Studies of binding interactions between Dufulin and southern rice black-streaked dwarf virus P9-1

Effects of charged polystyrene microplastics on the bioavailability of dufulin in tomato plant

Microplastics (MPs) and pesticides commonly exist in the environment, yet the interactions between them and their subsequent impacts on plants remain poorly understood. Thus, this study aimed to investigate the impacts of differently charged polystyrene (PS) MPs, including PS-COO-, PS and PS-NH3+ MPs, on the fate of 14C-labelled new antiviral pesticide Dufulin (DFL) in a hydroponic tomato system. The results showed that MPs greatly reduced the growth of tomato plants, with suppression of 18.4-30.2%. Compared to the control group, PS-COO-, PS and PS-NH3+ MPs also reduced the bioaccumulation of DFL in whole tomato plants by 40.3%, 34.5%, and 26.1%, respectively. Furthermore, MPs influenced the translocation of DFL in plant tissues, and the values decreased at the rates of 38.7%, 26.5% and 15.7% for PS-COO-, PS and PS-NH3+, respectively. Interestingly, compared to the control group, PS-COO- exhibited a profound inhibitory effect on DFL concentrations in tomatoes, potentially resulting in a lower dietary risk in the hydroponic tomato system. This may be due to the strong adsorption between PS-COO- and DFL, and PS-COO- may also inhibit the growth of tomato plants. Overall, our study could provide valuable insights into the risk assessment of DFL in the presence of MPs in plant systems.

Nonenantioselective environmental behavior of a chiral antiviral pesticide dufulin in aerobic soils

Dufulin is a promising chiral antiviral agent, but little is known about its fate in soils. In this study, the fate of dufulin enantiomers in aerobic soils was investigated using radioisotope tracing techniques. The result of the four-compartment model showed no significant differences in dissipation, generation of bound residues (BR) and mineralization between S-dufulin and R-dufulin during incubation. Dufulin dissipated most quickly in cinnamon soils, followed by fluvo-aquic and black soils and the half-lives of dufulin in these soils obtained by the modified model were 4.92-5.23, 32.39-33.32 and 60.80-61.34 d, respectively. After 120 d incubation, the percentage of radioactivity of BR increased to 18.2-38.4 % in the three soils. Dufulin formed most bound residues in the black soil, least in the cinnamon soil, and BRs rapidly formed in the cinnamon soil during the early culture period. In these three soils, the cumulative mineralization of ¹⁴CO₂ ranged from 25.0 to 26.7 %, 42.1 to 43.4 % and 33.8 to 34.4 %, respectively, which indicated that the environmental fate of dufulin was primarily influenced by soil characteristics. The study of microbial community structure revealed that the phyla Ascomycota, Proteobacteria and genus Mortierella might be related to the degradation of dufulin. These findings provide a reference for assessing the environmental impact and ecological safety of dufulin application.

Plant Protection against Viruses: An Integrated Review of Plant Immunity Agents

Plant viruses are an important class of pathogens that seriously affect plant growth and harm crop production. Viruses are simple in structure but complex in mutation and have thus always posed a continuous threat to agricultural development. Low resistance and eco-friendliness are important features of green pesticides. Plant immunity agents can enhance the resilience of the immune system by activating plants to regulate their metabolism. Therefore, plant immune agents are of great importance in pesticide science. In this paper, we review plant immunity agents, such as ningnanmycin, vanisulfane, dufulin, cytosinpeptidemycin, and oligosaccharins, and their antiviral molecular mechanisms and discuss the antiviral applications and development of plant immunity agents. Plant immunity agents can trigger defense responses and confer disease resistance to plants, and the development trends and application prospects of plant immunity agents in plant protection are analyzed in depth.

