Novel synthesized 2, 4-DAPG analogues: antifungal activity, mechanism and toxicology

Strategies for tailoring functional microbial synthetic communities

Natural ecosystems harbor a huge reservoir of taxonomically diverse microbes that are important for plant growth and health. The vast diversity of soil microorganisms and their complex interactions make it challenging to pinpoint the main players important for the life support functions microbes can provide to plants, including enhanced tolerance to (a)biotic stress factors. Designing simplified microbial synthetic communities (SynComs) helps reduce this complexity to unravel the molecular and chemical basis and interplay of specific microbiome functions. While SynComs have been successfully employed to dissect microbial interactions or reproduce microbiome-associated phenotypes, the assembly and reconstitution of these communities have often been based on generic abundance patterns or taxonomic identities and co-occurrences but have only rarely been informed by functional traits. Here, we review recent studies on designing functional SynComs to reveal common principles and discuss multidimensional approaches for community design. We propose a strategy for tailoring the design of functional SynComs based on integration of high-throughput experimental assays with microbial strains and computational genomic analyses of their functional capabilities.

2,4-Diacetylphloroglucinol (DAPG) derivatives rapidly eradicate methicillin-resistant staphylococcus aureus without resistance development by disrupting membrane

Methicillin-resistant Staphylococcus aureus (MRSA) causes severe public health challenges throughout the world, and the multi-drug resistance (MDR) of MRSA to antibiotics necessitates the development of more effective antibiotics. Natural 2,4-diacetylphloroglucinol (DAPG), produced by Pseudomonas, displays moderate inhibitory activity against MRSA. A series of DAPG derivatives was synthesized and evaluated for their antibacterial activities, and some showed excellent activities (MRSA MIC = 0.5-2 μg/mL). Among these derivatives, 7g demonstrated strong antibacterial activity without resistance development over two months. Mechanistic studies suggest that 7g asserted its activity by targeting bacterial cell membranes. In addition, 7g exhibited significant synergistic antibacterial effects with oxacillin both in vitro and in vivo, with a tendency to eradicate MRSA biofilms. 7g is a promising lead for the treatment of MRSA.

Antifungal molecular details of MNQ-derived novel carbon dots against Penicillium digitatum

It is urgent to develop high-efficiency and low-toxicity natural antifungal agents on green mold caused by Penicillium digitatum. The effect of 2-methoxy-1, 4-naphthoquinone (MNQ) inhibition of P. digitatum was not very satisfactory. MNQ-derived carbon dots (MNQ-CDs) synthesized through a solvothermal route were used as antifungal agents against P. digitatum. The antifungal activity of prepared MNQ-CDswas enhanced compared to MNQ, and the minimum inhibitory concentration was 2.8 μg/mL. A total of 441 genes and 122 metabolites have undergone significant changes. The omics data revealed that MNQ-CDs primarily modified the metabolism of aromatic amino acids and synthesis of the cell membrane in P. digitatum, thereby inhibiting its propagation. Furthermore, compared with MNQ, MNQ-CDs had a better control effect on the green mold of citrus fruits, and could more significantly inhibit the propagation of P. digitatum. This study provides a new idea for the design of new and efficient antifungal materials.

Mechanistic insight into the free radical scavenging and xanthine oxidase (XO) inhibitor potent of monoacetylphloroglucinols (MAPGs)

