Summary of Study ST003998
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR002503. The data can be accessed directly via it's Project DOI: 10.21228/M83N9S This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST003998 |
| Study Title | Untargeted Metabolomics and In silico Screening of Sisymbrium officinale: Identification of Flavonoid Glycosides as Potential Anti-Inflammatory Agents |
| Study Summary | Sisymbrium officinale (SO), often referred to as "the plant of singers," is a revered traditional Mediterranean medicinal herb known for its applications in treating inflammatory diseases. Despite its historical use, comprehensive metabolomics and in silico studies validating its anti-inflammatory effects remain scarce. The study reported here seeks to uncover and characterize the bioactive compounds within SO, providing a critical step in identifying potential anti-inflammatory agents. To achieve this, we extracted plant compounds using various solvents with differing polarities, i.e., water, methanol, ethanol, acetone, and chloroform. These extractions were followed by phase separation (polar phase and nonpolar phase) of crude extracts. Additionally, we employed GC-MS and LC-MS (polar phase and nonpolar phase) spectroscopy to obtain a preliminary quantification of the diverse functional groups in the SO extracts. GC-MS analysis resulted in the identification of SO primary metabolites including sugars (rhamnose, trehalose, fructopyranose, myo-inositol, etc.), amino acids (glycine, lysine, valine, etc.), and fatty acids (linolenic acid, norlinolenic acid, aminovaleric acid, etc.). The LC-MS analysis of both polar and nonpolar fraction resulted in diverse secondary metabolite groups including alkaloids (tetramethylpyrazine, pilocarpine), flavonoids (apigetrin, cynaroside, vitexin 4-O-glucoside, kaempferol, galangin, naringenin, etc.), and plant sterols (zymosterol). The bioassay analysis showed that methanol, ethanol, and acetone possess the highest anti-inflammatory activity through NO suppresion of RAW 264.7 macrophage cells. Further, chemometrics and in silico screening (molecular docking and ADMET) resulted in two flavonoid glycosides, apigetrin and 3-O-α-L-arabinopyranoside, as potential anti-inflammatory compounds that suppress the activity of human inducible NO synthase (iNOS, PDB ID: 3E7G), endothelial NOS (eNOS, PDB ID: 6AV7), and neuronal NOS (nNOS, PDB ID: 6CID). These findings pave the ways for further validation studies including isolation, purification, in vitro, and in vivo analysis. |
| Institute | King Abdullah University of Science and Technology |
| Last Name | Kahfi |
| First Name | Jordan |
| Address | Thuwal, Thuwal, Makkah, 23955, Saudi Arabia |
| jordan.kahfi@kaust.edu.sa | |
| Phone | 0541244806 |
| Submit Date | 2025-02-01 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | GC-MS/LC-MS |
| Release Date | 2025-07-15 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002503 |
| Project DOI: | doi: 10.21228/M83N9S |
| Project Title: | Untargeted Metabolomics and In silico Screening of Sisymbrium officinale: Identification of Flavonoid Glycosides as Potential Anti-Inflammatory Agents |
