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

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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
Email	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

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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

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.

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.

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

Analysis:

Analysis ID:	AN006589
Analysis Type:	MS
Chromatography ID:	CH005002
Num Factors:	5
Num Metabolites:	37
Units:	AUC

Analysis ID:	AN006590
Analysis Type:	MS
Chromatography ID:	CH005003
Num Factors:	5
Num Metabolites:	50
Units:	AUC

Analysis ID:	AN006591
Analysis Type:	MS
Chromatography ID:	CH005003
Num Factors:	5
Num Metabolites:	20
Units:	AUC

Analysis ID:	AN006592
Analysis Type:	MS
Chromatography ID:	CH005004
Num Factors:	5
Num Metabolites:	56
Units:	AUC