Three novel antioxidant candidates based on phenolic polyketide, monoacetylphloroglucinol (MAPG), a natural antibiotic compound produced by plant growth-promoting rhizobacteria (PGPR), Pseudomonas fluorescens F113 have been proposed. Initially, a green and highly efficient route to the synthesis of MAPG and its two analogues from phloroglucinol (PG) has been developed. Afterward, their rational mechanism of antioxidant activity has been investigated based on thermodynamic descriptors involved in the double ( 2H+/2e-) radical trapping processes. These calculations have been performed using the systematic density functional theory (DFT) method at the B3LYP/Def2-SVP level of theory in the gas phase and aqueous solution. Our findings reveal that the double formal hydrogen atom transfer (df-HAT) mechanism is preferred in the gas phase, while the double sequential proton loss electron transfer (dSPLET) mechanism is preferred in aqueous solution for all MAPGs. The 6-OH group represents the most favourable site for trapping radical species for all MAPGs, which is supported by the pK_a values obtained from DFT calculations. The role of acyl substituents on the PG ring has been comprehensively discussed. The presence of acyl substituents has a strong influence on the thermodynamic parameters of the phenolic O-H bond in PG. These results are supported by frontier molecular orbitals (FMOs) analysis, where the addition of acyl substituents increases the chemical reactivity of MAPGs significantly. Based on molecular docking and molecular dynamics simulations (MDs), MAPGs are also predicted to be promising candidates for xanthine oxidase (XO) inhibition.HighlightsThe antioxidant activity of the three synthesised MAPGs has been investigated using the DFT method.Acyl substituents increase the chemical reactivity and antioxidant activity of MAPGs.df-HAT is the preferred mechanism in the gas phase.dSPLET seems to be more favoured in aqueous solution.MAPGs are expected to be promising xanthine oxidase (XO) inhibitors.

Investigation of the dual role of acyl phloroglucinols as a new hope for antibacterial and anti-SARS-CoV-2 agents employing integrated in vitro and multi-phase in silico approaches

With the rapid spread of multi-drug-resistant bacteria and more infectious or aggressive variants of SARS-CoV-2, it is critical to develop drugs that can quickly adapt to evolving bacterial and viral mutations. In this study, encouraged by nature, we synthesized a series of phloroglucinol (PG) derivatives, acyl phloroglucinols (ACPLs) 2a-4c by mimicking the structure of the natural antifungal 2,4-diacetylphloroglucinol 3a (2,4-DAPG). According to the quantum chemical calculation, these compounds were expected to be exceptionally favourable for intermolecular interaction with protein receptors. Intriguingly, the in vitro study of Staphylococcus aureus (S. aureus) ATCC 25923 and Escherichia coli (E. coli) ATCC 25922, showed that the four ACPLs 3a-4a had good antibacterial activity and selectivity against gram-positive bacteria, S. aureus. These results were then supported by in silico molecular docking and molecular dynamics simulations (MDs) between these potent compounds and the S. aureus FtsA protein (PDB ID: 3WQU). Furthermore, with the aid of the knowledge base Virus-CKB along with the molecular docking study, it was found that the three ACPLs 4a-4c showed potential inhibitors against SARS-CoV-2 PLpro (PDB ID: 7CMD). Additionally, 100 ns of MDs was carried out in order to assess the stability behaviour of ACPLs at the docked site. Moreover, in silico ADME/T and drug likeness of all studied ACPLs were also predicted. Finally, shape-based screening of FDA-approved drugs was performed using the most prominent synthesized ACPLs as a template, enabling us to include several medications that could be utilized as antibacterial and antiviral drug candidates.Communicated by Ramaswamy H. Sarma.

2,4-Diacetylphloroglucinol producing Pseudomonas fluorescens JM-1 for management of ear rot disease caused by Fusarium moniliforme in Zea mays L

Maize (Zea mays L.) is a major cereal crop grown in a large number of countries. Loss in maize yield due to biotic stresses including fungal phytopathogens is a matter of immense concern. Control measures applied for eradication of fungal phytopathogens in maize are not up to the mark and more often involve harsh chemical(s)/pesticide(s) that cause deleterious effects both in humans and soil biota. Greener alternatives, such as the use of rhizosphere microbes in the form of bioinoculants, have proven to be very successful in terms of enhancing crop yield and suppressing fungal phytopathogens. In the present study, fluorescent pseudomonads were isolated from the maize rhizosphere and monitored for their plant growth-promoting (PGP) and biocontrol activities against Fusarium moniliforme. Based on various PGP traits and biocontrol potential, isolate JM-1 was found to be most effective and as per 16S rRNA gene sequencing analysis was identified as Pseudomonas fluorescens. Further experiments showed that the biocontrol potential of JM-1 against ear rot fungus involved the production of antifungal compound 2,4-diacetylphloroglucinol (DAPG). When examined for antagonistic interaction under scanning electron microscopy (SEM), structural abnormality, hyphal lysis, and deformity in fungal mycelium were observed. In the pot experiment, application of talc-based JM-1 containing bioformulation (in pot trials) showed significant enhancement in maize growth parameters (including the seed number and weight) in comparison to control even in presence of the phytopathogen. Ear fresh weight, dry weight, number of seeds per plant, and 100-grain weight were found to increase significantly by 34, 34, 52, and 18% respectively, in comparison to control. P. fluorescens JM-1 can therefore be used as a bioinoculant for ear rot disease control and sustainably enhancing maize yield.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03201-7.

