The raw data were imported into the metabolomics processing software Progenesis QI v3.0 (Waters Corporation, Milford, USA) for baseline filtering, peak identification, integration, retention time correction, and peak alignment, ultimately generating a data matrix containing retention time, mass-to-charge ratio (m/z), and peak intensity information. Subsequently, the software was employed for library search and identification of characteristic peaks by matching MS and MS/MS mass spectrometry data with metabolic databases. The MS mass error was set to less than 10 ppm, and metabolites were identified based on the matching scores from the secondary mass spectrometry.
The primary databases include mainstream public databases such as http://www.hmdb.ca/ and https://metlin.scripps.edu/, as well as self-built databases.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - negative - reverse-phase","Liquid Chromatography MS - positive - reverse-phase"],"chromatography_protocol":["Chromatographic conditions: The chromatographic column used was ACQUITY UPLC HSS T3 (100 mm × 2.1 mm i.d., 1.8 µm; Waters, Milford, USA). Mobile phase A consisted of 95% water and 5% acetonitrile (containing 0.1% formic acid), while mobile phase B was composed of 47.5% acetonitrile, 47.5% isopropanol, and 5% water (containing 0.1% formic acid). The injection volume was 3 μL, and the column temperature was maintained at 40°C.
"],"publication":["Discovery of isokurarinone as an ATCase-Engaging Lead with potent activity against methicillin-resistant Staphylococcus aureus."],"submitter_name":["Ding bosheng"],"submitter_affiliation":["Zhejiang Guangsha Vocational and Technical University of Construction"],"organism_part":["Bacteria"],"technology_type":["mass spectrometry"],"disease":[""],"extraction_protocol":["1. Transfer all samples to 1.5 mL centrifuge tubes; 2. Add 300 µL of extraction buffer (methanol:acetonitrile = 1:1 (v:v)) containing four internal standards (L-2-chlorophenylalanine (0.02 mg/mL), etc.); 3. Mix thoroughly for 30 seconds, followed by low-temperature ultrasonic extraction for 30 minutes (5°C, 40 kHz); 4. Store samples at-20°C for 30 minutes; 5. Centrifuge for 15 minutes (13,000 g, 4°C), transfer the supernatant, and dry with nitrogen; 6. Add 100 µL of reconstitution buffer (acetonitrile:water = 1:1) for resolubilization; 7. Mix thoroughly for 30 seconds, followed by low-temperature ultrasonic extraction for 5 minutes (5°C, 40 kHz); 8. Centrifuge for 10 minutes (13,000 g, 4°C), transfer the supernatant to a sample vial with an insert, and analyze on the instrument; 9. Additionally, take 20 µL of supernatant from each sample, mix them, and use as quality control samples.
The raw data were imported into the metabolomics processing software Progenesis QI v3.0 (Waters Corporation, Milford, USA) for baseline filtering, peak identification, integration, retention time correction, and peak alignment, ultimately generating a data matrix containing retention time, mass-to-charge ratio (m/z), and peak intensity information. Subsequently, the software was employed for library search and identification of characteristic peaks by matching MS and MS/MS mass spectrometry data with metabolic databases. The MS mass error was set to less than 10 ppm, and metabolites were identified based on the matching scores from the secondary mass spectrometry.
The primary databases include mainstream public databases such as http://www.hmdb.ca/ and https://metlin.scripps.edu/, as well as self-built databases.
"],"study_factor":["Association"],"submitter_email":["15700153239@163.com"],"sample_collection_protocol":["Bacteria were cultured until the logarithmic growth phase and bacterial density was adjusted to 2 × 105 CFU/mL. The treatment group was administered with drug to a final concentration of 1/2 × MIC, while the control group was treated with an equal volume of solvent. The samples were incubated for 4 h at 37°C and 180 rpm in a shaking incubator. After centrifugation, the culture medium was discarded and the bacterial pellet was washed thrice with 10 mL of pre-chilled sterile PBS buffer. The bacterial metabolism was quenched using liquid nitrogen.
"],"omics_type":["Metabolomics"],"study_design":["Methicillin-resistant Staphylococcus aureus","natural product","aspartate transcarbamoylase","isokurarinone","pyrimidine biosynthesis"],"curator_keywords":["natural product","Methicillin-resistant Staphylococcus aureus","aspartate transcarbamoylase","isokurarinone","pyrimidine biosynthesis"],"mass_spectrometry_protocol":["Scan range: m/z 70-1050; Sheath gas flow rate: 60 arb; Auxiliary gas flow rate: 20 arb; Heating temperature: 350°C; Capillary temperature: 320°C; Spray voltage (positive mode): 3400 V; Spray voltage (negative mode): -3000 V; S-Lens RF level: 70; Collision energy (normalized): 20,40,60%; Resolution (Full MS): 60,000; Resolution (MS2):15,000
"],"additional_accession":[]},"is_claimable":false,"name":"Discovery of isokurarinone as an ATCase-Engaging Lead with potent activity against methicillin-resistant Staphylococcus aureus","description":"The global proliferation of methicillin-resistant Staphylococcus aureus (MRSA) persists as a significant contributor to challenging infections, highlighting the urgent necessity for therapies that utilize novel mechanisms. Aspartate transcarbamoylase (ATCase), which catalyzes the initial committed step of de novo pyrimidine biosynthesis, represents a promising metabolic target with potential relevance to MRSA fitness and persistence. Through structure-based virtual screening and experimental validation, we identified the flavonoid isokurarinone as a compound targeting ATCase, demonstrating potent anti-MRSA activity. Docking and molecular dynamics simulations, along with surface plasmon resonance and differential scanning fluorimetry, provided evidence for direct binding, which was accompanied by a reduction in ATCase activity and a decrease in pyrB expression. Non-targeted metabolomics revealed a disruption of pyrimidine nucleotide homeostasis, coinciding with impaired membrane integrity, reduced proton motive force, decreased intracellular ATP levels, and increased oxidative stress. Isokurarinone also inhibited biofilm formation and altered the expression of virulence-associated genes. In a murine model of MRSA-infected wounds, isokurarinone accelerated wound closure, reduced bacterial burden, and attenuated local inflammatory mediators. Collectively, these findings support the notion of ATCase as a metabolism-guided target for MRSA and nominate isokurarinone as a promising lead scaffold for therapeutic development.
","dates":{"publication":"2026-01-14","submission":"2026-01-14"},"accession":"MTBLS13673","cross_references":{}}