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PLOS One logoLink to PLOS One
. 2022 Apr 15;17(4):e0265505. doi: 10.1371/journal.pone.0265505

LC-MS/MS metabolomics-facilitated identification of the active compounds responsible for anti-allergic activity of the ethanol extract of Xenostegia tridentata

Rinrada Suntivich 1, Worawat Songjang 2,3,#, Arunya Jiraviriyakul 2,3,#, Somsak Ruchirawat 4,5,6, Jaruwan Chatwichien 4,6,*
Editor: Branislav T Šiler7
PMCID: PMC9012362  PMID: 35427369

Abstract

In vivo and in vitro anti-allergic activities of ethanol extract of Xenostegia tridentata (L.) D.F. Austin & Staples were investigated using passive cutaneous anaphylaxis reaction assay and RBL-2H3 cell degranulation assay, respectively. The crude ethanol extract exhibited promising activities when compared with the known anti-allergic agents, namely dexamethasone and ketotifen fumarate. The ethyl acetate subfraction showed the highest anti-allergic activity among various sub-partitions and showed better activity than the crude extract, consistent with the high abundance of total phenolic and flavonoid contents in this subfraction. LC-MS/MS metabolomics analysis and bioassay-guided isolation were then used to identify chemical constituents responsible for the anti-allergic activity. The results showed that major components of the ethyl acetate subfraction consist of 3,5-dicaffeoylquinic acid, quercetin-3-O-rhamnoside, kaempferol-3-O-rhamnoside and luteolin-7-O-glucoside. The inhibitory activity of the isolated compounds against mast cell degranulation was validated, ensuring their important roles in the anti-allergic activity of the plant. Notably, besides showing the anti-allergic activity of X. tridentata, this work highlights the role of metabolomic analysis in identifying and selectively isolating active metabolites from plants.

Introduction

Allergic diseases including asthma, rhinitis, atopic dermatitis and food allergies are common chronic health problems worldwide [1], possibly leading to life-threatening conditions. Hypersensitivity reactions can be divided into type I—IV. Type I hypersensitivity is mediated by immunoglobulin E (IgE) and proceeds by a two-step mechanism; the first exposure (sensitization) and a subsequent exposure to a specific allergen, resulting in a process called mast cell degranulation [26]. Histamine and other proinflammatory mediators are then released from mast cells, causing symptoms such as a runny nose, coughing, itchiness and red rashes. Currently, there are different kinds of allergy medications with different modes of action such as anti-histamines, leukotriene receptor antagonists, mast-cell stabilizers, and corticosteroids. None of the available medications, however, can completely cure allergies. In addition, patients usually suffer from drug side effects or resistance after prolonged treatment [7]. Novel drugs for the treatment and prevention of allergies are therefore essential.

Secondary metabolites from plants have been shown to prevent or ameliorate allergic disorders [8]. Natural flavonoids and polyphenolic metabolites possess promising anti-allergic and immune-modulating effects [911]. Many flavonoids inhibit mast cell chemical mediator release and cytokine production [9, 10, 12]. Flavonoids such as ayanin, apigenin and fisetin were shown to inhibit IL-4 production with IC50 values of 2–5 μM [10]. Luteolin and diosmetin are two of the most potent anti-allergic flavonoids [13]. In vitro and in vivo studies have shown anti-allergic activity of luteolin and diosmetin against both the early and late phase reactions by inhibiting mast cell degranulation and IgE-mediated TNF-α and IL-4 productions [1214]. These findings have suggested the potential of utilizing flavonoid-rich plants for complementary or alternative treatment of allergic diseases.

Metabolomics is a comprehensive measurement of metabolites in biological systems. Metabolomics-based analysis usually aims to identify or quantify small molecules (<1000 Da) by using various analytical techniques such as nuclear magnetic resonance (NMR), gas chromatography mass spectrometry (GC-MS), and liquid chromatography mass spectrometry (LC-MS) [15]. Metabolomics accelerates the discovery of bioactive molecules by prioritizing compounds of interest before isolation steps [1618]. LC/MS-based metabolomics approach has proven to be an efficient tool for studying diverse plant metabolites [1921], which are estimated to be more than 200,000 metabolites [22]. Identification of compounds of interest can be done by first using the accurate mass obtained from an MS experiment to predict a possible chemical formula. Once the chemical formula is known, fragmentation information of MS/MS obtained from collision-induced dissociation (CID) and/or high collision dissociation (HCD) could guide compound identification [23, 24]. Compound annotation by matching MS/MS data to the database and integrating it with statistical analysis [25] can increase the level of confidence for identifying potential active compounds. Metabolomics could therefore serve as a powerful tool in plant-derived natural product research [20].

Xenostegia tridentata (L.) D.F. Austin & Staples (also known as Merremia tridentata (L.) Hallier f. or “Thao tot ma” in Thailand) is a medicinal plant widely distributed in tropical regions such as Africa, India, China, Australia and Southeast Asia [2628]. This plant is a perennial herb grown on disturbed sites such as roadsides, grasslands and cultivated areas. The plant has been reported as a component in Ayurvedic medicine for many diseases, including rheumatism, skin infections, fever, diabetes, diarrhea and urinary disorders [29, 30]. Studies have shown that X. tridentata possesses broad biological activities including anti-oxidant, anti-diabetic, anti-inflammatory, anti-arthritis, analgesic, wound healing, anti-microbial and larvicidal activities [3138]. These activities are attributed presumably to flavonoids, major phytochemical components present in this plant. X. tridentata extracts which are considered safe and have no observed toxicity in rats when orally administered at a concentration of up to 2000 mg/kg [31, 32, 34, 38].

Despite the availability of numerous studies on phytochemicals and bioactivities of X. tridentata, knowledge of the chemical structures of X. tridentata-derived compounds is limited [11, 26, 31, 39, 40]. Up to date, there have been only four flavonoids, including diosmetin, luteolin, diosmetin-7-O-β-D-glucoside and luteolin-7-O-β-D-glucoside isolated from this plant [11]. Moreover, in-depth identification of chemical constituents responsible for the bioactivities of this plant has never been revealed. Previous reports on the presence of luteolin and diosmetin and the anti-oxidant, anti-inflammatory and anti-arthritis properties that are closely related to anti-allergic activities prompted us to investigate the anti-allergic activity of X. tridentata, a never before investigated property. Herein, we studied the in vivo and in vitro inhibitory effects of the ethanol extract of X. tridentata on type I hypersensitivity. To identify the active components responsible for the activity, the crude ethanol extract was further fractionated and the resulting subfractions were evaluated for inhibitory activity on IgE-mediated degranulation of RBL-2H3 cells. Based on the assumption that fractions with high inhibitory activity contain high amount of the active compounds, LC-MS/MS metabolomics analysis to identify and quantify metabolites in each fraction was performed. The features that were highly abundant in the potent fraction, relative to the others, were listed, and their chemical structures and anti-allergic activities were validated.

Materials and methods

General information

All solvents and chemicals used were at least of analytical grade and were used without further purification. Folin & Ciocalteu′s phenol reagent and reference compounds (gallic acid, quercetin, luteolin and kaempferol) were purchased from Sigma Aldrich. Solvents were purchased from RCI Labscan Limited. Reagents for cell culture experiments including cell culture media, fetal bovine serum, penicillin-streptomycin, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and 2,4-dinitrophenylated bovine serum albumins (DNP-BSA) were purchased from Thermo Fisher Scientific (Thailand) Co., Ltd.

Plant material

The aerial part of X. tridentata was collected from Chonburi province, Thailand. The specimen was deposited at the PNU plant herbarium, Department of Biology, Faculty of Science, Naresuan University, Thailand (Voucher ID: 004662). The sample was rinsed with tap water and shade dried for 3 days before grinding to powder. The powder was kept at -20°C until used.

Preparation of X. tridentata extracts

Two hundred grams of X. tridentata powder was macerated in 2000 mL absolute ethanol (AR grade) for 48 hours. The supernatant was filtered through cotton and subsequently re-filtered through filter paper (Whatman No.1) by vacuum filtration. The clear filtrate was concentrated under vacuum (150 mbar, 40 °C) to yield 26.29 g of green oil (called F1: crude EtOH). Crude EtOH extract (24.5 g) was added with 100 mL of distilled water. Subsequent extractions with hexane (8 x 100 mL), ethyl acetate (5 x 100 mL) and n-butanol (3 x 100 mL) were performed. The resulting partitions were combined and concentrated under vacuum to yield four more fractions, namely F2: EtOH/Hex (green oil) 11.2 g, F3: EtOH/EtOAc (yellowish brown oil) 0.9 g, F4: EtOH/BuOH (brown oil) 2.6 g and F5: EtOH/H2O (brown oil) 4.6 g.