Understanding the metabolism of the novel plant antiviral agent dufulin by different positional 14C labeling in cherry radishes

Dufulin is a new type of plant antiviral agent. However, its metabolism in plants, which is very important for environmental risk assessment, is still unclear. In this study, we used ¹⁴C markers at different positions and high-performance liquid chromatography-quadrupole time-of-flight-mass spectrometry (HPLC-QTOF-MS) to qualitatively and quantitatively analyze dufulin metabolites in cherry radish. By combining ion pairs with unique abundance ratios, we clarified the metabolite structures, inferred the metabolic pathway of dufulin, and clarified the criteria for residues. The extractable residue of dufulin from cherry radish stem and leaf tissues was above 98 % and that in the succulent root was above 87 %. In the stem and leaf tissues and succulent root, dufulin underwent both phase I and phase II metabolism, and four metabolites were produced, including a conjugate of glucose malonate and hydroxylated dufulin, which was confirmed by comparison with a standard. However, the proportions and concentrations of the four metabolites did not meet the residue criteria, so only the dufulin precursor compound was included as a residue. This study provides reliable data for evaluating the impacts of dufulin on the environment and human health and for objectively examining the safety of dufulin.

Cysteine protease domain of potato virus Y: The potential target for urea derivatives

The cysteine protease structural domain (CPD) encoded by the potato virus Y (PVY) accessory component protein helper component-proteinase (HC-Pro) is an auxiliary component of aphid virus transmission and plays an important role in virus infection and replication. Urea derivatives have potential antiviral activities. In this study, the PVY HC-Pro C-terminal truncated recombinant protein (residues 307-465) was expressed and purified. The interactions of PVY CPD with urea derivatives HD1-36 were investigated. Microscale thermophoresis experiments showed that HD6, -19, -21 and - 25 had the strongest binding forces to proteins, with K_d values of 2.16, 1.40, 1.97 and 1.12 μM, respectively. An experiment verified the microscale thermophoresis results, and the results were as expected, with K_d values of 6.10, 4.78, 5.32, and 4.52 μM for HD6, -19, -21, and - 25, respectively. Molecular docking studies indicated that the interaction sites between PVY CPD and HD6, -19, -21, and - 25, independently, were aspartic acid 121, asparagine 48, and tyrosine 38, which played important roles in their binding. In vivo experiments verified that HD25 inhibited PVY more than the control agents ningnanmycin and urea. These data have important implications for the design and synthesis of novel urea derivatives.

Myricetin Derivative Targets Cucumber Mosaic Virus 2b Protein to Achieve In Vivo Antiviral Activity in Plants

Cucumber mosaic virus (CMV) 2b protein plays a key role in the process of CMV infecting plants and symptom formation and is a potential molecular target for the control of this important plant virus. The exploitation of antiviral compounds is one of the strategies with the highest input: output ratio in plant protection. In this study, the CMV 2b recombinant protein was cloned, purified, and identified as the target protein by mass spectrometry. Subsequently, we carried out preliminary functional screening of the LP series of myricetin derivatives designed and synthesized in our laboratory and commercial antiviral compounds by microscale thermophoresis (MST), which showed that LP compounds LP4, LP11, LP13, and LP20 interacted well with CMV 2b, with dissociation constant (K_d) values of 1.39, 0.88, 1.52, and 1.77 μM, respectively. Among the commercially available antiviral compounds, ningnanmycin (NNM) was the most active, with a K_d value of 4.09 μM. Then, the strongest binding force to CMV 2b was identified to be from LP11 by isothermal titration calorimetry (ITC) experiments, with a K_d of 1.19 μM. Among the commercial compounds, NNM had the strongest binding force with CMV 2b, with a K_d of 4.62 μM. Through the screening of commercial compounds and LP series compounds by MST and ITC, LP11, NNM (positive control), LP16 (negative control), and the blank control group were selected to test the in vivo impact of LP11 on CMV. Specifically, the screened compounds were sprayed onto CMV-inoculated Nicotiana benthamiana plants to determine their impact on the regulation of CMV pathogenic gene expression, symptoms, and virus titer. The results showed that LP11 had a strong ability to inhibit CMV infection of tobacco at the transcriptional and translational levels. By mutating the CMV 2b protein, the 15th amino acid leucine and the 18th amino acid methionine at the N-terminal region were shown to be potential sites for binding to compound LP11. This finding provided a theoretical basis for screening and developing anti-CMV agents.

