Computational metabolomics reveals overlooked chemodiversity of alkaloid scaffolds in Piper fimbriulatum DOI Creative Commons
Tito Damiani, Joshua David Smith, Téo Hebra

et al.

The Plant Journal, Journal Year: 2025, Volume and Issue: 121(5)

Published: March 1, 2025

Plant specialized metabolites play key roles in diverse physiological processes and ecological interactions. Identifying structurally novel metabolites, as well discovering known compounds new species, is often crucial for answering broader biological questions. The Piper genus (Piperaceae family) its special phytochemistry has been extensively studied over the past decades. Here, we investigated alkaloid diversity of fimbriulatum, a myrmecophytic plant native to Central America, using metabolomics workflow that combines untargeted LC-MS/MS analysis with range recently developed computational tools. Specifically, leverage open MS/MS spectral libraries data repositories metabolite annotation, guiding isolation efforts toward (i.e., dereplication). As result, identified several alkaloids belonging five different classes isolated one seco-benzylisoquinoline featuring linear quaternary amine moiety which named fimbriulatumine. Notably, many were never reported Piperaceae plants. Our findings expand this family demonstrate value revisiting well-studied families state-of-the-art workflows uncover previously overlooked chemodiversity. To contextualize our within context, employed automated mining literature reports scaffolds mapped results onto angiosperm tree life. By doing so, highlight remarkable provide framework generating hypotheses on biosynthetic evolution these metabolites. Many tools resources used study remain underutilized science community. This manuscript demonstrates their potential through practical application aims promote accessibility approaches.

Language: Английский

Machine learning-assisted structure annotation of natural products based on MS and NMR data DOI
Guilin Hu, Ming‐Hua Qiu

Natural Product Reports, Journal Year: 2023, Volume and Issue: 40(11), P. 1735 - 1753

Published: Jan. 1, 2023

This review presents a summary of the recent advancements in machine learning-assisted structure elucidation (MLASE) to establish structures natural products (NPs).

Language: Английский

Citations

17
Strategies for structure elucidation of small molecules based on LC–MS/MS data from complex biological samples DOI Creative Commons

Zhitao Tian,

Fangzhou Liu, Dongqin Li

et al.

Computational and Structural Biotechnology Journal, Journal Year: 2022, Volume and Issue: 20, P. 5085 - 5097

Published: Jan. 1, 2022

LC–MS/MS is a major analytical platform for metabolomics, which has become recent hotspot in the research fields of life and environmental sciences. By contrast, structure elucidation small molecules based on data remains challenge chemical biological interpretation untargeted metabolomics datasets. In years, several strategies using from complex samples have been proposed, these can be simply categorized into two types, one annotation mass spectra other retention time prediction. These helped many scientists conduct metabolite-related are indispensable development future tools. Here, we summarized characteristics current tools data, further discussed directions perspectives to improve power or elucidation.

Language: Английский

Citations

24
Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences DOI Creative Commons
Cecilia Deng, Sushma Naithani, Sunita Kumari

et al.

Database, Journal Year: 2023, Volume and Issue: 2023

Published: Jan. 1, 2023

Abstract Large-scale genotype and phenotype data have been increasingly generated to identify genetic markers, understand gene function evolution facilitate genomic selection. These datasets hold immense value for both current future studies, as they are vital crop breeding, yield improvement overall agricultural sustainability. However, integrating these from heterogeneous sources presents significant challenges hinders their effective utilization. We established the Genotype-Phenotype Working Group in November 2021 a part of AgBioData Consortium (https://www.agbiodata.org) review types resources that support archiving, analysis visualization needs plant research community. For 2021–22, we identified different examined metadata annotations related experimental design/methods/sample collection, etc. Furthermore, thoroughly reviewed publicly funded repositories raw processed well secondary databases knowledgebases enable integration context genome browser, pathway networks tissue-specific expression. Based on our survey, recommend need (i) additional infrastructural archiving many new types, (ii) development community standards annotation formatting, (iii) biocuration (iv) tools connect with enhance knowledge synthesis foster translational research. Although this paper only covers relevant community, expect similar issues shared by researchers working animals. Database URL: https://www.agbiodata.org.