Root-Associated Bacteria Are Biocontrol Agents for Multiple Plant Pests

Biological control is an important process for sustainable plant production, and this trait is found in many plant-associated microbes. This study reviews microbes that could be formulated into pesticides active against various microbial plant pathogens as well as damaging insects or nematodes. The focus is on the beneficial microbes that colonize the rhizosphere where, through various mechanisms, they promote healthy plant growth. Although these microbes have adapted to cohabit root tissues without causing disease, they are pathogenic to plant pathogens, including microbes, insects, and nematodes. The cocktail of metabolites released from the beneficial strains inhibits the growth of certain bacterial and fungal plant pathogens and participates in insect and nematode toxicity. There is a reinforcement of plant health through the systemic induction of defenses against pathogen attack and abiotic stress in the plant; metabolites in the beneficial microbial cocktail function in triggering the plant defenses. The review discusses a wide range of metabolites involved in plant protection through biocontrol in the rhizosphere. The focus is on the beneficial firmicutes and pseudomonads, because of the extensive studies with these isolates. The review evaluates how culture conditions can be optimized to provide formulations containing the preformed active metabolites for rapid control, with or without viable microbial cells as plant inocula, to boost plant productivity in field situations.

Phloroglucinol and Its Derivatives: Antimicrobial Properties toward Microbial Pathogens

Phloroglucinol (PG) is a natural product isolated from plants, algae, and microorganisms. Aside from that, the number of PG derivatives has expanded due to the discovery of their potential biological roles. Aside from its diverse biological activities, PG and its derivatives have been widely utilized to treat microbial infections caused by bacteria, fungus, and viruses. The rapid emergence of antimicrobial-resistant microbial infections necessitates the chemical synthesis of numerous PG derivatives in order to meet the growing demand for drugs. This review focuses on the use of PG and its derivatives to control microbial infection and the underlying mechanism of action. Furthermore, as future perspectives, some of the various alternative strategies, such as the use of PG and its derivatives in conjugation, nanoformulation, antibiotic combination, and encapsulation, have been thoroughly discussed. This review will enable the researcher to investigate the possible antibacterial properties of PG and its derivatives, either free or in the form of various formulations.

Partial purification and characterization of 2, 4-diacetylphloroglucinol producing Pseudomonas fluorescens VSMKU3054 against bacterial wilt disease of tomato

We find out the antimicrobial potential of partially purified 2,4-diacetylphloroglucinol (DAPG) against Ralstonia solanacearum and fungal plant pathogens isolated from tomato rhizobacterium Pseudomonas fluorescens VSMKU3054. The present study is mainly focused on the control of wilt disease of tomato by our isolate VSMKU3054 and DAPG. The cell free culture filtrate of P. fluorescens VSMKU3054 was significantly arrested the growth of R. solanacearum and fungal pathogens such as Rhizoctonia solani, Sclerotium rolfsii, Macrophomina phaseolina and Fusarium oxysporum compared to control. The existence of DAPG from the crude metabolites of P. fluorescens VSMKU3054 was confirmed on TLC with Rf value 0.34, which is coincide with that of authentic phloroglucinol. The partially purified DAPG exhibited much higher activity against R. solanacearum at 30 µg/ml than the fungal plant pathogens compared to control. The antimicrobial partially purified compound was identified as DAPG by UV, FT-IR and GC-MS analysis. The percentage of live cells of R. solanacearum when supplemented with DAPG at 30 µg/ml, significantly controlled the living nature of R. solanacearum up to 68% compared to tetracycline and universal control observed under high content screening analysis. The selected isolate P. fluorescens VSMKU3054 and DAPG significantly controlled wilt disease of tomato up to 59.5% and 42.12% on 3rd and 7th days compared to positive and negative control by detached leaf assay. Further, in silico analysis revealed that high interaction of DAPG encoding protease with lectin which is associated with R. solanacearum. Based on our findings, we confirmed that P. fluorescens VSMKU3054 and DAPG could be used a potential bio inoculants for the management of bacterial wilt disease of tomato.