The Discovery of Novel Ferulic Acid Derivatives Incorporating Substituted Isopropanolamine Moieties as Potential Tobacco Mosaic Virus Helicase Inhibitors

Target-based drug design, a high-efficiency strategy used to guide the development of novel pesticide candidates, has attracted widespread attention. Herein, various natural-derived ferulic acid derivatives incorporating substituted isopropanolamine moieties were designed to target the tobacco mosaic virus (TMV) helicase. Bioassays demonstrating the optimized A₁₉, A₂₀, A₂₉, and A₃₁ displayed excellent in vivo antiviral curative abilities, affording corresponding EC₅₀ values of 251.1, 336.2, 347.1, and 385.5 μg/mL, which visibly surpassed those of commercial ribavirin (655.0 μg/mL). Moreover, configurational analysis shows that the R-forms of target compounds were more beneficial to aggrandize antiviral profiles. Mechanism studies indicate that R-A₁₉ had a strong affinity (K_d = 5.4 μM) to the TMV helicase and inhibited its ability to hydrolyze ATP (50.61% at 200 μM). Meanwhile, A₁₉ could down-regulate the expression of the TMV helicase gene in the host to attenuate viral replication. These results illustrate the excellent inhibitory activity of A₁₉ towards the TMV helicase. Additionally, docking simulations uncovered that R-A₁₉ formed more hydrogen bonds with the TMV helicase in the binding pocket. Recent studies have unambiguously manifested that these designed derivatives could be considered as promising potential helicase-based inhibitors for plant disease control.

Plant Viral Coat Proteins as Biochemical Targets for Antiviral Compounds

Coat proteins (CPs) of RNA plant viruses play a pivotal role in virus particle assembly, vector transmission, host identification, RNA replication, and intracellular and intercellular movement. Numerous compounds targeting CPs have been designed, synthesized, and screened for their antiviral activities. This review is intended to fill a knowledge gap where a comprehensive summary is needed for antiviral agent discovery based on plant viral CPs. In this review, major achievements are summarized with emphasis on plant viral CPs as biochemical targets and action mechanisms of antiviral agents. This review hopefully provides new insights and references for the further development of new safe and effective antiviral pesticides.

Research on the Interaction Mechanism Between α Mino-Phosphonate Derivative Q-R and Harpin-Binding Protein 1 in Tobacco (Nicotiana tabacum) Plants

Amino-phosphonate derivative R-diphenyl-1-(4-methylbenzothiazole-2-amino)-1-(thiphene-2-yl)-methylphosphonate (Q-R) has a high protective anti-tobacco mosaic virus (TMV) activity. However, the mechanism responsible for Q-R's effect on TMV infection is largely unknown. Here, we studied the expression levels of harpin-binding protein 1 (HrBP1) and pathogenesis-related protein-1a (PR-1a) in TMV-infected tobacco plants by using reverse transcription quantitative real-time PCR. Then, we verified the interactions between Q-R and the HrBP1 protein from Escherichia coli using isothermal titration calorimetry and studied the Q-R-associated assembly of HrBP1 using size-exclusion chromatography. The results showed that the expression levels of HrBP1 and PR-1a genes were significantly increased by Q-R at the transcriptional level in TMV-infected tobacco plants, and the E. coli-expressed HrBP1 protein was assembled into oligomers by Q-R via binding to HrBP1 with a dissociation constant of 1.19 μM. We, therefore, concluded that Q-R activated the HrBP1 and PR-1a genes and enhanced the ability of HrBP1 to assemble in tobacco plants.

Joint effects of microplastic and dufulin on bioaccumulation, oxidative stress and metabolic profile of the earthworm (Eisenia fetida)

Microplastics and pesticides are identified as two environmental pollutants that have an adverse impact on the environment. The knowledge about the combined exposure of pesticides and microplastics may facilitate further assessment of their ecotoxicity. In this study, we investigated joint effects of microplastic and dufulin on bioaccumulation, oxidative stress and metabolic profile of the earthworm. Bioaccumulation analysis showed that the bio-soil accumulation factor of dufulin in earthworms reached its maximum value on the 14th day, and microplastics could significantly increase the bioaccumulation of dufulin in earthworms. Biochemical analysis showed that the oxidative damage of earthworms could be observed on the 14th day of the exposure to dufulin, while the oxidative damage of earthworms could be observed on the 7th day of the combined exposure to microplastics and dufulin, and it could still be observed on the 14th day. ¹H-NMR-based metabolomics revealed that the exposure of dufulin significantly altered the relative abundances of 14 metabolites and two metabolic pathways, but the combined exposure of dufulin and microplastics significantly changed the relative abundances of 21 metabolites and three metabolic pathways. It could be seen that microplastics could aggravate the oxidative damage and the interference with the metabolic profile caused by dufulin to earthworms. The results of this study could provide effective information for the risk assessment of dufulin and microplastic in environmental safety.

