Organic Chemistry Frontiers, Год журнала: 2023, Номер 10(19), С. 4740 - 4749
Опубликована: Янв. 1, 2023
Unprecedented sesquiterpenoid scaffolds, furnished by unexpected carbon–carbon linkage formation or cleavage, were targeted and isolated from Daphne aurantiaca following an integrated strategy.
Язык: Английский
Journal of Natural Products, Год журнала: 2021, Номер 84(11), С. 2795 - 2807
Опубликована: Окт. 18, 2021
Computational approaches such as genome and metabolome mining are becoming essential to natural products (NPs) research. Consequently, a need exists for an automated structure-type classification system handle the massive amounts of data appearing NP structures. An ideal semantic ontology NPs should go beyond simple presence/absence chemical substructures, but also include taxonomy producing organism, nature biosynthetic pathway, and/or their biological properties. Thus, holistic automatic framework could have considerable value comprehensively navigate relatedness NPs, especially so when analyzing large numbers NPs. Here, we introduce NPClassifier, deep-learning tool structural from counted Morgan fingerprints. NPClassifier is expected accelerate enhance discovery by linking structures underlying
Язык: Английский
Процитировано
290
Molecular Horticulture, Год журнала: 2022, Номер 2(1)
Опубликована: Июль 23, 2022
Over the past decade, systems biology and plant-omics have increasingly become main stream in plant research. New developments mass spectrometry bioinformatics tools, methodological schema to integrate multi-omics data leveraged recent advances proteomics metabolomics. These progresses are driving a rapid evolution field of research, greatly facilitating our understanding mechanistic aspects metabolisms interactions plants with their external environment. Here, we review MS-based metabolomics tools workflows special focus on applications research using several case studies related stress response, gene/protein function characterization, metabolic signaling pathways exploration, natural product discovery. We also present projection concerning future perspectives development including challenges for system biology. This is intended provide readers an overview how advanced MS technology, integrated application can be used advance
Язык: Английский
Процитировано
72
Computers in Biology and Medicine, Год журнала: 2024, Номер 178, С. 108702 - 108702
Опубликована: Июнь 7, 2024
Язык: Английский
Процитировано
52
Nature Communications, Год журнала: 2023, Номер 14(1)
Опубликована: Март 29, 2023
Abstract Metabolomics-driven discoveries of biological samples remain hampered by the grand challenge metabolite annotation and identification. Only few metabolites have an annotated spectrum in spectral libraries; hence, searching only for exact library matches generally returns a hits. An attractive alternative is so-called analogues as starting point structural annotations; are molecules which not but display high chemical similarity. However, current analogue search implementations yet very reliable relatively slow. Here, we present MS2Query, machine learning-based tool that integrates mass embedding-based similarity predictors (Spec2Vec MS2Deepscore) well detected precursor masses to rank potential matches. Benchmarking MS2Query on reference spectra experimental case studies demonstrate improved reliability scalability. Thereby, offers exciting opportunities further increase rate metabolomics profiles complex mixtures discover new biology.
Язык: Английский
Процитировано
49
Nature Protocols, Год журнала: 2024, Номер 19(9), С. 2597 - 2641
Опубликована: Май 20, 2024
Язык: Английский
Процитировано
30
Metabolomics, Год журнала: 2022, Номер 18(12)
Опубликована: Дек. 5, 2022
Untargeted metabolomics approaches based on mass spectrometry obtain comprehensive profiles of complex biological samples. However, average only 10% the molecules can be annotated. This low annotation rate hampers biochemical interpretation and effective comparison studies. Furthermore, de novo structural characterization spectral data remains a complicated time-intensive process. Recently, field computational has gained traction novel methods have started to enable large-scale reliable metabolite annotation. Molecular networking machine learning-based in-silico tools been shown greatly assist in diverse fields such as clinical natural product discovery.
Язык: Английский
Процитировано
59
Natural Product Reports, Год журнала: 2021, Номер 38(11), С. 2066 - 2082
Опубликована: Янв. 1, 2021
This review covers the current and potential use of mass spectrometry-based metabolomics data mining in natural products. Public data, metadata, databases analysis tools are critical. The value success rely on community participation.
Язык: Английский
Процитировано
58
Computational and Structural Biotechnology Journal, Год журнала: 2022, Номер 20, С. 2402 - 2414
Опубликована: Янв. 1, 2022
Inflammatory bowel disease (IBD), comprising Crohn’s (CD) and ulcerative colitis (UC), is a set of clinically chronic, relapsing gastrointestinal inflammatory lacks an absolute cure. Although the precise etiology unknown, developments in high-throughput microbial genomic sequencing significantly illuminate changes intestinal structure functions patients with IBD. The application metabolomics suggests that microbiota can influence IBD pathogenesis by producing metabolites, which are implicated as crucial mediators host-microbial crosstalk. This review aims to elaborate current knowledge perturbations microbiome–metabolome interface description altered composition metabolite profiles gut microbiota. We emphasized elaborated recent findings several potentially protective classes IBD, including fatty acids, amino acids derivatives bile acids. article will facilitate deeper understanding new therapeutic approach for applying metabolome-based adjunctive treatment.
Язык: Английский
Процитировано
57
Journal of the American Society for Mass Spectrometry, Год журнала: 2022, Номер 33(9), С. 1733 - 1744
Опубликована: Авг. 12, 2022
Spectrum alignment of tandem mass spectrometry (MS/MS) data using the modified cosine similarity and subsequent visualization as molecular networks have been demonstrated to be a useful strategy discover analogs molecules from untargeted MS/MS-based metabolomics experiments. Recently, neutral loss matching approach has introduced an alternative networking with implied performance advantage in finding that cannot discovered existing MS/MS spectrum strategies. To comprehensively evaluate scoring properties matching, similarity, measures 955 228 peptide pairs 10 million small molecule were compared. This comparative analysis revealed outperformed all cases. The further indicated depends on location type modification, well chemical compound class fragmented molecules.
Язык: Английский
Процитировано
50
Natural Product Reports, Год журнала: 2022, Номер 39(9), С. 1876 - 1896
Опубликована: Янв. 1, 2022
This review discusses genomics-, transcriptomics- and metabolomics-based plant biosynthetic pathway discovery, highlights the potential for integrative omics approaches.
Язык: Английский
Процитировано
50