Ethics statement

The animal experiment protocol was approved by Naresuan University Animal Care and Use Committee according to protocol number NU-AE630608. The mice were given free access to standard food and water, with 12-hour light-dark cycle at 22±2°C. For euthanasia, mice were intraperitoneally administered with sodium thiopental (> 100 mg/kg).

Passive cutaneous anaphylaxis reaction assay

Experiments were performed on 7-8-week-old adult ICR mice (Siam Nomura, Thailand). The experiments were carried out at the Center for Animal Research, Naresuan University. To induce a passive cutaneous anaphylaxis reaction, ears of ICR mice were intradermally injected with 0.5 μg of mouse anti-dinitrophenyl (DNP) IgE antibodies (Sigma Aldrich) or normal saline solution (NSS). After 24 hours, the filtered crude EtOH extract (F1) or dexamethasone resuspended in 1.2%TWEEN in NSS was orally administered at indicated concentrations. The 1.2%TWEEN in NSS was administered in the vehicle control group. One hour later, mice were intravenously injected with dinitrophenylated human serum albumin (DNP-HSA) 60 μg containing 0.5% Evans blue in phosphate buffer saline (PBS). Mice were observed for another hour and euthanized. Ears were photographed and removed for the Evans blue elution assay. The ears were cut into small pieces and dissolved in 400 μL of formamide at 63 ºC overnight. The resulting supernatant was then collected, and the absorbance was measured at 630 nm using a microplate reader (EnSpire Multimode Plate Reader, PerkinElmer, Inc.). Data was presented as absorbance compared to the control group. All efforts were made to minimize suffering and the number of mice needed to reach statistical significance and experimental reproducibility.

Determination of total phenol and total flavonoid contents

Total phenolic content

Total phenolic compounds content (TPC) was determined by Folin-Ciocalteu colorimetric method which compared absorbance at 765 nm (A765) of unknown samples to a standard curve of A765 of serial dilutions of gallic acid solution (0–200 μg/mL). The protocol reported by Siriwoharn et al. [41]. was followed with some modifications. Briefly, 100 μL of 1:10 diluted Folin-Ciocalteu Phenol reagent was added to 25 μL of gallic acid dilutions or unknown samples. The mixture was incubated in the dark for 5 minutes at ambient temperature, then 60 μL of 10% w/v sodium carbonate was added and incubated in the dark for 30 minutes. Absorbance at 765 nm was measured. Results were reported as mg of gallic acid equivalent (GAE) per g of crude extract. Each analysis of phenolic compounds in the extracts was done in triplicate.

Total flavonoid content

The total flavonoid content was determined by aluminum chloride colorimetric method, which compared the absorbance at 415 nm (A415) of unknown samples to a standard curve of A415 of serial dilutions of quercetin solution (0–200 μg/mL). The protocol reported by Chang et al. [42]. was followed with some modifications. Briefly, 75 μL of 95% ethanol (v/v) was added to 25 μL of quercetin dilutions or unknown samples. Then, 5 μL of 10% AlCl3.6H2O, 5 μL of 1M sodium acetate and 140 μL of deionized water were added, respectively. The mixtures were incubated for 30 minutes in the dark at ambient temperature. Absorbance at 415 nm was measured. Results were reported as mg of quercetin equivalent (QE) per g of crude extract. The experiment was done in triplicate.

LC-MS/MS profiling of the extracts of X. tridentata

Liquid chromatography—mass spectrometry was performed using Dionex Ultimate 3000 RS Ultra—High Performance Liquid Chromatography (UHPLC)—Orbitrap Fusion Tribrid Mass Spectrometer (Thermo, Massachusetts, USA), equipped with electrospray ionization (ESI) source. The samples were dissolved in MS-grade methanol to make a 1 mg/mL solution, followed by centrifugation at 14,000 x g for 5 minutes to remove insoluble debris. Subsequently, the methanol-dissolved samples were filtered through a 0.2 μm PVDF membrane filter and transferred to a glass-insert vial for LC injection. The liquid chromatography—mass spectrometry was performed on a BEH C18 column (1.7 μm diameter, 2.1 x 100 mm) maintained at 60°C. The optimal mobile phase system was 0.0–2.0 min, 5%-25%B; 2.0–5.0 min, 25%-30%B; 5.0–5.5 min, 30%-45%B; 5.5–9.0 min, 45%-95%B; 9.0–12.5 min, 95%-95%B; 12.5–12.6 min, 95%-5%B; 12.6–15.0 min and 5%-5%B where solvent A was water with 0.1% formic acid and solvent B was acetonitrile with 0.1% formic acid. The mass spectrometer was operated in both ESI positive and negative modes. Source-dependent parameters were as follows: sheath gas (N2), 45 arb; auxiliary gas (N2), 13 arb; sweep gas, 1 arb; ion spray voltage, 3.50 kV for ESI positive and 2.5kV for ESI negative; capillary temperature, 342 °C; vaporizer temperature, 358°C. The scan mode was a full MS1 scan followed by a data-dependent MS2 scan with a mass range of m/z 100–1200. The resolution of the full MS1 scan and the data-dependent MS2 scan were 120,000 and 15,000, respectively. For the data-dependent MS2 scan, the S-Lens RF level was set to 60%, and the automatic gain control (AGC) target was set to 1.0 x 105. Each sample was analyzed in triplicate. A pooled sample, combining an equal fraction of all ten samples, was injected every 10–15 samples to ensure system stability and reproducibility. The MS calibration was conducted using Pierce LTQ Velos ESI Positive Ion Calibration (PSP3A 88323) and Pierce ESI Negative Ion Calibration (PSP3A 88324) according to the manufacturer’s protocol.

Active compounds isolation and chemical structure determination

The fraction with the highest anti-allergic activity (F3: EtOH/EtOAc) was further purified to obtain major chemical components for structural identification and activity validation. One gram of the F3: EtOH/EtOAc fraction was purified by using medium-pressure liquid chromatography (MPLC; PuriFlash 450, Interchim, France) over reversed phase silica gel (PF-15C18AQ-F0080) and eluted with 3%-97% MeOH/H2O. The resulting fractions were examined by thin layer chromatography (TLC). The fractions containing identical compounds were combined and concentrated under vacuum. The NMR spectra of the isolated compounds were recorded on a Bruker Avance NMR spectrometer operating at 300 MHz for 1H and 75 MHz for 13C. High-resolution mass spectra were obtained using ESI on an Orbitrap Fusion Tribrid mass spectrometer (Thermo, Massachusetts, USA).

Measurement of RBL-2H3 cell viability

Rat basophilic leukemia cell line, RBL-2H3 (ATCC CRL-2256), was purchased from the American Type Culture Collection (ATCC). Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum, 100 U/mL penicillin and 100 μg/mL streptomycin at 37°C with 5% CO2.

The RBL-2H3 cells were seeded at 104 cells/well in a 96-well plate and allowed to grow for 24 hours. Plant extracts were added and allowed to incubate with the cells for 48 hours. The cell viability was determined by using the MTT viability assay. Briefly, culture media was removed. MTT solution (0.5 mg MTT in 1 mL of complete medium) was added and allowed to incubate at 37°C for 3 hours. The solution was then replaced with 100 μL of DMSO. Absorbance at 570 nm was measured using a microplate reader (Varioskan LUX multimode microplate reader, Thermo Scientific). Percent viability was calculated relative to the untreated control.

