Rapid screening of unprecedented sesquiterpenes with distinctive ring skeletons from Daphne aurantiaca employing an integrated strategy DOI

Shu-Hui Dong,

Jinling Han,

Xinyu Chang

и другие.

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

NPClassifier: A Deep Neural Network-Based Structural Classification Tool for Natural Products DOI Creative Commons
Hyun Woo Kim, Mingxun Wang, Christopher A. Leber

и другие.

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

Recent advances in proteomics and metabolomics in plants DOI Creative Commons
Shijuan Yan, Ruchika Bhawal, Zhibin Yin

и другие.

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

Advances in artificial intelligence for drug delivery and development: A comprehensive review DOI
Amol D. Gholap, Md Jasim Uddin, Md. Faiyazuddin

и другие.

Computers in Biology and Medicine, Год журнала: 2024, Номер 178, С. 108702 - 108702

Опубликована: Июнь 7, 2024

Язык: Английский

Процитировано

52

MS2Query: reliable and scalable MS2 mass spectra-based analogue search DOI Creative Commons
Niek De Jonge, Joris J. R. Louwen, Elena Chekmeneva

и другие.

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

Reproducible mass spectrometry data processing and compound annotation in MZmine 3 DOI
Steffen Heuckeroth, Tito Damiani, Aleksandr Smirnov

и другие.

Nature Protocols, Год журнала: 2024, Номер 19(9), С. 2597 - 2641

Опубликована: Май 20, 2024

Язык: Английский

Процитировано

30

Good practices and recommendations for using and benchmarking computational metabolomics metabolite annotation tools DOI Creative Commons
Niek De Jonge, Kevin Mildau, David Meijer

и другие.

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

Advancements in capturing and mining mass spectrometry data are transforming natural products research DOI
Scott A. Jarmusch, Justin J. J. van der Hooft, Pieter C. Dorrestein

и другие.

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

Gut microbial metabolome in inflammatory bowel disease: From association to therapeutic perspectives DOI Creative Commons
Mengfan Li,

Lijiao Yang,

Chenlu Mu

и другие.

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

Comparison of Cosine, Modified Cosine, and Neutral Loss Based Spectrum Alignment For Discovery of Structurally Related Molecules DOI
Wout Bittremieux, Robin Schmid, Florian Huber

и другие.

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

Integrative omics approaches for biosynthetic pathway discovery in plants DOI Creative Commons
Kumar Saurabh Singh, Justin J. J. van der Hooft, Saskia C. M. Van Wees

и другие.

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