Expert knowledge; MS/MS; Monoterpene indole alkaloids; Query; Scaffold; Similarity; Computer Science Applications; Physical and Theoretical Chemistry; Computer Graphics and Computer-Aided Design; Library and Information Sciences
Abstract :
[en] With over 3000 representatives, the monoterpene indole alkaloids (MIAs) class is among the most diverse families of plant natural products. The MS/MS spectral space exploration of these complex compounds using chemoinformatic and computational mass spectrometry tools offers a valuable opportunity to extract and share chemical insights from this emblematic family of natural products (NPs). In this work, we first present a substantially updated version of the MIADB, a database now containing 422 MS/MS spectra of MIAs that has been uploaded to the GNPS library versus 172 initial entries. We then introduce an innovative workflow that leverages hundreds of fragmentation spectra to support the FAIRification, extraction and dissemination of chemical knowledge. This workflow aims at the extraction of spectral patterns matching finely defined MIA skeletons. These extracted signatures can then be queried against complex biological extract datasets using MassQL. By applying this strategy to an LC-MS/MS dataset of 75 plant extracts, our results demonstrated the efficiency of this approach in identifying the diversity of MIA skeletons present in the analyzed samples. Additionally, our work enabled the digitization of structural data for diverse MIA skeletons by converting them into machine-readable formats and thereby enhancing their dissemination for the scientific community.Scientific contribution A comprehensive investigation of the monoterpene indole alkaloid chemical space, aiming to highlight skeleton-dependent fragmentation similarity trends and to generate valuable spectrometric signatures that could be used as queries.
Disciplines :
Pharmacy, pharmacology & toxicology
Author, co-author :
Szwarc, Sarah; Équipe, Chimie des Substances Naturelles, Université Paris-Saclay, CNRS, BioCIS, 17 avenue des Sciences, 91400, Orsay, France
Rutz, Adriano; Institute of Molecular Systems Biology, ETH Zürich, 8093, Zurich, Switzerland
Lee, Kyungha; College of Pharmacy and Research Institute of Pharmaceutical Sciences, Sookmyung Women's University, Seoul, 04310, Republic of Korea
Mejri, Yassine; Équipe, Chimie des Substances Naturelles, Université Paris-Saclay, CNRS, BioCIS, 17 avenue des Sciences, 91400, Orsay, France ; Université Paris-Dauphine, PSL Research University, CNRS, LAMSADE, 75016, PARIS, France
Bonnet, Olivier ; Université de Liège - ULiège > Unités de recherche interfacultaires > Centre Interdisciplinaire de Recherche sur le Médicament (CIRM)
Hazni, Hazrina; Department of Chemistry, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
Jagora, Adrien; Équipe, Chimie des Substances Naturelles, Université Paris-Saclay, CNRS, BioCIS, 17 avenue des Sciences, 91400, Orsay, France
Mbeng Obame, Rany B; Équipe, Chimie des Substances Naturelles, Université Paris-Saclay, CNRS, BioCIS, 17 avenue des Sciences, 91400, Orsay, France
Noh, Jin Kyoung; El Batan, Instituto de BioEconomia, Quito, 170135, Ecuador
Otogo N'Nang, Elvis; Département Science Fondamentale, Service Chimie-Biochimie, Université Des Sciences de La Santé, Owendo, Gabon
Alaribe, Stephenie C; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, College of Medicine, University of Lagos, Idiaraba Campus, Surulere, Lagos, Nigeria
Awang, Khalijah; Department of Chemistry, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
Bernadat, Guillaume; Équipe, Chimie des Substances Naturelles, Université Paris-Saclay, CNRS, BioCIS, 17 avenue des Sciences, 91400, Orsay, France
Choi, Young Hae; Natural Products Laboratory, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, the Netherlands
Courdavault, Vincent; EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Avenue Monge, 37200, Tours, France
Frederich, Michel ; Université de Liège - ULiège > Unités de recherche interfacultaires > Centre Interdisciplinaire de Recherche sur le Médicament (CIRM)
Gaslonde, Thomas; UMR 8038 CiTCoM, Faculté de Santé, Université Paris Cité, CNRS, 75006, Paris, France
Huber, Florian; Centre for Digitalisation and Digitality, Düsseldorf University of Applied Sciences, 40476, Düsseldorf, Germany
Kam, Toh-Seok; Department of Chemistry, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
Low, Yun Yee; Department of Chemistry, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
Poupon, Erwan; Équipe, Chimie des Substances Naturelles, Université Paris-Saclay, CNRS, BioCIS, 17 avenue des Sciences, 91400, Orsay, France
van der Hooft, Justin J J; Bioinformatics Group, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands ; Department of Biochemistry, University of Johannesburg, Johannesburg, 2006, South Africa
Kang, Kyo Bin; College of Pharmacy and Research Institute of Pharmaceutical Sciences, Sookmyung Women's University, Seoul, 04310, Republic of Korea
Le Pogam, Pierre; Équipe, Chimie des Substances Naturelles, Université Paris-Saclay, CNRS, BioCIS, 17 avenue des Sciences, 91400, Orsay, France. pierre.le-pogam-alluard@universite-paris-saclay.fr
Beniddir, Mehdi A; Équipe, Chimie des Substances Naturelles, Université Paris-Saclay, CNRS, BioCIS, 17 avenue des Sciences, 91400, Orsay, France. mehdi.beniddir@universite-paris-saclay.fr
ANR - Agence Nationale de la Recherche Campus France CNRS - Centre National de la Recherche Scientifique
Funding text :
This project has received financial support from the CNRS through the MITI interdisciplinary programs and was also supported by the National French Agency (ANR grant 20-CE43-0010) and by Campus France through STAR PHC fellowship. K.L. and K.B.K were supported by the National Research Foundation of Korea (NRF) grants funded by the Korean Government (Ministry of Science and ICT; 2021K1A3A1A21038059, 2022R1A5A2021216, 2022M3H9A2082952, and\u00A0RS-2024-00436674); Centre National de la Recherche Scientifique (MITIPRIME80); Ministry of Higher Education, Malaysia (FRGS/1/2020/SKK0/UM/01/5, FRGS/1/2023/STG04/UM/02/13).This work was also supported by the Korea Research Institute of Bioscience and Biotechnology (KRIBB) initiative program of Republic of Korea. We thank the Ethnobotanical Database of Bangladesh (EDB), Yunnan Academy of Agricultural Sciences (YAAS), the Instituto de BioEconomia, the National Biodiversity Institute of Costa Rica (INBio), the Institute of Traditional Medicine (ITM), the Universidad Nacional Aut\u00F3noma de Nicaragua (UNAN-Leon), the Universiti Putra Malaysia (UPM), the Institute of Ecology and Biological Resources (IEBR), University of Lagos, Nigeria, and International Biological Material Research Center (IBMRC) of KRIBB for providing the various plant extracts. Georges Massiot (Universit\u00E9 de Reims Champagne-Ardenne) is acknowledged for the three standards that contributed to enrich the MIADB.This project has received financial support from the CNRS through the MITI interdisciplinary programs and was also supported by the National French Agency (ANR grant 20-CE43-0010) and by Campus France through STAR PHC fellowship. K.L. and K.B.K were supported by the National Research Foundation of Korea (NRF) grants funded by the Korean Government (Ministry of Science and ICT; 2021K1A3A1A21038059, 2022R1A5A2021216, 2022M3H9A2082952, and RS-2024-00436674); Centre National de la Recherche Scientifique (MITIPRIME80); Ministry of Higher Education, Malaysia (FRGS/1/2020/SKK0/UM/01/5, FRGS/1/2023/STG04/UM/02/13).
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