The Microbiome of the Lebanese Wild Apple, Malus trilobata, is a Rich Source of Potential Biocontrol Agents for Fungal Post-harvest Pathogens of Apples

The widespread use of harmful fungicides in the agricultural sector has led to a demand for safer alternatives to protect against crop pathogens. The domestic apple is the second most highly consumed fruit in the world and encounters several pre- and post-harvest fungal and bacterial phytopathogens. The goal of this study was to explore the uncharacterized microbiome of a wild apple, Malus trilobata, as a potential source of novel biocontrol agents for two post-harvest fungi that affect commercial apples: Botrytis cinerea and Penicillium expansum. We sampled microflora associated with the leaves, bulk soil, and roots of Malus trilobata in two regions of Lebanon: Ehden reserve in the north and Dhour EL Choueir near Beirut. The two regions have different soil types Dhour EL Choueir and samples from the two regions showed very different microbial compositions, with greater microbial diversity among those from Ehden reserve. Molecular characterization revealed a wide variety of genera displaying activity against the two fungal pathogens, including several with previously unknown antifungal activity: Bosea, Microlunatus, Microbacterium, Mycetecola, Rhizobium and Paraphoma. In total, 92 strains inhibited Penicillium expansum (39%) and 87 strains inhibited Botrytis cinerea (38%) out of 237 screened. Further chemical and genetic characterization of one or more selected strains could pave the way for future development of new biocontrol agents for post-harvest applications.

Diacylphloroglucinol derivatives as antioxidant agents: green synthesis, optimisation, in vitro, and in silico evaluation

Several derivatives of diacylphloroglucinol (3a-3c and 5a-5b) as an analogue of natural product compound 2,4-diacetylphloroglucinol 3a, were successfully synthesised in an excellent yield via a greener Friedel-Craft acylation using methanesulfonic acid (MSA) as a catalyst under an ultrasound-assisted condition. Operational simplicity, excellent yield, expedient metal-free synthesis, energy-efficient and mild reaction conditions are the outstanding advantages in this procedure. A scaled-up reaction also revealed the practical suitability of this newly developed procedure. The effects of several process variables on 3a were carefully accomplished using response surface methodology (RSM). Moreover, the green credentials of the present protocol have been assessed using several established green metrics and compared to relevant procedures. Along with the monomers, dimeric diacylphloroglucinols (6a-6e) were also synthesised and their in vitro antioxidant activity of these species were carried out. Furthermore, drug-likeness, density functional theory (DFT), and molecular docking studies were also established.

Bacterial-Derived Plant Protection Metabolite 2,4-Diacetylphloroglucinol: Effects on Bacterial Cells at Inhibitory and Subinhibitory Concentrations

2,4-Diacetylphloroglucinol (2,4-DAPG) is a well-known bacterial secondary metabolite, however, its mechanism of inhibitory and subinhibitory action on bacterial cells is still poorly understood. The mechanism of 2,4-DAPG action on model bacterial strains was investigated using fluorescent spectroscopy and the action of the antibiotic was found to involve a rapid increase in membrane permeability that was accompanied by a reduction in its viability in nutrient-poor medium. At the same time, antibacterial action in nutrient-rich medium developed for several hours. Atomic force microscopy demonstrated time-dependent disturbances in the outer membrane of Escherichia coli when exposed to 2,4-DAPG, while Staphylococcusaureus cells have been visualized with signs of intracellular leakage. In addition, 2,4-DAPG inhibited the metabolic activity of S. aureus and E. coli bacterial cells in mature biofilms. Observed differences in the antibiofilm activity were dependent upon antibiotic concentration. The intracellular targets of the action of 2,4-DAPG were assessed using bacterial biosensors with inducible bioluminescence corresponding to DNA and protein damage. It was unable to register any positive response from either sensor. As a result, the bactericidal action of 2,4-DAPG is believed to be associated with the destruction of the bacterial barrier structures. The subinhibitory effect of 2,4-diacetylphloroglucinol was tested on quorum-sensing mediated processes in Pectobacterium carotovorum. Subinhibitory concentrations of 2,4-DAPG were found to lower the biosynthesis of acyl-homoserine lactones in P. carotovorum in a dose-dependent manner. Further investigation elucidated that 2,4-DAPG inhibits the metabolic activity of bacteria without affecting their viability.

