دورية أكاديمية
أعرض في EDS

Data Base similarity (DBsimilarity) of natural products to aid compound identification on MS and NMR pipelines, similarity networking, and more.

التفاصيل البيبلوغرافية
العنوان: Data Base similarity (DBsimilarity) of natural products to aid compound identification on MS and NMR pipelines, similarity networking, and more.
المؤلفون: Borges RM; Instituto de Pesquisas de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil., de Assis Ferreira G; Instituto de Pesquisas de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil., Campos MM; Instituto de Pesquisas de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil., Teixeira AM; Instituto de Pesquisas de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil., das Neves Costa F; Instituto de Pesquisas de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil., Chagas FO; Instituto de Pesquisas de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
المصدر: Phytochemical analysis : PCA [Phytochem Anal] 2024 Jan; Vol. 35 (1), pp. 93-101. Date of Electronic Publication: 2023 Aug 17.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Wiley Country of Publication: England NLM ID: 9200492 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1099-1565 (Electronic) Linking ISSN: 09580344 NLM ISO Abbreviation: Phytochem Anal Subsets: MEDLINE
أسماء مطبوعة: Original Publication: Chichester, Sussex, UK : Wiley, c1990-
مواضيع طبية MeSH: Biological Products*/chemistry, Magnetic Resonance Spectroscopy/methods ; Databases, Factual ; Plant Extracts/chemistry ; Anti-Bacterial Agents
مستخلص: Introduction: We developed Data Base similarity (DBsimilarity), a user-friendly tool designed to organize structure databases into similarity networks, with the goal of facilitating the visualization of information primarily for natural product chemists who may not have coding experience.
Method: DBsimilarity, written in Jupyter Notebooks, converts Structure Data File (SDF) files into Comma-Separated Values (CSV) files, adds chemoinformatics data, constructs an MZMine custom database file and an NMRfilter candidate list of compounds for rapid dereplication of MS and 2D NMR data, calculates similarities between compounds, and constructs CSV files formatted into similarity networks for Cytoscape.
Results: The Lotus database was used as a source for Ginkgo biloba compounds, and DBsimilarity was used to create similarity networks including NPClassifier classification to indicate biosynthesis pathways. Subsequently, a database of validated antibiotics from natural products was combined with the G. biloba compounds to identify promising compounds. The presence of 11 compounds in both datasets points to possible antibiotic properties of G. biloba, and 122 compounds similar to these known antibiotics were highlighted. Next, DBsimilarity was used to filter the NPAtlas database (selecting only those with MIBiG reference) to identify potential antibacterial compounds using the ChEMBL database as a reference. It was possible to promptly identify five compounds found in both databases and 167 others worthy of further investigation.
Conclusion: Chemical and biological properties are determined by molecular structures. DBsimilarity enables the creation of interactive similarity networks using Cytoscape. It is also in line with a recent review that highlights poor biological plausibility and unrealistic chromatographic behaviors as significant sources of errors in compound identification.
(© 2023 John Wiley & Sons Ltd.)
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معلومات مُعتمدة: 0001 Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq); 001 Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES); 210.489/2019APQ-1 Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ)
فهرسة مساهمة: Keywords: chemoinformatics; dereplication; metabolomics; natural products; structure similarity
المشرفين على المادة: 0 (Biological Products)
0 (Plant Extracts)
0 (Anti-Bacterial Agents)
تواريخ الأحداث: Date Created: 20230818 Date Completed: 20240109 Latest Revision: 20240109
رمز التحديث: 20240109
DOI: 10.1002/pca.3277
PMID: 37592443
قاعدة البيانات: MEDLINE
الوصف
تدمد:1099-1565
DOI:10.1002/pca.3277