| Project Summary: | Sisymbrium officinale (SO), often referred to as "the plant of singers," is a revered traditional Mediterranean medicinal herb known for its applications in treating inflammatory diseases. Despite its historical use, comprehensive metabolomics and in silico studies validating its anti-inflammatory effects remain scarce. The study reported here seeks to uncover and characterize the bioactive compounds within SO, providing a critical step in identifying potential anti-inflammatory agents. To achieve this, we extracted plant compounds using various solvents with differing polarities, i.e., water, methanol, ethanol, acetone, and chloroform. These extractions were followed by phase separation (polar phase and nonpolar phase) of crude extracts. Additionally, we employed GC-MS and LC-MS (polar phase and nonpolar phase) spectroscopy to obtain a preliminary quantification of the diverse functional groups in the SO extracts.We also carried out inflammatory bioassay analysis followed by chemometrics and in silico screening. |
| Institute: | King Abdullah University of Science and Technology |
| Last Name: | Kahfi |
| First Name: | Jordan |
| Address: | Thuwal, Thuwal, Makkah, 23955, Saudi Arabia |
| Email: | jordan.kahfi@kaust.edu.sa |
| Phone: | 0541244806 |
Subject:
| Subject ID: | SU004135 |
| Subject Type: | Plant |
| Subject Species: | Sisymbrium officinale |
| Taxonomy ID: | 203582 |
Factors:
Subject type: Plant; Subject species: Sisymbrium officinale (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Treatment |
|---|---|---|---|
| SA461241 | A5 | Leaves | Acetone Crude Extract |
| SA461242 | A2 | Leaves | Acetone Crude Extract |
| SA461243 | A1 | Leaves | Acetone Crude Extract |
| SA461244 | A4 | Leaves | Acetone Crude Extract |
| SA461245 | A3 | Leaves | Acetone Crude Extract |
| SA461246 | C2 | Leaves | Chloroform Crude Extract |
| SA461247 | C3 | Leaves | Chloroform Crude Extract |
| SA461248 | C4 | Leaves | Chloroform Crude Extract |
| SA461249 | C5 | Leaves | Chloroform Crude Extract |
| SA461250 | C1 | Leaves | Chloroform Crude Extract |
| SA461251 | E5 | Leaves | Ethanol Crude Extract |
| SA461252 | E4 | Leaves | Ethanol Crude Extract |
| SA461253 | E3 | Leaves | Ethanol Crude Extract |
| SA461254 | E2 | Leaves | Ethanol Crude Extract |
| SA461255 | E1 | Leaves | Ethanol Crude Extract |
| SA461256 | M2 | Leaves | Methanol Crude Extract |
| SA461257 | M3 | Leaves | Methanol Crude Extract |
| SA461258 | M4 | Leaves | Methanol Crude Extract |
| SA461259 | M5 | Leaves | Methanol Crude Extract |
| SA461260 | M1 | Leaves | Methanol Crude Extract |
| SA461261 | W1 | Leaves | Water Crude Extract |
| SA461262 | W2 | Leaves | Water Crude Extract |
| SA461263 | W3 | Leaves | Water Crude Extract |
| SA461264 | W4 | Leaves | Water Crude Extract |
| SA461265 | W5 | Leaves | Water Crude Extract |
| Showing results 1 to 25 of 25 |
Collection:
| Collection ID: | CO004128 |
| Collection Summary: | The leaf sample was collected from wild Sisymbrium officinale Plant grown in in the mountainous regions of Hebron, Palestine in February 2023. |
| Sample Type: | Leaves |
Treatment:
| Treatment ID: | TR004144 |
| Treatment Summary: | Sisymbrium officinale leaves were lyophilized and extracted with different type of solvent (water, ethanol, methanol, acetone, and chloroform). The dried crude extracts were subjected for liquid-liquid phase separation: polar phase and nonpolar phase prior GC-MS and LC-MS analysis |
Sample Preparation:
| Sampleprep ID: | SP004141 |
| Sampleprep Summary: | SO powder (25 mg) was mixed with 2.0 mL of each different solvent: water, methanol, ethanol, ethyl acetate, and acetone. The mixtures were sonicated in ice bath (15 minutes) to avoid excessive heating, macerated on a shaker overnight (25 °C, 1400 rpm, 17 hours) to ensure maximum extraction, and centrifuged (25 °C, 14,000X g, 10 minutes) to separate the debris and extracted materials. The supernatant was transferred into new labelled tubes (water, methanol, ethanol, ethyl acetate, and acetone) and stored at -20 °C. |
