.

Discovery of Novel N-Phenylphthalimide Protoporphyrinogen IX Oxidase Inhibitors

Developing new compounds with improved bioactivity is a crucial objective in herbicide research. To discover new compounds with high biological activity, a series of N-phenylphthalimide derivatives containing ether and oxime ether moieties were designed and synthesized. The assays demonstrated significant inhibitory effects of certain compounds on Nicotiana tabacum PPO (NtPPO). Among them, compound A4 exhibited the most potent inhibition of NtPPO, with a Ki value of 9.05 nM, surpassing both flumioxazin (Ki = 52.0 nM) and flumiclorac-pentyl (Ki = 46.3 nM). In addition, compound A4 exhibited complete inhibition against six weed species (Setaria viridis, Echinochloa crus-galli, Digitaria sanguinalis, Amaranthus retroflexus, Abutilon theophrasti, and Portulaca oleracea) and caused only 30-50% damage to maize and rice at 150 g a.i./ha. Molecular simulation analysis demonstrated that compound A4 exhibited stable binding to NtPPO due to the formation of a strong hydrogen bond with Arg98 (2.8 Å), surpassing the interactions of flumiclorac-pentyl (3.2 Å) and flumioxazin (3.1 Å). These findings suggest that compound A4 holds potential as a novel PPO inhibitor for the management of agricultural weeds.

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.

Discovery of Novel (5-Mercapto-4-phenyl-4H-1,2,4-triazol-3-yl)methyl Phenyl Carbamate as a Potent Phytoene Desaturase Inhibitor through Scaffold Hopping and Linker Modification

Phytoene desaturase (PDS) is a key rate-limiting enzyme in the carotenoid biosynthesis pathway. Although commercial PDS inhibitors have been developed for decades, it remains necessary to develop novel PDS inhibitors with higher bioactivity. In this work, we used the scaffold hopping and linker modification approaches to design and synthesize a series of compounds (7a-7o, 8a-8l, and 14a-14d). The postemergence application assay demonstrated that 8e and 7e separately showed the best herbicidal activity at 750 g a.i./ha and lower doses (187.5 g, 375g a.i./ha) without no significant toxicity to maize and wheat. The surface plasmon resonance revealed strong binding affinity between 7e and Synechococcus PDS (SynPDS). The HPLC analysis confirmed that 8e at 750 g a.i./ha caused significant phytoene accumulation in Arabidopsis seedlings. This work demonstrates the efficacy of structure-guided optimization through scaffold hopping and linker modification to design potent PDS inhibitors with enhanced bioactivity and crop safety.

Discovery of Benzothiazol-2-ylthiophenylpyrazole-4-carboxamides as Novel Succinate Dehydrogenase Inhibitors

Succinate dehydrogenase (SDH) has been considered an ideal target for discovering fungicides. To develop novel SDH inhibitors, in this work, 31 novel benzothiazol-2-ylthiophenylpyrazole-4-carboxamides were designed and synthesized using active fragment exchange and a link approach as promising SDH inhibitors. The findings from the tests on antifungal activity indicated that most of the synthesized compounds displayed remarkable inhibition against the fungi tested. Compound Ig N-(2-(((5-chlorobenzo[d]thiazol-2-yl)thio)methyl)phenyl)-3-(difluoromethyl)-1-methyl-1H-yrazole-4-carboxamide, with EC50 values against four kinds of fungi tested below 10 μg/mL and against Cercospora arachidicola even below 2 μg/mL, showed superior antifungal activity than that of commercial fungicide thifluzamide, and specifically compounds Ig and Im were found to show preventative potency of 90.6% and 81.3% against Rhizoctonia solani Kühn, respectively, similar to the positive fungicide thifluzamide. The molecular simulation studies suggested that hydrophobic interactions were the main driving forces between ligands and SDH. Encouragingly, we found that compound Ig can effectively promote the wheat seedlings and the growth of Arabidopsis thaliana. Our further studies indicated that compound Ig could stimulate nitrate reductase activity in planta and increase the biomass of plants.