Language: Английский

Citations

14
Chemical characterization of different parts of Forsythia suspensa and α-glucosidase and pancreatic lipase inhibitors screening based on UPLC-QTOF-MS/MS and plant metabolomics analysis DOI Creative Commons

Yan-Li Ji,

Feng Xie, Yaqing Chang

et al.

Arabian Journal of Chemistry, Journal Year: 2024, Volume and Issue: 17(5), P. 105723 - 105723

Published: March 12, 2024

Forsythia suspensa (Thunb.) Vahl (FS) is an important plant with high edible and medicinal values. The fruit of FS a common traditional medicine in China, Japan Korea. Compared to the research on phytochemistry pharmacology fruits, study other parts FS, such as leaves flowers still limited. In this study, integrated strategy based ultra-performance liquid chromatography quadrupole time flight mass spectrometry (UPLC-QTOF-MS/MS), metabolomics correlation analysis was established for comprehensively chemical characterization discovery α-glucosidase pancreatic lipase inhibitory metabolites. metabolic profiling performed by UPLC-QTOF-MS/MS, total 74 secondary metabolites, including 15 phenylethanoid glycosides, 20 lignans, 10 cyclohexanol derivatives, 11 organic acids, 9 flavonoids, 3 triterpenes, compounds were identified. Then, 29 differential metabolites that responsible distinguish further screened out multivariate statistical analysis. Meanwhile, inhibition different evaluated compared vitro experiments. results demonstrated showed highest IC50 0.17 ± 0.04 mg/mL 0.56 0.33 mg/mL, respectively. between enzyme activities investigated Pearson analysis, 12 potential inhibitors screen out. Additionally, five components, quercitrin, rutin, kaempferol-3-O-rutinoside, pinoresinol-4-O-glucoside phillyrin validated assays molecular docking all good effects lipase, binding enzymes mainly through hydrogen bonding, hydrophobic force, ionic bonding. This provided feasible comparison discrimination bioactive also useful information future utilization FS.

Language: Английский

Citations

5
FragHub: A Mass Spectral Library Data Integration Workflow DOI Creative Commons
Axel Dablanc,

Solweig Hennechart,

Amélie Perez

et al.

Analytical Chemistry, Journal Year: 2024, Volume and Issue: unknown

Published: July 19, 2024

Open mass spectral libraries (OMSLs) are critical for metabolite annotation and machine learning, especially given the rising volume of untargeted metabolomic studies development pipelines. Despite their importance, practical application OMSLs is hampered by lack standardized file formats, metadata fields, supporting ontology. Current libraries, often restricted to specific topics or matrices, such as natural products, lipids, human metabolome, may limit discovery potential studies. The goal FragHub provide users with capability integrate various into a single unified format, thereby enhancing accuracy reliability. addresses these challenges integrating multiple comprehensive database, data harmonizing metadata. It also proposes some generic filters spectrum using graphical user interface. Additionally, workflow generate in-house compatible proposed. dynamically segregates based on ionization modes chromatography techniques, utility in research. Python code publicly available under MIT license, at following repository: https://github.com/eMetaboHUB/FragHub. Generated can be accessed 10.5281/zenodo.11057687.

Language: Английский

Citations

5
In situnet fishing of α-glucosidase inhibitors from evening primrose (Oenothera biennis) defatted seeds by combination of LC-MS/MS, molecular networking, affinity-based ultrafiltration, and molecular docking DOI
Zhiqiang Wang,

Yuxian Zhang,

Hongyuan Yan

et al.