A greatly improved procedure for the synthesis of an antibiotic-drug candidate 2,4-diacetylphloroglucinol over silica sulphuric acid catalyst: multivariate optimisation and environmental assessment protocol comparison by metrics

Efforts toward the development of a straightforward greener Gram-scale synthesis of the antibiotic compound 2,4-diacetylphloroglucinol (DAPG) have been developed. This beneficial procedure was accomplished through the Friedel–Crafts acylation of phloroglucinol over inexpensive heterogeneous silica sulphuric acid (SSA) catalyst via ultrasound-assisted (US) synthesis under solvent-free condition. The influences of various parameters such as temperature, catalyst loading, and reaction time on the reaction performance were analysed using a multivariate statistical modelling response surface methodology (RSM). A high yield of DAPG (95%) was achieved at 60 °C after 15–20 min reaction with the presence of 10% (w/w) SSA as the catalyst. Column chromatography-free and a Gram scale-up reaction also exhibited the practical applicability of this newly developed protocol. The SSA catalyst was recovered and recycled up to 10 consecutive runs with no appreciable loss of activity. A plausible mechanism for the Friedel–Crafts acylation of phloroglucinol is proposed. Moreover, an environmental assessment has been carried out over this present method and compared with several established literature using the EATOS software and the Andraos algorithm to assess the consumption of the substrates, solvents, catalysts, and the production of coupled products or by-products. In addition, their energy consumptions were also determined. The data collected showed that the present method is the most promising one, characterised by the highest environmental impact profile against all the other reported methods. The physicochemical properties of the synthesised DAPG were assessed and exhibited reasonable oral bioavailability drug property as determined by Lipinski's rules.

A greatly improved procedure for the synthesis of antibiotic 2,4-diacetylphloroglucinol has been developed via a newly advanced synthetic method.

Multiplexed Gene Expression Tuning with Orthogonal Synthetic Gene Circuits

Understanding the individual and joint contribution of multiple protein levels toward a phenotype requires precise and tunable multigene expression control. Here we introduce a pair of mammalian synthetic gene circuits that linearly and orthogonally control the expression of two reporter genes in mammalian cells with low variability in response to chemical inducers introduced into the growth medium. These gene expression systems can be used to simultaneously probe the individual and joint effects of two gene product concentrations on a cellular phenotype in basic research or biomedical applications.

PhlG mediates the conversion of DAPG to MAPG in Pseudomonas fluorescens 2P24

The antibiotic 2,4-diacetylphoroglucinol (2,4-DAPG), produced by the Gram-negative rod-shaped bacterium Pseudomonas fluorescens 2P24, is active against various soil-borne bacterial and fungal pathogens that cause plant diseases. Biosynthesis of 2,4-DAPG is controlled by regulating expression of the phlACBD operon at the post-transcriptional level. The phlG gene is located between the phlF and phlH genes, upstream of the phlACBD biosynthetic operon. Herein, we cloned the phlG gene, generated a phlG deletion mutant, and investigated its regulatory role in 2,4-DAPG biosynthesis. The results showed that deletion of phlG had no effect on the biosynthesis of 2,4-DAPG, but it affected conversion of 2,4-DAPG to its precursor monoacetylphloroglucinol (MAPG). The global regulatory factor encoded by gacS positively regulated expression of phlG, while rsmE negatively regulated its expression. Deleting phlG did not alter the ability of the bacterium to colonise plants or promote plant growth. These results suggest that phlG collaborates with other factors to regulate production of the antibiotic 2,4-DAPG in P. fluorescens 2P24.