β-Hexosaminidase release assay

IgE-mediated mast cell degranulation was determined by measuring the release of β-hexosaminidase enzyme. Briefly, the RBL-2H3 cells were seeded in 24-well plates at 1 x 105 cells/well and grown for 24 hours. The cells were sensitized with 200 ng/mL DNP-specific IgE (Sigma Aldrich) for 24 hours. The IgE-sensitized RBL-2H3 cells were washed with PBS and incubated with plant extracts or ketotifen fumarate in Siraganian buffer (119 mM NaCl, 5 mM KCl, 5.6 mM glucose, 0.4 mM MgCl2, 25 mM PIPES, 40 mM NaOH, 1 mM CaCl2, and 0.1% BSA, pH 7.2) for 2 hours at 37°C. Subsequently, the cells were stimulated with DNP-BSA (1 μg/mL) for 1 hour at 37°C. To determine the amounts of β-hexosaminidase released into the supernatant, 50 μL of the supernatant was transferred into a 96-well plate and incubated with 50 μL of substrate solution (0.3 mg/mL p-nitrophenyl N-acetyl-D-glucosamine (Sigma Aldrich) in 0.1M citrate buffer (pH 4.5)) for 2 hours. The remaining cells were lysed with 200 μL of 1% (v/v) Triton X-100 in Siraganian buffer. The amount of β-hexosaminidase inside the cells was determined by incubating 50 μL of the cell lysate with the substrate as indicated above. The enzyme reaction was terminated by adding 200 μL of carbonate buffer containing 0.1 M Na2CO3 and 0.1 M NaHCO3 (pH 10), and absorbance at 405 nm (A405) was measured using a microplate reader (Varioskan LUX multimode microplate reader, Thermo Scientific). The experiment was performed in triplicate. The β-hexosaminidase release ratio (% of max) was calculated according to the following equations.

β-hexosaminidasereleasedratio=A405supernatant/A405supernatant+A405celllysate
β-hexosaminidasereleaseratio%ofmax=[β-hexosaminidasereleasedratiosample/β-hexosaminidasereleasedratiovehiclecontrol]x100

For compound 48/80-stimulated degranulation, RBL-2H3 cells (1 x 105 cells/ well) were grown on 24-well plates for 24 hours before being incubated for 2 hours at 37°C with a solution of tested samples or ketotifen fumarate in Siraganian buffer, having DMSO as a vehicle control. Subsequently, the cells were stimulated with compound 48/80 (10 μg/mL, Sigma Aldrich) for 1 hour at 37°C. The degree of degranulation was then measured in the same manner as in the case of IgE-mediation.

Measurement of intracellular reactive oxygen species (ROS) level

The intracellular levels of ROS were measured by using 2’,7’-dichlorofluorescein diacetate (DCFH-DA), a cell permeable dye that can be hydrolyzed by cellular esterase and rapidly oxidized to florescent 2’,7’-dichlorofluorescein (DCF) by intracellular oxidants. Briefly, the RBL-2H3 cells or IgE-sensitized cells (105 cells/well) in a 96-well plate were incubated with 5 μM DCFH-DA (Sigma Aldrich) for 1 hour at 37°C. The cells were washed twice with Hanks’ balanced salt solution (HBSS) and incubated with samples or DMSO in HBSS for 1 hour. After stimulation with compound 48/80 or DNP-BSA, the fluorescence (excitation/emission: 485/527 nm) of oxidized DCF was analyzed at 30-second intervals for 16 minutes using a microplate reader (Varioskan LUX multimode microplate reader, Thermo Scientific).

Statistical analysis

One-way analysis of variance (ANOVA) with Tukey’s multiple-comparison posttest was performed using GraphPad Prism 7.0 Software. All data were presented as mean ± standard error of the mean (SEM). Differences between groups were considered statistically significant at a P value of 0.05.

Results and discussion

In vivo effect of the crude ethanol extract of X. tridentata on type 1 hypersensitivity reaction

A passive cutaneous anaphylaxis reaction assay was performed to evaluate the ability of X. tridentata extract to attenuate type 1 allergic reaction. Mouse ears were sensitized with anti-DNP IgE. After orally administrated with the ethanol extract of X. tridentata (F1) or dexamethasone (a known immune suppressive agent), mice were intravenously challenged with antigen (DNP-HSA in 1% Evans blue dye) to stimulate a passive cutaneous anaphylaxis reaction, which could be determined from the vascular permeability of Evans blue dye into the ears. In mice treated with the extract (100 mg/kg) or dexamethasone (10 mg/kg), less Evans blue leakage was observed when compared with the vehicle control group (Fig 1), indicating that passive cutaneous anaphylaxis reaction was significantly suppressed by the extract, in the same manner as dexamethasone. The result suggested an anti-allergic potential of the ethanol extract of X. tridentata. However, treatment with the extract at 1000 mg/kg showed a less suppressive effect than at 100 mg/kg. The observed result was possibly related to the pharmacokinetics of the extract. Further study of molecular mechanisms and pharmacokinetics of the extract will therefore be important for optimizing the treatment doses and conditions.

Fig 1. In vivo inhibitory effect of crude EtOH (F1) on IgE-mediated passive cutaneous anaphylaxis reaction.

Fig 1

a) Experimental design of passive cutaneous anaphylaxis assay. Mouse ears were intradermally injected (i.d.) with anti-DNP-IgE. Twenty-four hours post sensitization, mice were orally administrated with F1 or dexamethasone then intravenously (i.v.) challenged with DNP antigen. Evans blue leakage was monitored at 2 hours after stimulation. b) Evans blue leakage after the antigen challenge. Dexamethasone was used as a positive control. c) Evans blue extracted from each ear was quantified using a spectrophotometer. Data are presented as mean ± SEM (n = 5 per group). *p < 0.05, compared with the vehicle control group.

Inhibitory activity of the extracts on IgE-mediated mast cell degranulation

To determine anti-allergic components in X. tridentata, the crude ethanol extract (F1) was dissolved in water and further separated by subsequent extractions with hexane, ethyl acetate and n-butanol, yielding samples F2-F5, respectively (Scheme 1). In vitro inhibitory activity of the resulting extracts on mast cell degranulation was performed on DNP-specific IgE-sensitized RBL-2H3 cells. The degree of degranulation was determined by the amount of β-hexosaminidase release upon stimulation with the antigen (DNP-BSA). As shown in Table 1, similar to the effect of ketotifen fumarate (a known anti-allergic agent), the F1-F3 extracts possessed mast cell degranulation inhibitory activity on IgE-mediated in a dose-dependent manner. Among them, the ethyl acetate fraction (F3) exhibited the highest anti-allergic activity and showed improved activity over the crude ethanol extract (F1), without being cytotoxic to the cells at the concentration up to 2000 μg/mL. The butanol fraction (F4) showed weak activity at 500 μg/mL and was over 20% toxic to the cells at the higher concentrations. The water fraction (F5) also exerted weak activity and did not inhibit the degranulation in a dose-dependent manner. Markedly, at the concentrations of 1000 and 2000 μg/mL, F3 exhibited significantly higher inhibitory activity than F5: EtOH/H2O (p<0.001). Moreover, to assure that the observed effects of the extracts on the inhibition of mast cell degranulation were not from the inhibition of the enzyme activity, β-hexosaminidase inhibitory activity of each extract was determined. The results showed that no significant inhibition was observed for all tested samples (S1 Table).

Table 1. Effects of X. tridentata extracts on IgE-mediated mast cell degranulation and cell viability of RBL-2H3 cells.

Sample β-hexosaminidase release ratio (% of max) a
Treatment concentration (μg/mL)
25 100 500 1000 2000
F1: crude EtOH ND ND 66.2±8.2 34.8±5.5** N/A
F2: EtOH/Hex ND ND 66.4±8.7 37.3±6.2** 28.9±6.5**
F3: EtOH/EtOAc ND ND 48.2±2.4** 28.1±5.9** 13.8±2.3**
F4: EtOH/BuOH ND ND 77.8±2.5 N/A N/A
F5: EtOH/H2O ND ND 53.2±2.1** 63.0±2.1** 68.0±4.8
ketotifen fumarate 70.8±4.4* 37.6±4.9** ND ND ND
% Cell viability b
F1: crude EtOH ND ND 97.6±1.2 85.9±3.6 64.1±4.3
F2: EtOH/Hex ND ND 112.6±14.5 111.5±5.5 109.6±3.2
F3: EtOH/EtOAc ND ND 119.4±14.9 107.4±7.0 116.9±3.4
F4: EtOH/BuOH ND ND 90.2±10.0 46.6±5.3** 13.3±0.6**
F5: EtOH/H2O ND ND 102.4±3.2 103.6±7.7 98.4±1.2
ketotifen fumarate 100.1±3.7 77.4±4.8 ND ND ND

The values are presented as means ± SEM (n = 3–6).

*p < 0.05,

**p < 0.001, compared with the vehicle control.

a 2- hour incubation time.

b 48-hour incubation time.

N/A indicates over 20% cytotoxicity was observed at 2- hour incubation time. ND means Not Determined.