Review on Structures of Pesticide Targets

Molecular targets play important roles in agrochemical discovery. Numerous pesticides target the key proteins in pathogens, insect, or plants. Investigating ligand-binding pockets and/or active sites in the proteins' structures is usually the first step in designing new green pesticides. Thus, molecular target structures are extremely important for the discovery and development of such pesticides. In this manuscript, we present a review of the molecular target structures, including those of antiviral, fungicidal, bactericidal, insecticidal, herbicidal, and plant growth-regulator targets, currently used in agrochemical research. The data will be helpful in pesticide design and the discovery of new green pesticides.

Screening anti-TMV agents targeting tobacco mosaic virus helicase protein

Tobacco mosaic virus helicase (TMV-Hel) plays important roles in viral multiplication. TMV-Hel is a potential target of anti-TMV agents. Our previous studies expressed and purified TMV-Hel as target protein for cytosinpeptidemycin. In this study, we preform molecular docking to study the binding sites of commercial antiviral agents with TMV-Hel. Then we verify the interactions between the potential anti-TMV agents and TMV-Hel in vitro using Microscale Thermophoresis experiment and study the inhibiting expression of TMV-Hel with the potential anti-TMV agents in vivo using Western-blot (WB) method. The results showed that ribavirin bound to TMV-Hel with a dissociation constant of 1.55 μM by direct interaction with eight binding sites, which was consistent with the docking studies. Ribavirin inhibited the expression of TMV-Hel in Nicotiana benthamiana. Docking studies combined Microscale Thermophoresis and WB experiment provided a new method to screen anti-TMV agents targeting TMV-Hel.

Synthesis and antiviral activity of novel myricetin derivatives containing ferulic acid amide scaffolds

A variety of myricetin derivatives bearing ferulic acid amide scaffolds were designed and synthesized.

Dufulin Intervenes the Viroplasmic Proteins as the Mechanism of Action against Southern Rice Black-Streaked Dwarf Virus

Southern rice black-streaked dwarf virus (SRBSDV) causes disease in crops, which reduces the quality and yield. Several commercial antiviral agents are available to control the SRBSDV induced disease. However, the mechanism of antiviral agents controlling SRBSDV is largely unknown. Identifying targets in SRBSDV is a key step of antiviral agent discovery. Here, we investigated the potential protein target of the antiviral agent dufulin. We cloned and expressed a soluble viroplasmic P6 protein in the prokaryote Escherichia coli and the eukaryote Spodoptera frugiperda 9. The dissociation constants of dufulin with the purified P6 protein from E. coli and S. frugiperda 9 expression systems were 4.49 and 4.95 μM, respectively, indicating a strong binding affinity between dufulin and P6 protein. In vivo, dufulin significantly inhibited the expression of both P6 protein and P6 gene in the SRBSDV-infected rice leaves. This inhibition on P6 protein expression was also observed in transformed Nicotiana benthamiana where the P6 was overexpressed. Our data also showed that dufulin inhibited the duplication of SRBSDV in a dose-dependent manner in infected rice leaves with a half maximum effective concentration of 3.32 mM. It is therefore concluded that dufulin targets the viroplasmic protein P6 to inhibit the virulence of SRBSDV.

Design, synthesis, antiviral bioactivities and interaction mechanisms of penta-1,4-diene-3-one oxime ether derivatives containing a quinazolin-4(3H)-one scaffold

Background

penta-1,4-diene-3-one oxime ether and quinazolin-4(3H)-one derivatives possess favorable agricultural activities. Aiming to discover novel molecules with highly-efficient agricultural activities, a series of penta-1,4-diene-3-one oxime ether derivatives containing a quinazolin-4(3H)-one scaffold were synthesized and evaluated for their antiviral activities.