Fluorinated benzoxazinones designed via MIA-QSAR, docking and molecular dynamics as protoporphyrinogen IX oxidase inhibitors

BACKGROUND

Fluorine plays a significant role in agrochemical science because approximately 25% of herbicides licensed worldwide contain this element. In a pool of previously synthesized benzoxazinones, some compounds contained fluorine and demonstrated inhibitory activities against protoporphyrinogen IX oxidase (PPO). Therefore, three data sets of benzoxazinone derivatives with known inhibitory activity against PPO were employed to build a multivariate image analysis applied to a quantitative structure-activity relationships (MIA-QSAR) model to identify improved analogs with at least one fluorine substituent.

RESULTS

The QSAR model was vigorously validated and demonstrated to be highly predictive (r2 = 0.85, q2 = 0.71, and r2 pred = 0.88); thus, the model can provide reliable estimations for the PPO inhibitory activity of unknown derivatives. From these compounds, a couple of N-substituted benzoxazinones that contained the -CH2CHF2 group were found with predicted pKi values larger than 8 (Ki in mol L-1) and higher lipophilicity than the most active data set compounds. In addition, we carried out a systematic investigation of the binding mode of PPO by performing computational docking followed by molecular dynamics simulations. The proposed binding mode was consistent with experimental studies, and several potential key residues were identified.

CONCLUSION

Two new proposed benzoxazinones exhibited better performance than compounds of the data set, and fluorine substituents played pivotal roles in describing the biological activities. © 2024 Society of Chemical Industry.

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.

Understanding the Effects of Ligand Configuration on Protoporphyrinogen IX Oxidase with Rationally Designed 3-(N-Phenyluracil)but-2-enoates

Protoporphyrinogen IX oxidase (PPO, EC 1.3.3.4) is a promising target for green herbicide discovery. However, the ligand configuration effects on PPO activity were still poorly understood. Herein, we designed 3-(N-phenyluracil)but-2-enoates using our previously developed active fragments exchange and link (AFEL) approach and synthesized a series of novel compounds with nanomolar ranges of Nicotiana tabacum PPO (NtPPO) inhibitory potency and promising herbicidal potency. Our systematic structure-activity relationship investigations showed that the E isomers of 3-(N-phenyluracil)but-2-enoates displayed improved bioactivity than their corresponding Z isomers. Using molecular simulation studies, we found that the E isomers showed a relatively lower entropy change and could sample more stable binding conformation to the receptor than the Z isomers. Our density functional theory (DFT) calculations showed that the E isomers showed higher chemical reactivity and lower electronic chemical potential than their corresponding Z isomers. Compound E-Ic emerged as the optimal compound with a Ki value of 3.0 nM against NtPPO, exhibiting a broader spectrum of weed control than saflufenacil at 37.5-75 g ai/ha and also safe to maize at 75 g ai/ha, which could be considered as a promising lead herbicide for further development.

Discovery of Benzothiazolylpyrazole-4-Carboxamides as Potent Succinate Dehydrogenase Inhibitors through Active Fragment Exchange and Link Approach

Succinate dehydrogenase (SDH) is an attractive target for developing green fungicides to manage agricultural pathogens in modern agriculture research. Herein, in this work, we report the discovery of benzothiazolylpyrazole-4-carboxamides I-III as potent SDH inhibitors using active fragment exchange and link approach. The results of the fungicidal activity assays showed that some of the synthesized compounds exhibited excellent inhibition against the tested fungi. Systematic structure-activity relationship studies led to the discovery of compound Ip, N-(1-((4,6-difluorobenzo[d]thiazol-2-yl)thio)propan-2-yl)-3-(difluoromethyl)-N-methoxy-1-methyl-1H-pyrazole-4-carboxamide, which showed higher fungicidal activity against Fusarium graminearum Schw (EC50 = 0.93 μg/mL) than the commercial fungicides thifluzamide (EC50 > 50 μg/mL) and boscalid (EC50 > 50 μg/mL). The molecular simulation studies suggested that hydrophobic interactions were the primary driving forces between ligands and SDH. Promisingly, we found that Ip could stimulate the growth of wheat seedlings and Arabidopsis thaliana and increase the biomass of the treated plants. Preliminary studies on the plant growth promoter mechanism of Ip indicated that it could increase nitrate reductase activity in planta, that, in turn, stimulates the growth of plants.