Scheme 1. Preparation of the crude extract and sub-partitions from X. tridentata.

graphic file with name pone.0265505.e003.jpg

Total phenolic and total flavonoid contents of X. tridentata extracts

According to previous reports on the high content of flavonoids and phenolic compounds present in X. tridentata and known anti-allergic activity of these classes of metabolites, preliminarily phytochemical screening on total phenolic and total flavonoid contents of the extracts was determined by Folin-Ciocalteu and aluminium chloride colorimetric methods, respectively. The results shown in Table 2 indicated that the EtOH/EtOAc fraction (F3) contained the highest amount of total phenolic and total flavonoid compounds, corresponding to its inhibitory potency on mast cell degranulation.

Table 2. Total phenolic and total flavonoid contents of the extracts of X. tridentata.

Sample Total phenolic content Total flavonoid content
mg GAE/g extract mg QE/g extract
F1: crude EtOH 29.2±2.9** 52.7±3.8**
F2: EtOH/Hex 25.6±7.0** 95.2±0.3**
F3: EtOH/EtOAC 405.1±7.6 159.7±1.7
F4: EtOH/BuOH 136.9±6.5** -3.2±0.6**
F5: EtOH/H2O 31.7±5.9** -16.7±0.5**

The values are presented as means ± SEM (n = 3).

**p < 0.001, compared with F3: EtOH/EtOAc.

Metabolomics analysis approach in identification of anti-allergic compounds present in the ethanol extracts of X. tridentata

LC-MS/MS metabolomics analysis was performed to identify active compounds responsible for anti-allergic activity. Firstly, five extracts (F1-F5) were analyzed with LC-MS/MS in both ESI positive and negative modes to obtain metabolite profiles (S1 Appendix). For data analysis, the MS raw files were subjected to peak alignment, peak picking, adduct grouping and normalization using Compound Discoverer 3.1 software (CD3.1). The parameters in CD3.1 for data analysis were set to be compatible with the chromatographic data obtained from this experiment. A retention time (RT) alignment step was obtained with a 5-ppm mass tolerance and a 2-min maximum shift. An unknown compound detection step was achieved with a 5-ppm mass tolerance, a signal to noise ratio of 3 and minimum peak intensity of 1x104. Unknown compound grouping step was performed with a 5-ppm mass tolerance and a 0.2-min RT tolerance. The Area Under the Curve (AUC) of each metabolite was determined and normalized with that of pooled samples. Among 3,863 features obtained from the analysis, 2,860 features were detected only in positive ionization mode, 767 features were detected only in negative ionization mode, and 236 features were detected in both ionization modes. The data suggested that both positive and negative ionizations were needed for full metabolome coverage of the X. tridentata extracts.

Principal Component Analysis (PCA) is a pattern recognition method used to visualize general clustering trends. In PCA, data are not given or labeled with a primary classification but clustered to find all unknown patterns. PCA is therefore an unsupervised analysis. In this work, PCA was used to compare the chemical profiles of F1-F5 without classifying or pre-grouping the samples. The score plots of each sample in positive and negative ionization modes are shown in Fig 2a and 2b. Principal component 1 (PC1) represents the maximal variation of data, whereas principal component 2 (PC2) is orthogonal to the PC1 axis and accounts for the second highest variation. PC1 and PC2 are the first and second principal components accounted for 38.7% and 32.4% of the total variance in the data respectively in ESI positive mode and explained for 48.3% and 24.6% of the total variance in the data respectively in ESI negative mode. Herein, two-component PCA models accounted for the total variance of 71.1% and 72.9% for ESI positive and negative, respectively. Each point represents an individual LC-MS injection. The scatter of data dictates the similarities or differences of metabolites in each sample. Samples containing similar metabolite content are congregated, while those containing different metabolite content are disseminated in PCA. The result showed that all pooled samples were closely clustered together demonstrating the reproducibility and robustness of the LC-MS system. The metabolite profiles of the EtOH/EtOAc fraction (F3) and other fractions (F1, F2, F4, and F5) were strongly discriminated in PCA in both positive and negative ionization modes. The metabolites abundantly present in the F3 fraction were of our interest since they potentially contributed to the strong discrimination in PCA and were possibly attributed to the anti-allergic activity.

Fig 2. Principle component analysis and heat map visualization of X.tridentata extracts metabolic profiles.

Fig 2

Principal component 1 (PC1) represents the maximal variation of data. Principal component 2 (PC2) is orthogonal to the PC1 axis and accounts for the second highest variation. a) Principle component analysis for ESI positive mode b) Principle component analysis for ESI negative mode. Each point represents an individual LC-MS injection. c) Heat map of 35 features with the highest fold change of F3/F5 observed in ESI positive mode and d) in ESI negative mode.

To determine the features with significant association to the anti-allergic activity, the metabolomics data analysis focused on features that were high abundant in the F3 fraction and low abundant in the F5 fraction, since F3 and F5 possessed the highest and lowest anti-allergic activities, respectively. In the first filtering step using % coefficient of variation (%CV) less than 30%, 3,863 normalized ions were determined. The magnitude of difference between the two sample groups, so called fold change (FC), was then applied in the second filtering step. The FC of AUC (Area Under the Curve) of F3 vs F5 (AUCEtOH/EtOAc/ AUCEtOH/H2O) was used to determine the significant features. As a result, top 35 features (FC = 590 for data in ESI positive mode and FC = 280 for data in ESI negative mode) were determined and then selected for hierarchical clustering to discover trends within the partition samples (Fig 2c and 2d). In both positive and negative ionization modes, all features were predominantly presented in the F3 fraction and minimally observed in other fractions.

To facilitate the compound annotation step, an in-house mass list of reported compounds found in Xenostegia tridentata (L.) D.F. Austin & Staples or plant species in the Convolvulaceae family (Merremia tridentata, Ipomoea carnea, Evolvulus alsinoides, Evolvulus nummularius, Ipomoea batatas, Argyreia speciose and Argyreia cuneate) was constructed. The literature curation was performed by searching the following keywords: “Xenostegia tridentata”, “Merremia tridentata”, “Convolvulaceae”, and “Thao tot ma”. The list contains 116 compounds (S2 Table) with information including compound name, chemical formula, molecular weight, m/z, chemical structure, InChIKey, CAS number, IUPAC name, common name, Chem Spider ID, ChemSpider link, reported plant species with reference publications and reported activities with references. Reported mass spectroscopic information on public databases (mzCloud and METLIN) was also included to facilitate further compound annotation with MS techniques.

In this work, the LC-MS data acquisition was designed to obtain both MS1 and MS2 data simultaneously. MS1 data from high-resolution mass spectrometer (< 5 ppm mass accuracy) were used to predict the chemical formula and match it against MS1 public databases, including ChemSpider, NIST Chemistry WebBook, Phenol-Explorer, Planta Piloto de Química Fina, Universidad de, PlantCyc and Sigma-Aldrich. In addition, various MS2 fragmentations were performed to increase the confidence of the annotation step. The MS2 spectra were matched with the mzCloud database to aid compound annotation (S3 Table). The significant features that contributed to the discrimination between F3 and F5 fractions were identified according to the metabolomics standard initiative (MSI) [43]. MSI level 1–4 were proposed as a minimal reporting standard for chemical analysis. MSI level 4 refers to unidentified or unclassified compounds that can be detected using spectral data. MSI level 3 includes compounds that can be putatively characterized or classified by using physicochemical properties or spectral similarity to a chemical class. MSI level 2 is for putatively annotated compounds with spectral similarity to known compounds in public/commercial spectral libraries. MSI level 1 is for novel and non-novel identified compounds. Novel MSI I metabolites can be characterized by elemental analysis, NMR, IR, UV and accurate mass measurement, while non-novel MSI I metabolite identification can be validated with commercial standard compounds by comparison of a minimum of two independent and orthogonal data under identical experimental conditions.