Result

Antiviral bioassays indicated that some title compounds exhibited significant antiviral activity against tobacco mosaic virus (TMV). In particular, compounds 8c, 8j and 8k possessed appreciable curative activities against TMV in vivo, with half-maximal effective concentration (EC₅₀) values of 138.5, 132.9 and 125.6 μg/mL, respectively, which are better than that of ningnanmycin (207.3 μg/mL). Furthermore, the microscale thermophoresis experiments (MST) on the interaction of compound 8k with TMV coat protein (TMV CP) showed 8k bound to TMV CP with a dissociation constant of 0.97 mmol/L. Docking studies provided further insights into the interaction of 8k with the Arg90 of TMV CP.

Conclusions

Sixteen penta-1,4-diene-3-one oxime ether derivatives containing a quinazolin-4(3H)-one scaffold were designed, synthesized, and their antiviral activities against TMV were evaluated. Antiviral bioassays indicated that some target compounds exhibited remarkable antiviral activities against TMV. Furthermore, through the MST and docking studies, we can speculate that 8k inhibited the virulence of TMV by binding Arg90 in TMV CP. These results indicated that this kind of penta-1,4-diene-3-one oxime ether derivatives containing a quinazolin-4(3H)-one scaffold could be further studied as potential alternative templates in the search for novel antiviral agents.

Electronic supplementary material

The online version of this article (10.1186/s13065-019-0547-1) contains supplementary material, which is available to authorized users.

Novel Phosphorylated Penta-1,4-dien-3-one Derivatives: Design, Synthesis, and Biological Activity

A series of novel phosphorylated penta-1,4-dien-3-one derivatives were designed and synthesized. The structures of all title compounds were determined by ¹H-NMR, ¹³C-NMR, ³¹P-NMR, and high-resolution mass spectrometry (HRMS). Bioassay results showed that several of the title compounds exhibited remarkable antibacterial and antiviral activities. Among these, compound 3g exhibited substantial antibacterial activity against Xanthomonas oryzae pv. Oryzae (Xoo), with a 50% effective concentration (EC₅₀) value of 8.6 μg/mL, which was significantly superior to bismerthiazol (BT) (58.8 µg/mL) and thiodiazole-copper (TC) (78.7 μg/mL). In addition, compound 3h showed remarkable protective activity against tobacco mosaic virus (TMV), with an EC₅₀ value of 104.2 μg/mL, which was superior to that of ningnanmycin (386.2 μg/mL). Furthermore, the microscale thermophoresis and molecular docking experiments on the interaction of compounds 3h and 3j with TMV coat protein (TMV CP) were also investigated. Compounds 3h and 3j bound to TMV CP with dissociation constants of 0.028 and 0.23 μmol/L, which were better than that of ningnanmycin (0.52 μmol/L). These results suggest that novel phosphorylated penta-1,4-dien-3-one derivatives may be considered as an activator for antibacterial and antiviral agents.

Cucumber mosaic virus coat protein: The potential target of 1, 4-pentadien-3-one derivatives

Cucumber mosaic virus coat protein (CMV CP) plays a key role in cell-to-cell movement in host organisms. 1,4-Pentadien-3-one derivatives have excellent antiviral activities. In this study, we cloned, expressed and purified a CP recombinant protein. Then, we studied the binding interactions of CMV CP and 1, 4-pentadien-3-one derivatives N1-N20. Microscale thermophoresis experiments showed that N12 and N16 bound to CMV CP with dissociation constants of 0.071 and 0.11 μM, respectively. Docking and site-directed mutagenesis studies provided further insights into the interactions of N12 and N16 with Ile210, Thr69 and Ser213of CMV CP. Thus, these CMV CP residues may be important binding sites for the 1,4-pentadien-3-one derivatives N12 and N16. The data are important for designing and synthesizing new pentadienone derivatives.

Biological activity evaluation and action mechanism of chalcone derivatives containing thiophene sulfonate

