The Three Pillars of Natural Product Dereplication. Alkaloids from the Bulbs of <i>Urceolina peruviana</i> (C. Presl) J.F. Macbr. as a Preliminary Test Case
The role and importance of the identification of natural products are discussed in the perspective of the study of secondary metabolites. The rapid identification of already reported compounds, or structural dereplication, is recognized as a key element in natural product chemistry. The biological t...
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doaj-952981a91008416184415fa8f1519b402021-01-27T00:06:22ZengMDPI AGMolecules1420-30492021-01-012663763710.3390/molecules26030637The Three Pillars of Natural Product Dereplication. Alkaloids from the Bulbs of <i>Urceolina peruviana</i> (C. Presl) J.F. Macbr. as a Preliminary Test CaseMariacaterina Lianza0Ritchy Leroy1Carine Machado Rodrigues2Nicolas Borie3Charlotte Sayagh4Simon Remy5Stefan Kuhn6Jean-Hugues Renault7Jean-Marc Nuzillard8Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, ItalyUniversité de Reims Champagne Ardenne, CNRS, ICMR UMR 7312, 51097 Reims, FranceUniversité de Reims Champagne Ardenne, CNRS, ICMR UMR 7312, 51097 Reims, FranceUniversité de Reims Champagne Ardenne, CNRS, ICMR UMR 7312, 51097 Reims, FranceUniversité de Reims Champagne Ardenne, CNRS, ICMR UMR 7312, 51097 Reims, FranceUniversité de Reims Champagne Ardenne, CNRS, ICMR UMR 7312, 51097 Reims, FranceSchool of Computer Science and Informatics, De Montfort University, Leicester LE1 9BH, UKUniversité de Reims Champagne Ardenne, CNRS, ICMR UMR 7312, 51097 Reims, FranceUniversité de Reims Champagne Ardenne, CNRS, ICMR UMR 7312, 51097 Reims, FranceThe role and importance of the identification of natural products are discussed in the perspective of the study of secondary metabolites. The rapid identification of already reported compounds, or structural dereplication, is recognized as a key element in natural product chemistry. The biological taxonomy of metabolite producing organisms, the knowledge of metabolite molecular structures, and the availability of metabolite spectroscopic signatures are considered as the three pillars of structural dereplication. The role and the construction of databases is illustrated by references to the KNApSAcK, UNPD, CSEARCH, and COCONUT databases, and by the importance of calculated taxonomic and spectroscopic data as substitutes for missing or lost original ones. Two NMR-based tools, the PNMRNP database that derives from UNPD, and KnapsackSearch, a database generator that provides taxonomically focused libraries of compounds, are proposed to the community of natural product chemists. The study of the alkaloids from <i>Urceolina peruviana</i>, a plant from the Andes used in traditional medicine for antibacterial and anticancer actions, has given the opportunity to test different approaches to dereplication, favoring the use of publicly available data sources.https://www.mdpi.com/1420-3049/26/3/637natural productsdereplicationdatabasesspectroscopytaxonomymolecular structures |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Mariacaterina Lianza Ritchy Leroy Carine Machado Rodrigues Nicolas Borie Charlotte Sayagh Simon Remy Stefan Kuhn Jean-Hugues Renault Jean-Marc Nuzillard |
spellingShingle |
Mariacaterina Lianza Ritchy Leroy Carine Machado Rodrigues Nicolas Borie Charlotte Sayagh Simon Remy Stefan Kuhn Jean-Hugues Renault Jean-Marc Nuzillard The Three Pillars of Natural Product Dereplication. Alkaloids from the Bulbs of <i>Urceolina peruviana</i> (C. Presl) J.F. Macbr. as a Preliminary Test Case Molecules natural products dereplication databases spectroscopy taxonomy molecular structures |
author_facet |
Mariacaterina Lianza Ritchy Leroy Carine Machado Rodrigues Nicolas Borie Charlotte Sayagh Simon Remy Stefan Kuhn Jean-Hugues Renault Jean-Marc Nuzillard |
author_sort |
Mariacaterina Lianza |
title |
The Three Pillars of Natural Product Dereplication. Alkaloids from the Bulbs of <i>Urceolina peruviana</i> (C. Presl) J.F. Macbr. as a Preliminary Test Case |
title_short |
The Three Pillars of Natural Product Dereplication. Alkaloids from the Bulbs of <i>Urceolina peruviana</i> (C. Presl) J.F. Macbr. as a Preliminary Test Case |
title_full |
The Three Pillars of Natural Product Dereplication. Alkaloids from the Bulbs of <i>Urceolina peruviana</i> (C. Presl) J.F. Macbr. as a Preliminary Test Case |
title_fullStr |
The Three Pillars of Natural Product Dereplication. Alkaloids from the Bulbs of <i>Urceolina peruviana</i> (C. Presl) J.F. Macbr. as a Preliminary Test Case |
title_full_unstemmed |
The Three Pillars of Natural Product Dereplication. Alkaloids from the Bulbs of <i>Urceolina peruviana</i> (C. Presl) J.F. Macbr. as a Preliminary Test Case |
title_sort |
three pillars of natural product dereplication. alkaloids from the bulbs of <i>urceolina peruviana</i> (c. presl) j.f. macbr. as a preliminary test case |
publisher |
MDPI AG |
series |
Molecules |
issn |
1420-3049 |
publishDate |
2021-01-01 |
description |
The role and importance of the identification of natural products are discussed in the perspective of the study of secondary metabolites. The rapid identification of already reported compounds, or structural dereplication, is recognized as a key element in natural product chemistry. The biological taxonomy of metabolite producing organisms, the knowledge of metabolite molecular structures, and the availability of metabolite spectroscopic signatures are considered as the three pillars of structural dereplication. The role and the construction of databases is illustrated by references to the KNApSAcK, UNPD, CSEARCH, and COCONUT databases, and by the importance of calculated taxonomic and spectroscopic data as substitutes for missing or lost original ones. Two NMR-based tools, the PNMRNP database that derives from UNPD, and KnapsackSearch, a database generator that provides taxonomically focused libraries of compounds, are proposed to the community of natural product chemists. The study of the alkaloids from <i>Urceolina peruviana</i>, a plant from the Andes used in traditional medicine for antibacterial and anticancer actions, has given the opportunity to test different approaches to dereplication, favoring the use of publicly available data sources. |
topic |
natural products dereplication databases spectroscopy taxonomy molecular structures |
url |
https://www.mdpi.com/1420-3049/26/3/637 |
work_keys_str_mv |
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