LC-MS metabolite profiles of five extracts (F1-F5) in both ESI positive and negative (S1 Appendix) were subjected to metabolomics data analysis as previously described. The LC-MS profile is a base peak ion chromatogram showing the relative abundance of peaks presented in each sample. The major peak for five extracts analyzed in ESI positive mode at 5.15–5.22 min in S1 Appendix was predicted to be a compound with a molecular weight of 324.21996 and a chemical formula of C21H28N2O. For compound identification, MS2 showed no match to any spectrum on mzCloud database. Based on MS1 data, this major peak at 5.15–5.22 min could be predicted with the lowest mass error of -0.64 ppm to several compounds including 4,4’-bis(diethylamino)benzophenone, 1-(9H-carbazol-9-yl)-3-(dipropylamino)-2-propanol, N-[4-(diethylamino)phenyl]-4-(2-methyl-2-propanyl)benzamide, diampromide and N2-butyl-N-(1,2-diphenylethyl)-N2-methylglycin-amide. The significant features in positive and negative ionization modes that contributed to the discrimination between F3 and F5 fractions were summarized in Tables 3 and 4, respectively. The identification level of significant features was determined by following MSI guidelines. For example, feature 270.05306_5.128 showed a high percentage of MS2 matching to several compounds on mzCloud (S3 Table). This feature showed the highest matching score to apigenin in both positive and negative ionization modes. It is noted that the observed m/z 117.0346 at HCD 40 under ESI negative mode was only matched with similar intensity and pattern to that of apigenin but not to other compounds including genistein. Using metabolomics data, feature 270.05306_5.128 was therefore putatively identified as apigenin with MSI level 2. To increase the level of identification to MSI level 1, commercial apigenin will be needed for comparing RT, MS1 and MS2. In another example, with MS1 information, feature 516.12723_3.168 could be 4,5-dicaffeoylquinic acid, 3,5-dicaffeoylquinic acid, 3,4-di-O-caffeoylquinic acid, or 1,3-di-O-caffeoylquinic acid. However, only one hit of 4,5-dicaffeoylquinic acid was obtained from MS2 matching (S3 Table). This result was potentially from the fact that 4,5-dicaffeoylquinic acid was the only isomer identified from both positive and negative MS2 spectra on mzCloud database. Therefore, with metabolomics data, feature 516.12723_3.168 was putatively identified as dicaffeoylquinic acid with MSI level 3. To increase the level of identification shown in Tables 3 and 4 to MSI level 1, either standard or purified compounds would need to be analyzed to ensure matching RT, MS1 and MS2 under good separation conditions. As a result, fraction F3 was further purified and the resulting pure compounds were subjected to NMR experiments to confirm the chemical structures.

Table 3. Summary of metabolite features contributed to the discrimination between F3: EtOH/EtOAc and F5: EtOH/H2O fractions in ESI positive mode.

NO. ESI FEATURE PREDICTED FORMULA PUTATIVE IDENTIFIED COMPOUND1
1 Pos 248.13884_3.543 C11 H16 N6 O
2 Pos 270.05306_5.128 C15 H10 O5 Apigenin 2
3 Pos 283.12085_3.847 C17 H17 N O3 (2E)-3-(4-Hydroxyphenyl)-N-[2-(4-hydroxyphenyl)ethyl]acrylamide 2
4 Pos 286.04762_3.608 C15 H10 O6 Flavonoids 3
5 Pos 286.04762_3.212 C15 H10 O6 Flavonoids 3
6 Pos 292.20366_6.335 C18 H28 O3
7 Pos 302.0424_3.377 C15 H10 O7 Flavonoids 3
8 Pos 302.04244_2.959 C15 H10 O7 Flavonoids 3
9 Pos 302.04245_3.253 C15 H10 O7 Flavonoids 3
10 Pos 311.18852_6.41 C14 H26 N5 O P
11 Pos 312.19101_6.293 C13 H24 N6 O3
12 Pos 313.13132_4.124 C18 H19 N O4
13 Pos 324.21996_5.206 C21 H28 N2 O
14 Pos 432.10586_3.357 C21 H20 O10 Apigetrin (Apigenin-7-O-glucoside) 2
15 Pos 432.10612_3.604 C21 H20 O10 Afzelin (Kaempferol-3-O-rhamnoside) 2
16 Pos 448.1005_3.147 C21 H20 O11 Flavonoid glycosides 3
17 Pos 448.10052_3.328 C21 H20 O11 Flavonoid glycosides 3
18 Pos 448.10082_3.034 C21 H20 O11 Cynaroside (luteolin-7-O-glucoside) 2
19 Pos 448.10088_3.492 C21 H20 O11 Flavonoid glycosides 3
20 Pos 448.10108_3.251 C21 H20 O11 Quercitrin (Quercetin-3-O-rhamnoside) 2
21 Pos 458.11871_3.523 C10 H26 N4 O14 S
22 Pos 458.21517_7.888 C23 H30 N4 O6
23 Pos 462.11648_3.521 C22 H22 O11 Methoxy flavonoid glycosides 3
24 Pos 482.12103_3.77 C25 H22 O10 Silymarin (flavonolignans) 3
25 Pos 482.12115_3.515 C25 H22 O10 Silymarin (flavonolignans) 3
26 Pos 498.11685_4.286 C26 H18 N4 O7
27 Pos 512.13159_3.981 C22 H20 N6 O9
28 Pos 512.13175_4.317 C23 H16 N10 O5
29 Pos 516.12723_3.168 C25 H24 O12 Dicaffeoylquinic acid 3
30 Pos 526.14751_4.721 C27 H26 O11 Viscutin 1 3
31 Pos 530.14304_4.313 C26 H26 O12 Flavonoid glycoside derivatives 3
32 Pos 530.14304_3.973 C26 H26 O12 Flavonoid glycoside derivatives 3
33 Pos 530.14305_3.717 C26 H26 O12 Flavonoid glycoside derivatives 3
34 Pos 535.09984_3.341 C16 H23 N7 O10 P2
35 Pos 1070.20008_3.165 C43 H53 N4 O18 P3 S2

1 Putative identified compounds were determined as level 1–4 according to the Metabolomics Standard Initiative (MSI).

2 Compounds with MSI level 2 were putatively annotated based on spectral similarity to available databases.

3 Compounds with MSI level 3 that putatively characterized by their compound classes according to spectral similarity to known compounds in that chemical class.

4 Unknown compounds with MSI level 4 can be distinguished from spectra data but remain unclassified or unidentified based on MS and MS/MS data.

Table 4. Summary of metabolite features contributed to the discrimination between F3: EtOH/EtOAc and F5: EtOH/H2O fractions in ESI negative mode.

NO. ESI FEATURE PREDICTED FORMULA PUTATIVE IDENTIFIED COMPOUND
1 Neg 250.06648_3.766 C13 H14 O3 S
2 Neg 283.12085_3.847 C17 H17 N O3 (2E)-3-(4-Hydroxyphenyl)-N-[2-(4-hydroxyphenyl)ethyl]acrylamide 2
3 Neg 288.23061_6.625 C16 H32 O4
4 Neg 313.13132_4.124 C18 H19 N O4
5 Neg 328.22551_6.388 C18 H32 O5 Corchorifatty acid F 2
6 Neg 328.22573_6.293 C18 H32 O5 Corchorifatty acid F 2
7 Neg 330.24103_6.566 C18 H34 O5
8 Neg 370.22629_5.188 C20 H35 O4 P
9 Neg 392.11154_2.845 C19 H20 O9
10 Neg 432.1063_3.741 C21 H20 O10 Flavonoid glycosides 3
11 Neg 434.0856_3.072 C20 H18 O11 Flavonoid glycosides 3
12 Neg 448.10088_3.492 C21 H20 O11 Flavonoid glycosides 3
13 Neg 448.10108_3.251 C21 H20 O11 Quercitrin (Quercetin-3-O-rhamnoside) 2
14 Neg 448.10124_3.392 C21 H20 O11 Flavonoid glycosides 3
15 Neg 452.11113_3.673 C24 H20 O9 Flavan-3-ol derivatives 3
16 Neg 453.11447_3.215 C16 H20 N7 O7 P
17 Neg 476.22668_7.876 C23 H32 N4 O7
18 Neg 495.10201_3.599 C22 H17 N5 O9
19 Neg 498.11685_4.286 C26 H18 N4 O7
20 Neg 498.1171_3.862 C26 H18 N4 O7
21 Neg 498.11711_3.793 C22 H14 N10 O5
22 Neg 500.13232_3.767 C25 H24 O11
23 Neg 500.13278_3.465 C25 H24 O11
24 Neg 516.12723_3.168 C25 H24 O12 Dicaffeoylquinic acid 3
25 Neg 530.14304_4.313 C26 H26 O12 Flavonoid glycoside derivatives 3
26 Neg 530.14304_3.973 C26 H26 O12 Flavonoid glycoside derivatives 3
27 Neg 530.14305_3.717 C26 H26 O12 Flavonoid glycoside derivatives 3
28 Neg 530.14308_3.913 C26 H26 O12 Flavonoid glycoside derivatives 3
29 Neg 544.1587_5.275 C28 H24 N4 O8
30 Neg 544.15876_4.435 C29 H20 N8 O4
31 Neg 544.15887_4.713 C28 H24 N4 O8
32 Neg 570.13851_3.609 C23 H23 N8 O8 P
33 Neg 678.15954_4.308 C34 H30 O15 3,4,5-tri-O-caffeoylquinic acid 3
34 Neg 897.20656_3.385 C37 H41 N9 O12 P2 S
35 Neg 1032.25617_3.168 C52 H40 N8 O16

1 Putative identified compounds were determined as level 1–4 according to the Metabolomics Standard Initiative (MSI).

2 Compounds with MSI level 2 that were putatively annotated based on spectral similarity to available databases.

3 Compounds with MSI level 3 that were putatively characterized by their compound classes according to spectral similarity to known compounds in that chemical class.