Silencing Dicer-Like Genes Reduces Virulence and sRNA Generation in Penicillium italicum, the Cause of Citrus Blue Mold

The Dicer protein is one of the most important components of RNAi machinery because it regulates the production of small RNAs (sRNAs) in eukaryotes. Here, Dicer1-like gene (Pit-DCL1) and Dicer2-like gene (Pit-DCL2) RNAi transformants were generated via pSilent-1 in Penicillium italicum (Pit), which is the causal agent of citrus blue mold. Neither transformant showed a change in mycelial growth or sporulation ability, but the pathogenicity of the Pit-DCL2 RNAi transformant to citrus fruits was severely impaired, compared to that of the Pit-DCL1 RNAi transformant and the wild type. We further developed a citrus wound-mediated RNAi approach with a double-stranded fragment of Pit-DCL2 generated in vitro, which achieved an efficiency in reducing Pi-Dcl2 expression and virulence that was similar to that of protoplast-mediated RNAi in P. italicum, suggesting that this approach is promising in the exogenous application of dsRNA to control pathogens on the surface of citrus fruits. In addition, sRNA sequencing revealed a total of 69.88 million potential sRNAs and 12 novel microRNA-like small RNAs (milRNAs), four of which have been predicated on target innate immunity or biotic stress-related genes in Valencia orange. These data suggest that both the Pit-DCL1 and Pit-DCL2 RNAi transformants severely disrupted the biogenesis of the potential milRNAs, which was further confirmed for some milRNAs by qRT-PCR or Northern blot analysis. These data suggest the sRNAs in P. italicum that may be involved in a molecular virulence mechanism termed cross-kingdom RNAi (ck-RNAi) by trafficking sRNA from P. italicum to citrus fruits.

Inhibitory Effect of 7-Demethoxytylophorine on Penicillium italicum and its Possible Mechanism

7-demethoxytylophorine (DEM) is a phenanthroindolizidine alkaloid, which is reported to be effective in inhibiting leucocytes and regulation of human immunity. However, few studies reported the inhibitory effect of DEM against plant-pathogenic fungi, particularly postharvest pathogen Penicillium italicum (P. italicum). Current studies have investigated the antifungal activity of DEM through membrane damage and energy deficit in P. italicum. The results showed that the DEM potentially inhibits the growth of P. italicum in a dose-dependent manner. In vitro (mycelial growth and spore germination) tests showed great minimal inhibitory concentration (MIC) (1.56 µg mL-1) and minimum fugicide concentration (MFC) (6.25 µg mL-1). Microscopic analyses showed that mycelial morphology of P. italicum was severely damaged following DEM treatment. Moreover, relative electrical conductivity and lysis ability assays showed that DEM treatment aids in destroying the integrity of plasma membranes that deplete reducing sugars and soluble proteins. The activity of malate dehydrogenase (MDH) and succinate dehydrogenase (SDH) demonstrated that DEM led to the disruption of TCA cycle in P. italicum mycelia. The results of this study led us to conclude that, DEM could be used as a natural antifungal agent for controlling postharvest blue mold disease of citrus fruits caused by P. italicum.

Mitochondrial Signs and Subcellular Imaging Provide Insight into the Antifungal Mechanism of Carabrone against Gaeumannomyces graminis var. tritici

Carabrone, a botanical bicyclic sesquiterpenic lactone, has broad-spectrum antifungal activity and is particularly efficient against the devastating phytopathogen Gaeumannomyces graminis var. tritici (Ggt). The antifungal mechanism of carabrone against Ggt, however, remains unclear. The main objective of this study was to investigate the subcellular localization of carabrone in Ggt to gain a better understanding of its mechanism of action. When Ggt was exposed to carabrone (EC₅₀ value of 28.45 μg/mL) for 7 days, a decline in mitochondrial concentration together with some obvious alternations in mitochondrial structure, including hazy outlines, medullary transitions, excess accumulation of unclear settlings, and vacuolar degeneration, were observed, indicating that carbrone may act on the mitochondria directly. A fluorescent conjugate (TTY) was thus designed and synthesized as a surrogate of carabrone that possessed comparable antifungal activity against Ggt (EC₅₀ of 33.68 μg/mL). Additionally, a polyclonal antibody specific to carabrone and with a high titer (256 000) was also prepared by immunizing mice. Subsequently, two imaging techniques, the use of the fluorescent conjugate (FC) and immunofluorescence (IF), were applied to determine the subcellular localization of carabrone. Both FC and IF fluorescent signals demonstrated its mitochondrial localization with a Pearson's coefficient of 0.83 for FC and 0.86 for IF. These results imply that carabrone exerts its antifungal activity against Ggt by interfering with mitochondrial function.