A series of novel chalcone derivatives containing a thiophene sulfonate group were designed and synthesized. The structures of all title compounds were determined by ¹H-NMR, ¹³C-NMR and HRMS. Antibacterial bioassays indicated that, compound 2l demonstrated excellent antibacterial activities against Xanthomonas axonopodis pv. citri (Xac), with an EC₅₀ value of 11.4 μg mL⁻¹, which is significantly superior to those of bismerthiazol (BT) (51.6 μg mL⁻¹) and thiodiazole-copper (TC) (94.7 μg mL⁻¹). Meanwhile, the mechanism of action of compound 2l was confirmed by using scanning electron microscopy (SEM). In addition, compound 2e showed remarkable inactivation activity against Tobacco mosaic virus (TMV), with an EC₅₀ value of 44.3 μg mL⁻¹, which was superior to that of ningnanmycin (120.6 μg mL⁻¹). Microscale thermophoresis (MST) also showed that the binding of compounds 2e and 2h to Tobacco mosaic virus coat protein (TMV-CP) yielded K_d values of 0.270 and 0.301 μmol L⁻¹, which are better than that of ningnanmycin (0.596 μmol L⁻¹). At the same time, molecular docking studies for 2e and 2h with TMV-CP (PDB code: 1EI7) showed that the compound was embedded well in the pocket between the two subunits of TMV-CP in each case. These results suggested that chalcone derivatives containing a thiophene sulfonate group may be considered as activators in the design of antibacterial and antiviral agents.

Synthesis, antibacterial, antiviral activities and action mechanism of chalcone derivatives containing thiophene sulfonate.

Synthesis, antiviral and antibacterial activities and action mechanism of penta-1,4-dien-3-one oxime ether derivatives containing a quinoxaline moiety

A series of penta-1,4-dien-3-one oxime ether derivatives containing a quinoxaline moiety were synthesized, and their bioactivities and action mechanism were evaluated.

Toxicokinetics, Tissue Distribution, and Excretion of Dufulin Racemate and Its R ( S)-Enantiomers in Rats

Dufulin is a plant antiviral agent with a novel molecular structure and has been used widely to prevent and control tobacco and rice viral diseases. In this study, an UHPLC-MS/MS method was developed for rapid determination of dufulin racemate ( rac-DFL) and its R ( S)-enantiomers in rat plasma, tissues, urine, and feces. A MALDI-MSI method was further used for visual research on tissue distribution after intragastric administration of the three analytes. Toxicokinetic study showed that both ( R)-enantiomer of dufulin (( R)-DFL) and ( S)-enantiomer of dufulin (( S)-DFL) had a faster ability to reach C_max than that of rac-DFL. ( R)-DFL and ( S)-DFL had a similar T_1/2, though both were significantly lower than rac-DFL. C_max of rac-DFL was obviously higher than ( R)-DFL or ( S)-DFL. Meanwhile, C_max of ( S)-DFL was only about 60% of ( R)-DFL. Rac-DFL and its R ( S)-enantiomers had a dose-dependent toxicokinetic profile. Tissue distribution results revealed rac-DFL, ( R)-DFL, and ( S)-DFL mainly distributed in the liver and kidney, but the maximum concentration was only ng/g grade and could significantly degrade within 3 h. This indicates that dufulin does not cause liver and kidney toxicity in animals. In addition, rac-DFL and its R ( S)-enantiomers have not been detected in brain tissue. Cumulative excretion of rac-DFL and its R ( S)-enantiomers within 24 h in urine and feces were less than 22.85% indicating that they mainly excreted as metabolites. These results could provide evidence for the in-depth toxicity evaluation of dufulin pesticide. In addition, its metabolic selectivity information in vivo has also been obtained.

Binding studies between cytosinpeptidemycin and the superfamily 1 helicase protein of tobacco mosaic virus

Tobacco mosaic virus (TMV) helicases play important roles in viral multiplication and interactions with host organisms. They can also be targeted by antiviral agents. Cytosinpeptidemycin has a good control effect against TMV. However, the mechanism of action is unclear. In this study, we expressed and purified TMV superfamily 1 helicase (TMV-Hel) and analyzed its three-dimensional structure. Furthermore, the binding interactions of TMV-Hel and cytosinpeptidemycin were studied. Microscale thermophoresis and isothermal titration calorimetry experiments showed that cytosinpeptidemycin bound to TMV-Hel with a dissociation constant of 0.24–0.44 μM. Docking studies provided further insights into the interaction of cytosinpeptidemycin with the His375 of TMV-Hel. Mutational and Microscale thermophoresis analyses showed that cytosinpeptidemycin bound to a TMV-Hel mutant (H375A) with a dissociation constant of 14.5 μM. Thus, His375 may be the important binding site for cytosinpeptidemycin. The data are important for designing and synthesizing new effective antiphytoviral agents.

Tobacco mosaic virus (TMV) helicases play important roles in viral multiplication and interactions with host organisms.