4 Unknown compounds with MSI level 4 that can be distinguished from spectra data but remain unclassified or unidentified based on MS and MS/MS data.

Validation of chemical structures of the significant metabolites

Among the sub-partitions, F3 contained the highest contents of flavonoid and phenolic compounds and exhibited the highest inhibitory activity on mast cell degranulation. Further purification of this fraction was therefore performed. One gram of F3 was subjected to the MPLC separation. The chromatogram of F3 displays four major peaks (Fig 3). The collected pure compounds of each peak were subjected to LC-MS/MS under the same conditions as the metabolite profiling experiment. The accurate mass, MS2 fragmentation patterns with various energies and RT were well-matched to mass spectra of the F3: EtOH/EtOAc (S1 Appendix). The results showed that peak 1–4 were features 516.12723_3.168, 448.10082_3.034, 448.10108_3.251 and 432.10612_3.604, respectively. The four features obtained from metabolite profiling and the isolated compounds were in good agreement with only 0.02 min of RT difference and 3 ppm of mass difference. The NMR and HRMS analysis of the collected fractions of each peak revealed that peak 1–4 corresponded to four known compounds, 3,5-dicaffeoylquinic acid (0.06 g, 6.3%), luteolin-7-O-glucoside (0.09 g, 8.8%), quercetin-3-O-rhamnoside (0.15 g, 14.8%) and kaempferol-3-O-rhamnoside (0.03 g, 3.1%), respectively. Relative metabolite levels were obtained from the average area under the curve (AUC) of each feature in the extracts F1-F5, as shown in Fig 4. The level of the four identified metabolites was significantly elevated in the F3 fraction potentially suggesting their contribution to the anti-allergic activity.

Fig 3. Isolation of major compounds from F3: EtOH/EtOAc.

Fig 3

a) Chromatogram of subfraction F3 from MPLC separation on a reversed phase silica gel column eluted with gradient system of MeOH and H2O (3–97%). The chromatographic signals at 256 nm (black) and 366 nm (orange) were detected. b) Chemical structures of the known compounds corresponding to peak1-4 (see S1 and S2 Appendices for the HRMS and NMR spectra, respectively).

Fig 4. The levels of four significant metabolite features in different subfractions.

Fig 4

a) ESI+516.12723_3.168, b) ESI+448.10082_3.034, c) ESI+448.10108_3.251 and d) ESI+432.10612_3.604.

Validation of anti-allergic activity of the isolated pure compounds

The phenolic and flavonoid compounds identified from the metabolomics analysis have been widely reported for their bioactivities including anti-allergic activities [10, 4451]. For example, 3,5-dicaffeoylquinic acid, quercetin-3-O-rhamnoside and luteolin-7-O-glucoside exhibited dose-dependent in vitro and in vivo inhibitions of mast cell degranulation induced by compound 48/80, a non-IgE-mediated mast cell degranulation agent [44, 50, 51]. Kaempferol-3-O-rhamnoside showed inhibitory effects on OVA-induced airway allergic inflammation in vivo [52]. To validate the anti-allergic activities of these compounds in our assay, the IgE-mediated and compound 48/80-stimulated mast cell degranulation assays were performed. The results shown in Figs 5b and 6a confirmed the inhibitory activities of the four isolated compounds and ketotifen fumarate on the degranulation activated by both stimulants.

Fig 5. Inhibitory effects on IgE-mediated RBL-2H3 cell degranulation.

Fig 5

a) The effects of the extracts (100 μg/mL) and active compounds (25 μM) derived from X. tridentata on intracellular ROS generation b) The effects of active compounds and ketotifen fumarate (25 and 100 μM) on β-hexosaminidase release. Ketotifen fumarate was used as a positive control. The values are presented as means ± SEM (n = 3). *p<0.05 and **p < 0.001, compared with the vehicle control.

Fig 6. Inhibitory effects on compound 48/80-stimulated RBL-2H3 cell degranulation.

Fig 6

a) The effects of the active compounds and ketotifen fumarate (25 and 100 μM) on β-hexosaminidase release. Ketotifen fumarate was used as a positive control. The values are present as means ± SEM (n = 4). *p<0.05 and **p < 0.001, compared with the vehicle control. b) The effects of active compounds (25 μM) derived from X. tridentata on intracellular ROS generation.

Generation of intracellular reactive oxygen species (ROS) within mast cells upon activation with chemical agents or antigens has been known to play important roles in the production of proinflammatory cytokines and degranulation [53, 54]. Attenuation of ROS generation could therefore impair degranulation and subsequently diminish the allergic cascade. To examine the inhibitory effect of X. tridentata extracts on ROS production, RBL-2H3 cells were loaded with DCFH-DA, a redox-sensitive dye, incubated with X. tridentata extracts and activated with anti-DNP-IgE and DNP-BSA or compound 48/80. After activation, the fluorescence signal, representative of ROS generation, was measured for 16 minutes using a microplate reader (30-second intervals). The results shown in Figs 5a and 6b indicate that the extracts and the four isolated compounds could suppress ROS generation in the RBL-2H3 cells activated by IgE-dependent activation or compound 48/80.

In summary, crude ethanol extract of X. tridentata exhibited in vivo and in vitro inhibitory effects on IgE-mediated mast cell degranulation, a process relating to type I hypersensitivity. Among the subfractions, the ethyl acetate subfraction (F3) showed the highest inhibitory activity on IgE-mediated RBL-2H3 cell degranulation, presumably due to its high flavonoid and phenolic contents. From LC-MS/MS metabolomics analysis, luteolin-7-O-glucoside, quercetin-3-O-rhamnoside, kaempferol-3-O-rhamnoside and 3,5-dicaffeoylquinic acid were listed among the top 35 features that were found in more abundance in F3 than in other subfractions. These four compounds corresponded to the four major metabolites isolated from F3. The chemical structures were confirmed by NMR and HRMS techniques. As reported previously, the isolated compounds showed inhibitory effects on mast cell degranulation and intracellular ROS generation, assuring their important roles in the anti-allergic property of X tridentata. Notably, this work highlights the utilization of LC-MS/MS metabolomics analysis as an efficient tool for active metabolite identification in plants. Moreover, anti-allergic activity of X.tridentata and the presence of quercetin-3-O-rhamnoside, kaempferol-3-O-rhamnoside and 3,5-dicaffeoylquinic in this plant are reported. To apply this plant as complementary or alternative medicine for allergic diseases, studies on molecular responses according to the extracts and the active components are underway in our laboratory to fulfill understanding of their modes of action.

Supporting information

S1 Appendix. LC-MS metabolite profiling and comparison of MS and MS/MS data of the features obtained from metabolite profiling to isolated compounds.

(PDF)

S2 Appendix. NMR spectra of the isolated compounds.

(PDF)

S1 Table. Extraction yields, β-hexosaminidase inhibitory activity of the extracts, cytotoxicity of the isolated compounds and previously reported anti-allergic activities of the isolated compounds.

(PDF)

S2 Table. Library for LC-MS.

(XLSX)

S3 Table. Metabolite identification of features contributed to the discrimination between F3:EtOH/EtOAc and F5:EtOH/H2O fractions.

(PDF)

Acknowledgments

The authors would like to extend sincerest appreciation to Dr. Pranee Nangam at Faculty of Science, Naresuan University, Thailand, for her kind help on plant species identification and Program in Environmental Toxicology, Chulabhorn Graduate Institute, for providing the equipment for the cell culture experiments. The authors gratefully acknowledge Dr. Ubolsree Lertsakulpanich, Dr. Suganya Yongkiettrakul, and Dr. Warangkhana Songsungthong at National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA) and Mrs. Suwalya Khemvaraporn at Thammasat University for guidance and manuscript revision.