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

Protoporphyrinogen IX oxidase (PPO/Protox, E.C. 1.3.3.4) is recognized as one of the most important targets for herbicide discovery. In this study, we report our ongoing research efforts toward the discovery of novel PPO inhibitors. Specifically, we identified a highly potent new compound series containing a pyrimidinedione moiety and bearing a versatile building block-benzoxazinone scaffold. Systematic bioassays resulted in the discovery of compound 7af, ethyl 4-(7-fluoro-6-(3-methyl-2,6-dioxo-4-(trifluoromethyl)-3,6-dihydropyrimidin-1(2H)-yl)-3-oxo-2,3-dihydro-4H-benzo[b][1,4]oxazin-4-yl)butanoate, which exhibited broad-spectrum and excellent herbicidal activity at the dosage of 37.5 g a.i./ha through postemergence application. The inhibition constant (Ki) value of 7af to Nicotiana tabacum PPO (NtPPO) was 14 nM, while to human PPO (hPPO), it was 44.8 μM, indicating a selective factor of 3200, making it the most selective PPO inhibitor to date. Moreover, molecular simulations further demonstrated the selectivity and the binding mechanism of 7af to NtPPO and hPPO. This study not only identifies a candidate that showed excellent in vivo bioactivity and high safety toward humans but also provides a paradigm for discovering PPO inhibitors with improved performance through molecular simulation and structure-guided optimization.

Design, synthesis and antifungal activity of novel 1,4-benzoxazin-3-one derivatives containing an acylhydrazone moiety

A series of 1,4-benzoxazin-3-one derivatives containing an acylhydrazone moiety were designed, synthesized and evaluated for their in vitro antifungal activities against Gibberella zeae, Pellicularia sasakii, Phytophthora infestans, Capsicum wilt, and Phytophthora capsica. The structures of target compounds were characterized by 1H NMR, 13H NMR, 19F NMR and HRMS. The preliminary antifungal evaluation of all target compounds showed that some target compounds possessed moderate to good activities against G. zeae, P. sasakii, P. infestans and C. wilt. Among them, compounds 5L and 5o exhibited noticeable inhibition effects against G. zeae with the EC50 values (effective concentration for 50% activity) of 20.06 and 23.17 μg/ml, respectively, which were even nearly double effective than that of hymexazol (40.51 μg/ml). Meanwhile, compound 5q displayed a notable inhibitory effect toward P. sasakii, with the EC50 value of 26.66 μg/ml, which was better than that of hymexazol (32.77 μg/ml). In addition, compound 5r yielded the EC50 value of 15.37 μg/ml against P. infestans, which was less than those of hymexazol (18.35 μg/ml) and carbendazim (34.41 μg/ml). Eventually, compound 5p showed higher inhibitory effect against C. wilt, with EC50 value of 26.76 μg/ml, which was better than that of hymexazol (>50 μg/ml).

Design and synthesis of novel PPO-inhibiting pyrimidinedione derivatives safed towards cotton

Developing innovative and effective herbicides is of utmost importance since weed management has become a worldwide agricultural production concern, resulting in severe economic losses every year. In this study, a series of new pyrimidinedione compounds were developed via combination of pyrimidinediones with N-phenylacetamide moiety. The herbicidal activity test (37.5-150 g of ai/ha) indicated that most of the new derivatives exhibited excellent herbicidal activity against dicotyledonous weeds, but less against grasses. Among them, compound 34 was identified as the best postemergence herbicidal activities against six species of weeds (Amaranthus retrof lexus, AR; Abutilon theophrasti, AT; Veronica polita, VP; Echinochloa crusgalli, EC; Digitaria sanguinalis, DS; Setaria viridis, SV), which were comparable to the commercial control agent saflufenacil (≥90%). The protoporphyrinogen oxidase (PPO; EC. 1.3.3.4) activity experiment suggested that compound 34 could significantly reduce the PPO content in weeds, the relative expression levels of the PPO gene were verified by real-time quantitative polymerase chain reaction (RT-qPCR), and the results were consistent with the trend of the enzyme activity data. Molecular docking showed that compound 34 could occupy the PPO enzyme catalytic substrate pocket, which played an excellent inhibitory effect on the activity of receptor protein. Meanwhile, the tolerance of compound 34 to cotton was better than that of the commercial agent saflufenacil at 150 g of ai/ha. Thus, compound 34 exhibits the potential to be a new PPO herbicide for weed control in cotton fields. This study provided a basis for the subsequent structural modification and mechanism research of pyrimidinedione derivatives.

