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Allard PM, Gaudry A, Quirós-Guerrero LM, Rutz A, Dounoue-Kubo M, Walker TWN, Defossez E, Long C, Grondin A, David B, Wolfender JL. Open and reusable annotated mass spectrometry dataset of a chemodiverse collection of 1,600 plant extracts. Gigascience 2023; 12:6980761. [PMID: 36649739 PMCID: PMC9845059 DOI: 10.1093/gigascience/giac124] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 09/15/2022] [Accepted: 11/29/2022] [Indexed: 01/19/2023] Open
Abstract
As privileged structures, natural products often display potent biological activities. However, the discovery of novel bioactive scaffolds is often hampered by the chemical complexity of the biological matrices they are found in. Large natural extract collections are thus extremely valuable for their chemical novelty potential but also complicated to exploit in the frame of drug-discovery projects. In the end, it is the pure chemical substances that are desired for structural determination purposes and bioactivity evaluation. Researchers interested in the exploration of large and chemodiverse extract collections should thus establish strategies aiming to efficiently tackle such chemical complexity and access these structures. Establishing carefully crafted digital layers documenting the spectral and chemical complexity as well as bioactivity results of natural extracts collections can help prioritize time-consuming but mandatory isolation efforts. In this note, we report the results of our initial exploration of a collection of 1,600 plant extracts in the frame of a drug-discovery effort. After describing the taxonomic coverage of this collection, we present the results of its liquid chromatography high-resolution mass spectrometric profiling and the exploitation of these profiles using computational solutions. The resulting annotated mass spectral dataset and associated chemical and taxonomic metadata are made available to the community, and data reuse cases are proposed. We are currently continuing our exploration of this plant extract collection for drug-discovery purposes (notably looking for novel antitrypanosomatids, anti-infective and prometabolic compounds) and ecometabolomics insights. We believe that such a dataset can be exploited and reused by researchers interested in computational natural products exploration.
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Affiliation(s)
- Pierre-Marie Allard
- Correspondence address. Pierre-Marie Allard, Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland. E-mail:
| | - Arnaud Gaudry
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211 Geneva, Switzerland,School of Pharmaceutical Sciences, University of Geneva, 1211 Geneva, Switzerland
| | - Luis-Manuel Quirós-Guerrero
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211 Geneva, Switzerland,School of Pharmaceutical Sciences, University of Geneva, 1211 Geneva, Switzerland
| | - Adriano Rutz
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211 Geneva, Switzerland,School of Pharmaceutical Sciences, University of Geneva, 1211 Geneva, Switzerland
| | - Miwa Dounoue-Kubo
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, 770-8514 Tokushima, Japan
| | - Tom W N Walker
- Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Emmanuel Defossez
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland,Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Christophe Long
- Direction Scientifique Naturactive, Pierre Fabre Medicament, 81100 Castres, France
| | - Antonio Grondin
- Green Mission Pierre Fabre, Institut de Recherche Pierre Fabre, 31562 Toulouse, France
| | - Bruno David
- Green Mission Pierre Fabre, Institut de Recherche Pierre Fabre, 31562 Toulouse, France
| | - Jean-Luc Wolfender
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211 Geneva, Switzerland,School of Pharmaceutical Sciences, University of Geneva, 1211 Geneva, Switzerland
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