Data Availability

All relevant data are within the manuscript and its Supporting information files.

Funding Statement

This work was supported by the Agricultural Research Development Agency (Public Organization) [grant numbers CRP6305030720] and the National Science and Technology Development Agency [grant number FDA-CO-2563-12800-TH]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.:JC.

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Decision Letter 0

Branislav T Šiler

26 Oct 2021

PONE-D-21-29347LC-MS/MS metabolomics-facilitated identification of the active compounds responsible for anti-allergic activity of the ethanol extract of Xenostegia tridentataPLOS ONE

Dear Dr. Chatwichien,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

Please be careful when  providing information about the studied species, since several synonyms have been and are still in use. Moreover, do introduce these synonyms in the Introduction section. Some of methodological approaches used in the study are not properly performed as being pointed out in the Reviewer's report. These concerns should be meticulously checked and additional experiments performed where needed. Statistical analyzes also deserve more authors' attention. Language usage should be considerably improved. It is highly recommended to have the manuscript read and copy-edited by a native English speaker or a professional editing agency.

Please submit your revised manuscript by Dec 10 2021 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

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If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

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We look forward to receiving your revised manuscript.

Kind regards,

Branislav T. Šiler, Ph.D.

Academic Editor

PLOS ONE

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Reviewers' comments:

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Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Partly

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

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3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

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4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

**********

5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: Authors describe the anti-allergic effects of plant Merrenia (X.) tridentata in vitro and in vivo and use LC-MS/MS to identify several compounds with the following isolation to confirm the identity and the activity, as well in relation to the references. The work is interesting and well designed, with the logical sequence. The metabolomic approach is interesting, but the lack of proper library data makes the actual compound identification challenging. It is valuable that authors isolated the major compounds and tested them for activity as well. The data however, often show limitations and some parts are not clear. Data statisticts and viability should be concerned, following also other comments below:

1. “Xenostegia tridentata (L.) D.F. Austin & Staples is a synonym of Merremia tridentata(L.) Hallier f.”, please see below link and correct the statements about the first isolations from the plant (e.g., the last paragraph “for the first time” is not appropriate, because many previous studies of Merrenia were shown, also in the end of Abstract P. 2. Line 15). P. 3 please mention the synonym of the plant. For plant synonyms, please check theplantlist.org. here: http://www.theplantlist.org/tpl1.1/record/tro-8502902

2. Timing of the assays. The errors of the assays, SEM show high error. The viability window for F4 (BuOH) and ketotifen doesn’t fit the antigen-induced assay. Ketotifen is approx. 25% toxic at 100uM which would seriously affect the assay response considering sensitivity of antigen-induced assay in RBL cells (unless the timing of treatments was significantly different which is not shown in the Table 1)? Was the samples treatment time in Table 1. For MTT 48 hr and for beta-hexo assay 2hr? Please describe and explain why the cytotoxic samples (including kerotifen at 100uM with over 20% toxicity) were used in antigen-induced beta-hexo assay and the effects of butanol layer are not fitting their toxic levels? Is it because of the different time treatment?

3.

4. In the procedure, long incubation times may cause statistical errors particularly in the antigen induced assays.

5. P. 6. Line 10 Was the solubility of extracts in tween saline solution good enough? Was the sample filtered before administration? Was the solvent and vehicle the same? Please describe clearly.

6. Isolation scheme and Table 1. Considering that all the samples were oily, and the major fraction was hexane layer (11 g), while ethyl acetate layer was the minor (0.9 g) one. Referring also to Table 4 that content of these compounds is low in crude extract, while 3.034 is high in BuOH. => Is it possible that the most active fraction is hexane layer and maybe due to its unsaturated fatty acid content which exerts strong anti-inflammatory properties? It would be useful to investigate more on the content of this fraction.

7. Why Compound 48/80 was chosen as inducer, what is its mechanism of action?

8. P. 21. Line 13 Mention the level of activity, IC50 or values would be useful as well as the comparison with literature values. There was no concentration manner observed from Fig. 5 and 6 for pure compounds activity, is it reasonable I comparison with literature??

9. Vehicle control in Fig. 4 ROS is very unstable.

10. Ketotifen at 100 (ug/mL or uM?) should not be used if was toxic by over 20% in Table 1. And why it’s values differ so much from Fig. 5 and 6 (35 vs 60 for 100ug/ml or uM?). The concentration unit is also unclear?

11. Why MS2 in mzcloud give sometimes no hit, while often many hits, which fragment (product) ion was considered?

12. Please explain abbreviations: What does NSS, ICR mean.

13. Figure 1 The description of in vivo results may be clarified. The fact that the high concentration of extract was not inhibiting PCA in the same manner as control dexamethasone (also because the concentration used was different). Even the top concentration of extract did not statistically inhibit PCA. Is it due to a statistical error or is similar concentration effect observed in vitro as well? The cause may be too short pre-treatment in vivo with only a single dose??

14. Table 1. The statistics is not reasonable. Stars are missing for ketotifen at 100 and crude or water at 2000 ug/mL. It is not reasonable to evaluate the effects of the samples toxic to the cells, such as when the cell death is over 20%, especially for butanol layer. Also the concentrations used were extremely high. Is there a reasoning for it? It would be useful to see thte IC50 values for clarification in the text, because the current description is very brief and often skips the inconsistent results.

15. Is the beta-hexo release ratio percentage of max, meaning max is triton or inducer alone?

16. What is AGC and it’s value of 1x105?

17. How authors could use 1 g of EA fraction when only 0.9 g was obtained?

18. P. 13. Line 18 The statement “The parameters were adjusted to fit to the chromatographic data obtained from this experiment” it’s not clear, how the parameters were adjusted and if in objective manner?

19. Do the features represent the mass?

20. How the authors ensure that the isolated compounds were matching the metabolomics study?

21. Except the in-house mass list, was there another database available and used for MS2 except mzcloud which often gave no result?

22. Metabolomics Standard Initiative MSI levels 1-4 and the differences between them should be described. The resulting compounds identification such as four isolated compounds or apigenin should be given.

23. The effects of compounds on viability and hexosaminidase enzymatic activity should be mentioned clearly in the text (currently in Sup data), while negative values of EA layer should be explained, and methodology reviewed, -46.1 ± 0.9 (1000ug/mL) -89.5 ± 0.5 (2000 ug/mL)

24. P. 29. Line 8-9. The condition should be mentioned in Materials section. The further purification besides MPLC should be described and purity level estimated. The Fig. 3 MPLC chromatogram peaks are overlapping.

25. What represents the last four number of each “feature”?

26. Please unify a reference style, there are missed capital for Genus name or the style is inconsistent. Capitalization, please unify

27. LC-MS/MS in S1 show only few peaks, on which basis they were identified and what could be the major peak at 5.17?

There are many syntax and grammar errors or misspellings, please see following as examples only:

P. 6 l. 12 by intraperitoneal administration

What does NSS, ICR mean.

P13, l. 3 screening was

P.14, l. 9 discrimination possibly be attributed to

P.3 lines 21-25 rephrase please. Statistic treatment,

P. 4 knowledges.

P. 4 Line 13 contributed

P. 21. Line 6 bioassay-guided is not so clear

P. 13. Line 16 detect

P. 14 Unsupervised analysis could be explained. Figure 2 is not very clear.

P. 15. Line 1-2 rephrase please.

P. 29 cpd 24 name

Conclusion. Please specify statements: P. 23. Line 2 “Some proinflammatory factors” is too vague

Line 8-10 please rephrase

Line12-15 “to its highly abundance” rephrase and consider about role of hexane layer

Line14-16 please rephrase

PCA (same for in vivo experiment) abbreviation should not be used for “Fig 2. Principle component analysis (PCA) and Heat map visualization of X.tridentata extracts.”

Also, the analysis and discrimination of layers is not clear.

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Reviewer #1: Yes: Michal Korinek

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PLoS One. 2022 Apr 15;17(4):e0265505. doi: 10.1371/journal.pone.0265505.r002

Author response to Decision Letter 0


9 Dec 2021

Please kindly find our responses to reviewers, detail about our revision and our explanation to the reviewer’s concerns in the “response to reviewers” file.