Food & Function, Journal Year: 2022, Volume and Issue: 13(5), P. 2545 - 2558

Published: Jan. 1, 2022

Defatted seeds of evening primrose (DSEP), the by-product oil manufacture, exhibit potential α-glucosidase inhibitory activity; however, presently they are routinely discarded as waste. In this study, an

Language: Английский

Citations

21
Stable isotope-resolved metabolomics based on mass spectrometry: Methods and their applications DOI
Di Yu, Lina Zhou, Xinyu Liu

et al.

TrAC Trends in Analytical Chemistry, Journal Year: 2023, Volume and Issue: 160, P. 116985 - 116985

Published: Feb. 11, 2023

Language: Английский

Citations

13
Metabolomic Analysis Reveals Association between Decreased Ovarian Reserve and In Vitro Fertilization Outcomes DOI Creative Commons
Na An, Min Zhang, Quan‐Fei Zhu

et al.

Metabolites, Journal Year: 2024, Volume and Issue: 14(3), P. 143 - 143

Published: Feb. 27, 2024

In vitro fertilization (IVF) is a highly effective treatment for infertility; however, it poses challenges women with decreased ovarian reserve (DOR). Despite the importance of understanding impact DOR on IVF outcomes, limited research has explored this relationship, particularly using omics approaches. Hence, we conducted study to investigate association between and employing metabolomic approach. We analyzed serum samples from 207 undergoing treatment, including 89 118 normal (NOR). Our findings revealed that was significantly associated unfavorable characterized by reduced oocyte count, lower embryo quality, rates pregnancy live births. Furthermore, identified 82 metabolites displayed significant alterations in patients, impacting diverse metabolic pathways. Notably, distinct panel metabolites, palmitic acid, stearic LysoPC(9:0(CHO)/0:0), PC(18:0/9:0(CHO)), PC(16:0/9:0(CHO)), exhibited discriminatory power NOR groups, showcasing strong correlation outcomes. These emphasize crucial role disruptions influencing outcomes among DOR.

Language: Английский

Citations

4
Comprehensive Analysis of 11 Species of Euodia (Rutaceae) by Untargeted LC-IT-TOF/MS Metabolomics and In Vitro Functional Methods DOI Creative Commons

Xuhong Yong,

Wang Bi, Mengdi Wang

et al.

Molecules, Journal Year: 2024, Volume and Issue: 29(5), P. 1059 - 1059

Published: Feb. 28, 2024

The Euodia genus comprises numerous untapped medicinal plants that warrant thorough evaluation for their potential as valuable natural sources of herbal medicine or food flavorings. In this study, untargeted metabolomics and in vitro functional methods were employed to analyze fruit extracts from 11 significant species the genus. An investigation distribution metabolites (quinolone indole quinazoline alkaloids) these indicated E. rutaecarpa (Euodia rutaecarpa) was most widely distributed species, followed by compacta compacta), glabrifolia glabrifolia), austrosinensis austrosinensis), fargesii fargesii). There have been reports on close correlation between alkaloids anti-tumor activity, especially fruits which exhibit effectiveness against various types cancer, such SGC-7901, Hela, A549, other cancer cell lines. Additionally, plant contains alkaloids, possess remarkable antibacterial properties. Our results offer novel insights into utilization resources pharmaceutical industry.

Language: Английский

Citations

4
Metabolomics and Genomics Enable the Discovery of a New Class of Nonribosomal Peptidic Metallophores from a Marine Micromonospora DOI
Qihao Wu,

Bailey A. Bell,

Jia‐Xuan Yan

et al.

Journal of the American Chemical Society, Journal Year: 2022, Volume and Issue: 145(1), P. 58 - 69

Published: Dec. 19, 2022

Although microbial genomes harbor an abundance of biosynthetic gene clusters, there remain substantial technological gaps that impair the direct correlation newly discovered clusters and their corresponding secondary metabolite products. As example one approach designed to minimize or bridge such gaps, we employed hierarchical clustering analysis principal component (

Language: Английский

Citations

17