Combined analysis:
| Analysis ID | AN006589 | AN006590 | AN006591 | AN006592 |
|---|---|---|---|---|
| Chromatography ID | CH005002 | CH005003 | CH005003 | CH005004 |
| MS ID | MS006288 | MS006289 | MS006290 | MS006291 |
| Analysis type | MS | MS | MS | MS |
| Chromatography type | GC | Reversed phase | Reversed phase | Reversed phase |
| Chromatography system | Thermo Trace 1310 | Thermo Vanquish | Thermo Vanquish | Thermo Vanquish |
| Column | Thermo Scientific Trace GOLD TG-5SilMS (30m × 0.25mm, 0.25um) | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) |
| MS Type | EI | ESI | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap | Orbitrap | QTOF |
| MS instrument name | Thermo Orbitrap Exploris 240 | Thermo Orbitrap ID-X Tribrid | Thermo Orbitrap ID-X Tribrid | Bruker timsTOF PRO |
| Ion Mode | POSITIVE | POSITIVE | NEGATIVE | POSITIVE |
| Units | AUC | AUC | AUC | AUC |
Chromatography:
| Chromatography ID: | CH005002 |
| Chromatography Summary: | A Thermo Trace 1310, was used for the analysis of the primary metabolites. Helium was used as the carrier gas, with a flow rate of 1.2mL/min. |
| Instrument Name: | Thermo Trace 1310 |
| Column Name: | Thermo Scientific Trace GOLD TG-5SilMS (30m × 0.25mm, 0.25um) |
| Column Temperature: | Programmed temperature gradient: The oven temperature was maintained initially at 70°C for 2 min and increased to 220 °C at a rate of 8°C/min, then increased to 325 °C at a rate of 16°C/min and was held for 10 min. |
| Flow Gradient: | - |
| Flow Rate: | 1.2 mL/min |
| Solvent A: | - |
| Solvent B: | - |
| Chromatography Type: | GC |
| Chromatography ID: | CH005003 |
| Chromatography Summary: | A Thermo Vanquish was used for the analysis of the polar phase secondary metabolites. Chromatographic separation of the liquid-phase chemical components was achieved using a C18 column (2.1 × 100 mm, 1.7µm) Waters, Milford, MA, USA, coupled to a UPLC BEH C18 column (2.1 × 10mm, 1.7µm) with a flow rate of 0.4 mL/min. Two solutions were used for the mobile phase, namely Solution A (100% water; 0.1% formic acid) and Solution B (100% acetonitrile; 0.1% formic acid). |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) |
| Column Temperature: | 35°C |
| Flow Gradient: | The gradient was linearly changed as follows: 0−2 min, 100% B; 2−9 min from 100% B to 85% B; 9−14 min from 85% B to 50% B; 14−17 min from 50% B to 100%B, 17.1−20 min, 100% B for column re-equilibration. |
| Flow Rate: | 0.4 mL/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH005004 |
| Chromatography Summary: | The nonpolar phase measurement was performed using Thermo Vanquish. UPLC BEH C18 column (2.1 × 10mm, 1.7µm) with a flow rate of 0.4 mL/min. Two solutions were used for the mobile phase, namely Solution A (60% acetonitrile/40% water; 0.1% formic acid; 10mM ammonium formate) and Solution B (10% acetonitrile/90% isopropanol; 0.1% formic acid; 10mM ammonium formate). |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) |
| Column Temperature: | 55°C |
| Flow Gradient: | The gradient was changed as follow: 0-2 minutes, 43% B; 2-18 minutes, from 43% B to 99% B; 18-20 minutes, 99%B; 20-22 minutes, from 99% B to 43% B. |
| Flow Rate: | 0.4 mL/min |
| Solvent A: | 60% acetonitrile/40% water; 0.1% formic acid; 10mM ammonium formate |
| Solvent B: | 10% acetonitrile/90% isopropanol; 0.1% formic acid; 10mM ammonium formate |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS006288 |
| Analysis ID: | AN006589 |
| Instrument Name: | Thermo Orbitrap Exploris 240 |
| Instrument Type: | Orbitrap |