Synthesis of 3-(Pyridin-2-yl)quinazolin-2,4(1H,3H)-diones via Annulation of Anthranilic Esters with N-pyridyl Ureas

A new route for the synthesis of quinazolin-2,4(1H,3H)-diones and thieno [2,3-d]pyrimidine-2,4(1H,3H)-diones substituted by pyridyl/quinolinyl moiety in position 3 has been developed. The proposed method concluded in an annulation of substituted anthranilic esters or 2-aminothiophene-3-carboxylates with 1,1-dimethyl-3-(pyridin-2-yl) ureas. The process consists of the formation of N-aryl-N'-pyridyl ureas followed by their cyclocondensation into the corresponding fused heterocycles. The reaction does not require the use of metal catalysts and proceeds with moderate to good yields (up to 89%). The scope of the method is more than 30 examples, including compounds with both electron-withdrawing and electron-donating groups, as well as diverse functionalities. At the same time, strong electron-acceptor substituents in the pyridine ring of the starting ureas reduce the product yield or even prevent the cyclocondensation step. The reaction can be easily scaled to gram quantities.

Identifying novel selective PPO inhibitors through structure-based virtual screening and bio-evaluation

Protoporphyrinogen oxidase (PPO) is a key enzyme in chlorophyll and heme biosynthesis, and the development of its inhibitors is of great importance both in the pharmaceutical and pesticide industries. However, the currently developed PPO inhibitors have insignificant bio-selectivity and have a serious impact on non-target organisms. In this study, a docking-based virtual screening approach combined with bio-activity testing was used to obtain novel selective inhibitors of PPO. The results of the bio-activity test showed that thirteen compounds showed 10-fold selectivity over human PPO. And the best selective compound, ZINC70338, has a K _i value of 2.21 μM for Nicotiana tabacum PPO and >113-fold selectivity for human PPO. The selectivity mechanism of ZINC70338 in different species of PPO was then analyzed by molecular dynamics simulations to provide a design basis and theoretical guidance for the design of novel selective inhibitors.

Design, Synthesis, and Metabolism Studies of N-1,4-Diketophenyltriazinones as Protoporphyrinogen IX Oxidase Inhibitors

Protoporphyrinogen IX oxidase (PPO, EC 1.3.3.4) is an established site for green herbicide discovery. In this work, based on structural analysis, we develop an active fragment exchange and link (AFEL) approach to designing a new class of N-1,4-diketophenyltriazinones I-III as potent Nicotiana tabacum PPO (PPO) inhibitors. After systematic structure-activity relationship optimizations, a series of new compounds with Ki values in the single-digit nanomolar range toward NtPPO and promising herbicidal activity were discovered. Among them, Ii (Ki = 0.11 nM) displays 284- and 90-fold improvement in NtPPO inhibitory activity over trifludimoxazin (Ki = 31 nM) and saflufenacil (Ki = 10 nM), respectively. In addition, Ip (Ki = 2.14 nM) not only exhibited good herbicidal activity at 9.375-37.5 g ai/ha but also showed high crop safety to rice at 75 g ai/ha by the postemergence application, indicating that Ip could be developed as a potential herbicide for weed control in rice fields. Additionally, our molecular dynamic simulation clarified the molecular basis for the interactions of these molecules with NtPPO. The metabolism studies in planta showed that IIIc could be converted to Ic, which displayed higher herbicidal activity than IIIc. The density functional theory analysis showed that due to the effect of two sulfur atoms at the triazinone moiety, IIIc is more reactive than Ic, making it more easily degraded in planta. Our work indicates that the AFEL strategy could be used to design new molecules with improved bioactivity.

