Advanced Methods for Natural Products Discovery: Bioactivity Screening, Dereplication, Metabolomics Profiling, Genomic Sequencing, Databases and Informatic Tools, and Structure Elucidation

Natural Products (NP) are essential for the discovery of novel drugs and products for numerous biotechnological applications. The NP discovery process is expensive and time-consuming, having as major hurdles dereplication (early identification of known compounds) and structure elucidation, particula...

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Autores: Gaudêncio, Susana P., Bayram, Engin, Bilela, Lada Lukic, Cueto, Mercedes, Díaz-Marrero, Ana Raquel, Haznedaroglu, Berat Z., Jimenez, Carlos, Mandalakis, Manolis, Pereira, Florbela, Reyes, Fernando, Tasdemir, Deniz
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2023
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:dnet:digitalcsic_::3ed9b331448ff27ac42d1918a9005b89
Acceso en línea:http://hdl.handle.net/10261/309327
Access Level:acceso abierto
Palabra clave:Blue biotechnology
Natural products
high-throughput screening (HTS)
mode of action (MoA)
molecular networking
dereplication
natural products databases
Global Natural Product Social Molecular Networking (GNPS)
informatic chemometrics
high-throughput genome sequencing (HTGS)
computer assisted structure elucidation (CASE)
relative and absolute configuration determination in structure elucidation
http://metadata.un.org/sdg/3
Ensure healthy lives and promote well-being for all at all ages
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dc.title.none.fl_str_mv Advanced Methods for Natural Products Discovery: Bioactivity Screening, Dereplication, Metabolomics Profiling, Genomic Sequencing, Databases and Informatic Tools, and Structure Elucidation
title Advanced Methods for Natural Products Discovery: Bioactivity Screening, Dereplication, Metabolomics Profiling, Genomic Sequencing, Databases and Informatic Tools, and Structure Elucidation
spellingShingle Advanced Methods for Natural Products Discovery: Bioactivity Screening, Dereplication, Metabolomics Profiling, Genomic Sequencing, Databases and Informatic Tools, and Structure Elucidation
Gaudêncio, Susana P.
Blue biotechnology
Natural products
high-throughput screening (HTS)
mode of action (MoA)
molecular networking
dereplication
natural products databases
Global Natural Product Social Molecular Networking (GNPS)
informatic chemometrics
high-throughput genome sequencing (HTGS)
computer assisted structure elucidation (CASE)
relative and absolute configuration determination in structure elucidation
http://metadata.un.org/sdg/3
Ensure healthy lives and promote well-being for all at all ages
title_short Advanced Methods for Natural Products Discovery: Bioactivity Screening, Dereplication, Metabolomics Profiling, Genomic Sequencing, Databases and Informatic Tools, and Structure Elucidation
title_full Advanced Methods for Natural Products Discovery: Bioactivity Screening, Dereplication, Metabolomics Profiling, Genomic Sequencing, Databases and Informatic Tools, and Structure Elucidation
title_fullStr Advanced Methods for Natural Products Discovery: Bioactivity Screening, Dereplication, Metabolomics Profiling, Genomic Sequencing, Databases and Informatic Tools, and Structure Elucidation
title_full_unstemmed Advanced Methods for Natural Products Discovery: Bioactivity Screening, Dereplication, Metabolomics Profiling, Genomic Sequencing, Databases and Informatic Tools, and Structure Elucidation
title_sort Advanced Methods for Natural Products Discovery: Bioactivity Screening, Dereplication, Metabolomics Profiling, Genomic Sequencing, Databases and Informatic Tools, and Structure Elucidation
dc.creator.none.fl_str_mv Gaudêncio, Susana P.
Bayram, Engin
Bilela, Lada Lukic
Cueto, Mercedes
Díaz-Marrero, Ana Raquel
Haznedaroglu, Berat Z.
Jimenez, Carlos
Mandalakis, Manolis
Pereira, Florbela
Reyes, Fernando
Tasdemir, Deniz
author Gaudêncio, Susana P.
author_facet Gaudêncio, Susana P.
Bayram, Engin
Bilela, Lada Lukic
Cueto, Mercedes
Díaz-Marrero, Ana Raquel
Haznedaroglu, Berat Z.
Jimenez, Carlos
Mandalakis, Manolis
Pereira, Florbela
Reyes, Fernando
Tasdemir, Deniz
author_role author
author2 Bayram, Engin
Bilela, Lada Lukic
Cueto, Mercedes
Díaz-Marrero, Ana Raquel
Haznedaroglu, Berat Z.
Jimenez, Carlos
Mandalakis, Manolis
Pereira, Florbela
Reyes, Fernando
Tasdemir, Deniz
author2_role author
author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv European Cooperation in Science and Technology
Fundação para a Ciência e a Tecnologia (Portugal)
European Commission
Ministerio de Ciencia e Innovación (España)
Agencia Estatal de Investigación (España)
Consejo Superior de Investigaciones Científicas (España)
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Blue biotechnology
Natural products
high-throughput screening (HTS)
mode of action (MoA)
molecular networking
dereplication
natural products databases
Global Natural Product Social Molecular Networking (GNPS)
informatic chemometrics
high-throughput genome sequencing (HTGS)
computer assisted structure elucidation (CASE)
relative and absolute configuration determination in structure elucidation
http://metadata.un.org/sdg/3
Ensure healthy lives and promote well-being for all at all ages
topic Blue biotechnology
Natural products
high-throughput screening (HTS)
mode of action (MoA)
molecular networking
dereplication
natural products databases
Global Natural Product Social Molecular Networking (GNPS)
informatic chemometrics
high-throughput genome sequencing (HTGS)
computer assisted structure elucidation (CASE)
relative and absolute configuration determination in structure elucidation
http://metadata.un.org/sdg/3
Ensure healthy lives and promote well-being for all at all ages
description Natural Products (NP) are essential for the discovery of novel drugs and products for numerous biotechnological applications. The NP discovery process is expensive and time-consuming, having as major hurdles dereplication (early identification of known compounds) and structure elucidation, particularly the determination of the absolute configuration of metabolites with stereogenic centers. This review comprehensively focuses on recent technological and instrumental advances, highlighting the development of methods that alleviate these obstacles, paving the way for accelerating NP discovery towards biotechnological applications. Herein, we emphasize the most innovative high-throughput tools and methods for advancing bioactivity screening, NP chemical analysis, dereplication, metabolite profiling, metabolomics, genome sequencing and/or genomics approaches, databases, bioinformatics, chemoinformatics, and three-dimensional NP structure elucidation.