| MS Type: | EI |
| MS Comments: | The Thermo Orbitrap Exploris 240 mass spectrometer was used. This instrument was operated in electron ionization (EI) which was set at 300 ˚C, and the electron energy was set to 70eV with an emission current of 50µA. The acquisition mode was set to full scan with a scan range of 35-700 Da and an orbitrap resolution of 60000 (FWHM, measured at m/z 200). The AGC target was set to standard and the maximum injection time was set to auto mode. The data acquisition was lock-mass corrected using GC column bleed siloxane masse of m/z 207. The Trace 1310 GC operated with an injection volume of 1 µl of sample that was injected using a 10 µL syringe into a single gooseneck with glass wool Thermo Scientific™ Liner GOLD. The inlet mode was set to Split mode with a split flow of 40ml/min and a purge flow of 5 ml/min. The helium carrier rate was set to 1.2 ml/min. The oven temperature was maintained initially at 70°C for 2 min and increased to 220 °C at a rate of 8°C/min, then increased to 325 °C at a rate of 16°C/min and was held for 10 min. |
| Ion Mode: | POSITIVE |
| MS ID: | MS006289 |
| Analysis ID: | AN006590 |
| Instrument Name: | Thermo Orbitrap ID-X Tribrid |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The Thermo Orbitrap ID-X tribrid was used. This instrument was operated using following parameters were: sheath gas at 50 arb, auxiliary gas at 10 arb, spray voltage at +3.5 kV in positive mode and 2.5kV, capillary temperature at 300 ◦C, auxiliary gas heater temperature at 350°C, s-lens RF level at 60%. Full scan parameters: m/z range from 50 to 500; mass resolution, 60,000; AGC target, 3e6; maximum IT, 100ms. DDA parameters: m/z range from 50 to 500, TopN, 3 (fragments the 3 ions with top intensities from the previous full scan spectrum); intensity threshold to trigger MS/MS acquisition, 2e4; dynamic exclusion, 6 s; combined MSMS CE at 10, 30, 40, 70, 90 eV, mass resolution, 30,000; AGC target, 1e5; maximum IT, 50ms; m/z isolation window within 1. |
| Ion Mode: | POSITIVE |
| MS ID: | MS006290 |
| Analysis ID: | AN006591 |
| Instrument Name: | Thermo Orbitrap ID-X Tribrid |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The Thermo Orbitrap ID-X tribrid was used. This instrument was operated using following parameters: sheath gas at 50 arb, auxiliary gas at 10 arb, spray voltage at +3.5 kV in positive mode and 2.5kV, capillary temperature at 300 ◦C, auxiliary gas heater temperature at 350°C, s-lens RF level at 60%. Full scan parameters: m/z range from 50 to 500; mass resolution, 60,000; AGC target, 3e6; maximum IT, 100ms. DDA parameters: m/z range from 50 to 500, TopN, 3 (fragments the 3 ions with top intensities from the previous full scan spectrum); intensity threshold to trigger MS/MS acquisition, 2e4; dynamic exclusion, 6 s; combined MSMS CE at 10, 30, 40, 70, 90 eV, mass resolution, 30,000; AGC target, 1e5; maximum IT, 50ms; m/z isolation window within 1. |
| Ion Mode: | NEGATIVE |
| MS ID: | MS006291 |
| Analysis ID: | AN006592 |
| Instrument Name: | Bruker timsTOF PRO |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | The Bruker timsTOF PRO was used. This instrument was operated using following parameters: the end plate offset voltage was 500V, capillary voltage was 4500V, nebulizer pressure was 2.2 Bar, dry gas flow was 10 L/min, and dry gas temperature was 220°C. The MS scan ranged between 100–1350 m/z. For the ion mobility detector, the 1/K0 scan ranged between 0.55–1.83V s/cm2, ramp time was 100ms, accumulation time was 100ms, and ramp rate was 9.42 Hz. |
| Ion Mode: | POSITIVE |