Synthesis of Novel α-Trifluoroanisole Derivatives Containing Phenylpyridine Moieties with Herbicidal Activity

To find novel herbicidal compounds with high activity and broad spectrum, a series of phenylpyridine moiety-containing α-trifluoroanisole derivatives were designed, synthesized, and identified via nuclear magnetic resonance (NMR) and high-resolution mass spectrometry (HRMS). Greenhouse-based herbicidal activity assays revealed that compound 7a exhibited > 80% inhibitory activity against Abutilon theophrasti, Amaranthus retroflexus, Eclipta prostrate, Digitaria sanguinalis, and Setaria viridis at a dose of 37.5 g a.i./hm2, which was better than fomesafen. Compound 7a further exhibited excellent herbicidal activity against Abutilon theophrasti and Amaranthus retroflexus in this greenhouse setting, with respective median effective dose (ED50) values of 13.32 and 5.48 g a.i./hm2, both of which were slightly superior to fomesafen (ED50 = 36.39, 10.09 g a.i./hm2). The respective half-maximal inhibitory concentration (IC50) for compound 7a and fomesafen when used to inhibit the Nicotiana tabacum protoporphyrinogen oxidase (NtPPO) enzyme, were 9.4 and 110.5 nM. The docking result of compound 7a indicated that the introduction of 3-chloro-5-trifluoromethylpyridine and the trifluoromethoxy group was beneficial to the formation of stable interactions between these compounds and NtPPO. This work demonstrated that compound 7a could be further optimized as a PPO herbicide candidate to control various weeds.

A Competitive Edge: Competitor Inspired Scaffold Hopping in Herbicide Lead Optimization

Over the years, scaffold hopping has proven to be a powerful tool in the agrochemical optimization process. It offers the opportunity to modify known molecular lead structures to improve a range of parameters, including biological efficacy and spectrum, physicochemical properties, toxicity, stability, and to secure new intellectual property. Very often the disclosure of a new chemical structure can spark a multitude of competitor activities, where scaffold hopping plays a crucial role in the optimization process as well as for the generation of new intellectual property. Herein, recent examples of scaffold hopping in early phase herbicide research based on competitor inspired activities will be discussed using examples of how these research campaigns can often result in the registration of new crop protection products.

Discovery of (5-(Benzylthio)-4-(3-(trifluoromethyl)phenyl)-4H-1,2,4-triazol-3-yl) Methanols as Potent Phytoene Desaturase Inhibitors through Virtual Screening and Structure Optimization

Phytoene desaturase (PDS) is not only an important enzyme in the biosynthesis of carotenoids but also a promising target for herbicide discovery. However, in recent years, no expected PDS inhibitors with new scaffolds have been reported. Hence, a solution for developing PDS inhibitors is to search for new compounds with novel chemotypes based on the PDS protein structure. In this work, we integrated structure-based virtual screening, structure-guided optimization, and biological evaluation to discover some PDS inhibitors with novel chemotypes. It is noteworthy that the highly potent compound 1b, 1-(4-chlorophenyl)-2-((5-(hydroxymethyl)-4-(3-(trifluoromethyl)phenyl)-4H-1,2,4-triazol-3-yl)thio)ethan-1-one, exhibited a broader spectrum of post-emergence herbicidal activity at 375-750 g/ha against six kinds of weeds than the commercial PDS inhibitor diflufenican. Surface plasmon resonance (SPR) assay showed that the affinity of our compound 1b (K_D = 65.9 μM) to PDS is slightly weaker but at the same level as diflufenican (K_D = 38.3 μM). Meanwhile, determination of the phytoene content and PDS mRNA quantification suggested that 1b could induce PDS mRNA reduction and phytoene accumulation. Moreover, 1b also caused the increase of reactive oxygen species (ROS) and the change of ROS-associated enzyme activity in albino leaves. Hence, all these results indicated the feasibility of PDS protein structure-based virtual screen and structure optimization to search for highly potent PDS inhibitors with novel chemotypes for weed control.