publishDate 2023
dc.date.none.fl_str_mv 2023
2023
2023
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/309327
url http://hdl.handle.net/10261/309327
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
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info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/RTI2018-093634-B-C22
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2020-115979RR-C32
https://doi.org/10.3390/md21050308
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Multidisciplinary Digital Publishing Institute
publisher.none.fl_str_mv Multidisciplinary Digital Publishing Institute
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
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spelling Advanced Methods for Natural Products Discovery: Bioactivity Screening, Dereplication, Metabolomics Profiling, Genomic Sequencing, Databases and Informatic Tools, and Structure ElucidationGaudêncio, Susana P.Bayram, EnginBilela, Lada LukicCueto, MercedesDíaz-Marrero, Ana RaquelHaznedaroglu, Berat Z.Jimenez, CarlosMandalakis, ManolisPereira, FlorbelaReyes, FernandoTasdemir, DenizBlue biotechnologyNatural productshigh-throughput screening (HTS)mode of action (MoA)molecular networkingdereplicationnatural products databasesGlobal Natural Product Social Molecular Networking (GNPS)informatic chemometricshigh-throughput genome sequencing (HTGS)computer assisted structure elucidation (CASE)relative and absolute configuration determination in structure elucidationhttp://metadata.un.org/sdg/3Ensure healthy lives and promote well-being for all at all agesNatural Products (NP) are essential for the discovery of novel drugs and products for numerous biotechnological applications. The NP discovery process is expensive and time-consuming, having as major hurdles dereplication (early identification of known compounds) and structure elucidation, particularly the determination of the absolute configuration of metabolites with stereogenic centers. This review comprehensively focuses on recent technological and instrumental advances, highlighting the development of methods that alleviate these obstacles, paving the way for accelerating NP discovery towards biotechnological applications. Herein, we emphasize the most innovative high-throughput tools and methods for advancing bioactivity screening, NP chemical analysis, dereplication, metabolite profiling, metabolomics, genome sequencing and/or genomics approaches, databases, bioinformatics, chemoinformatics, and three-dimensional NP structure elucidation.This publication is based upon work from COST Action CA18238 (Ocean4Biotech), funded by the European Cooperation in Science and Technology (COST) Program in the period 2019–2023. SPG: This work is financed by national funds from FCT—Fundação para a Ciência e a Tecnologia, I.P., in the scope of the projects UIDP/04378/2020 and UIDB/04378/2020 of the Research Unit on Applied Molecular Biosciences—UCIBIO and the project LA/P/0140/2020 of the Associate Laboratory Institute for Health and Bioeconomy—i4HB. LLB: The publication is part of a project that has received funding from the Erasmus + Project No. ECOBIAS_609967-EPP-1-2019-1-RS-EPPKA2-CBHE-JP; GA.2019-1991/001-001. Development of master curricula in ecological monitoring and aquatic bioassessment for Western Balkans HEIs/ECOBIAS. CJ: This work was supported by grants PID2021-122732OB-C22 from MCIN/AEI/10.13039/501100011033/FEDER “A way to make Europe” (AEI, Spanish State Agency for Research and FEDER Programme from the European Union) and RTI2018-093634-B-C22 from the State Agency for Research (AEI) of Spain, co-funded by the FEDER Programme from the European Union, and BLUEBIOLAB (0474_BLUEBIOLAB_1_E), Programme INTERREG V A of Spain-Portugal (POCTEP). FP: This work is financed by national funds from FCT—Fundação para a Ciência e a Tecnologia, I.P., in the scope of the project UIDB/50006/2020 of the Research Unit on Associated Laboratory for Green Chemistry (LAQV) of the Network of Chemistry and Technology (REQUIMTE) and for an Assistant Research Position (CEECIND/01649/2021). MC: INTERREG-MAC2/1.1b/279 (AHIDAGRO) and the Ministerio de Ciencia e Innovación (Spain) (grant PID2020-115979RR-C32). ARDM is supported with funds from Proyecto Intramural Especial CSIC [Ref. 202280I032].Peer reviewedMultidisciplinary Digital Publishing InstituteEuropean Cooperation in Science and TechnologyFundação para a Ciência e a Tecnologia (Portugal)European CommissionMinisterio de Ciencia e Innovación (España)Agencia Estatal de Investigación (España)Consejo Superior de Investigaciones Científicas (España)Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202320232023info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/309327reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PID2021-122732OB-C22info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/RTI2018-093634-B-C22info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2020-115979RR-C32https://doi.org/10.3390/md21050308Síinfo:eu-repo/semantics/openAccessoai:dnet:digitalcsic_::3ed9b331448ff27ac42d1918a9005b892026-05-22T06:33:51Z
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