Attachment

Submitted filename: Response to Reviewers.pdf

Decision Letter 1

Branislav T Šiler

10 Jan 2022

PONE-D-21-29347R1LC-MS/MS metabolomics-facilitated identification of the active compounds responsible for anti-allergic activity of the ethanol extract of Xenostegia tridentataPLOS ONE

Dear Dr. Chatwichien,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

Although the authors have amended the manuscript according to the Reviewer's report, these is still a room for improvement. Please meticulously check the new report and supplement the manuscript with the necessary information.

Please submit your revised manuscript by Feb 24 2022 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

  • A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.

  • A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.

  • An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Branislav T. Šiler, Ph.D.

Academic Editor

PLOS ONE

Journal Requirements:

Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

**********

2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: Authors addressed the comments in comprehensive manner and although there are limitations such as the high doses used in bioassays (the plant is not food), low ratio of identified components based on the metabolomics study, the overall quality was improved and the manuscript is suitable for publication. The approach authors chose may serve as a template for future discovery of antiallergic drugs from herbal medicines.

Minor comments:

1. The role of LC-MS/MS metabolomics in current study may be exaggerated since the methods failed to identify the major compounds in the first place.

2. The PC 1 and PC 2 descriptors were not explained in Fig. 2.

3. Dicaffeoylquinic was identified as 4,5 by MS/MS but 3,5 by isolation.

4. Information could be shared in Supporting Information:

The list of 116 collected samples related to this plant may have been shared in Supporting information or online database.

The collected literature data on previously reported bioactivity (Reply 8) could also be added to Supporting information, taken that authors spent time to analyze the data (Note. cynaroside % Inh values must be mistaken 0.21 and 0.59).

The table with yields of extraction. (Reply 17)

The fact that vehicle control being activated by antigen in M&M (Reply 15)

HPLC chromatograms of isolated compounds (Reply 24).

The possible identity of major peak at 5.15-5.22 (could be mentioned in the main text).

5. Very nice and clear NMR analysis and literature comparison in Supporting Information. On which basis author confirmed the correct position of glucoside luteolin-7-O-glucoside when there is no HMBC correlation H1'' to C-7?

6. Semi-quantification is based on AUC of detected mass. Could relative amount per g of plant extract be calculated?

6. Some English errors could be corrected:

p.17 l.13, l.16 was/were (*MSI 1)

Supporting: diCaffeoyl, lutoelin-7-O-D-glucoside etc.

p.4 line 7 *considered as safe

p.11 l.18 *is possibly related

**********

7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: Yes: Michal Korinek

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PLoS One. 2022 Apr 15;17(4):e0265505. doi: 10.1371/journal.pone.0265505.r004

Author response to Decision Letter 1


24 Jan 2022

In the revised version, we have re-checked and corrected the reference list. References 28 and 33 are replaced with other relevant papers. DOI of reference 23 is corrected. The author’s names and journal abbreviations are completed and corrected. The titles are now displayed in sentence-format (capitalize the first letter of the first word). According to the reviewer’s comments, the experimental data including extraction yields, HPLC chromatograms of isolated compounds and the in-house library of compounds related to X.tridentata are added into supporting information. Typos and grammatical errors in the manuscript and supporting information are reviewed and corrected. In addition, we have updated the name of affiliation #6 since it has been recently changed (Jan 6, 2022). Please kindly find more detail about our responses to the reviewer in the “Response to Reviewers” file

Attachment

Submitted filename: Response to Reviewers.pdf

Decision Letter 2

Branislav T Šiler

18 Feb 2022

PONE-D-21-29347R2LC-MS/MS metabolomics-facilitated identification of the active compounds responsible for anti-allergic activity of the ethanol extract of Xenostegia tridentataPLOS ONE

Dear Dr. Chatwichien,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

==============================

The authors did not fully address Reviewer's and Academic Editor's concerns. Specifically, PC1 and PC2 descriptors should be given in the caption for Figure 2, regardless of their introduction in the main text. Figure captions should stand alone and be readable without referencing to the main text.

Regarding Reviewer's suggestion about expressing compound masses as relative amounts per gram, I am really convinced that the reviewer asked the authors to present such a calculation (as a table, presumably), not just to answer if this possibility exist.

Please do not randomly capitalize words (compounds particularly), even if abbreviation is provided in parenthesis (e.g., P5L6, P5L7, P10L21, P10L23, P18L10-11, and further in the text).

Citations in square brackets in the text should stand before a comma.

Please do not spell out "nanometers" (P7L15). Using "nm" only is quite acceptable. Also, using "AlCl3" without previous description is also perfectly fine (P7L14). Do not express centrifugation speed in rpm (P8L1). Use "g" instead (it needs computing), since equal rotation (rpm) in rotors with different diameters produce different g force. Therefore, g is a constant, while rpm is not. Do not use semicolons when listing items after colons, but use commas instead.

Merremia tridentata is a synonym of the studied plant species and cannot be referred to as "other plants in the Convolvulaceae family" (P17L4). Moreover, using vernacular expressions such as "other plants" (might present other individuals) instead of "plant species" is not scientifically justified.

==============================

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Academic Editor

PLOS ONE

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Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

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Reviewers' comments:

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

PLoS One. 2022 Apr 15;17(4):e0265505. doi: 10.1371/journal.pone.0265505.r006

Author response to Decision Letter 2


2 Mar 2022

In the revised version, we have added the descriptions of PC1 and PC2 to the caption for Fig 2. The words that were randomly capitalized or unnecessary to be spelled out are corrected according to editor’s suggestions. The citations in square brackets are moved to stand before commas and periods. The word “in other plants” in P17L4 is replaced with the more appropriate word “plant species”. Fig 4 is revised to show the relative levels of the four significant metabolite features from the same ionization mode (ESI+ mode). The word “semi-quantitation” in main text is replaced with “relative metabolite level”, to avoid any misunderstanding that the AUC values could be directly used for quantification. The changes are highlighted in yellow in the “Revised Manuscript with Track Changes” file. In addition, please kindly find more detail about our responses in the “Response to Reviewers” file.

Regarding the reviewer’s suggestion on the calculation of relative amount of compound per gram extract, we think that, based on the results that we currently have, we can not obtain the accurate values. Further quantitative analysis by using standard compounds will need to be performed (which is beyond our focus for this work). However, the putative values could be calculated based on assumptions. The calculation and result are shown in the “Response to Reviewers” file.

Attachment

Submitted filename: Responses to reviewers.pdf

Decision Letter 3

Branislav T Šiler

3 Mar 2022

LC-MS/MS metabolomics-facilitated identification of the active compounds responsible for anti-allergic activity of the ethanol extract of Xenostegia tridentata

PONE-D-21-29347R3

Dear Dr. Chatwichien,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

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Kind regards,

Branislav T. Šiler, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Acceptance letter

Branislav T Šiler

23 Mar 2022

PONE-D-21-29347R3

LC-MS/MS metabolomics-facilitated identification of the active compounds responsible for anti-allergic activity of the ethanol extract of Xenostegia tridentata

Dear Dr. Chatwichien:

I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department.

If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org.

If we can help with anything else, please email us at plosone@plos.org.

Thank you for submitting your work to PLOS ONE and supporting open access.

Kind regards,

PLOS ONE Editorial Office Staff

on behalf of

Dr. Branislav T. Šiler

Academic Editor

PLOS ONE

Associated Data

    This section collects any data citations, data availability statements, or supplementary materials included in this article.

    Supplementary Materials

    S1 Appendix. LC-MS metabolite profiling and comparison of MS and MS/MS data of the features obtained from metabolite profiling to isolated compounds.

    (PDF)

    S2 Appendix. NMR spectra of the isolated compounds.

    (PDF)

    S1 Table. Extraction yields, β-hexosaminidase inhibitory activity of the extracts, cytotoxicity of the isolated compounds and previously reported anti-allergic activities of the isolated compounds.

    (PDF)

    S2 Table. Library for LC-MS.

    (XLSX)

    S3 Table. Metabolite identification of features contributed to the discrimination between F3:EtOH/EtOAc and F5:EtOH/H2O fractions.

    (PDF)

    Attachment

    Submitted filename: Response to Reviewers.pdf

    Attachment

    Submitted filename: Response to Reviewers.pdf

    Attachment

    Submitted filename: Responses to reviewers.pdf

    Data Availability Statement

    All relevant data are within the manuscript and its Supporting information files.


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