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Cited by 433Mass Spectrometry Techniques and ApplicationsComputational Drug Discovery MethodsMetabolomics and Mass Spectrometry Studies

Bioactivity-Based Molecular Networking for the Discovery of Drug Leads in Natural Product Bioassay-Guided Fractionation

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Nothias, Louis-Félix, Nothias-Esposito, Mélissa, da Silva, Ricardo, Wang, Mingxun, Protsyuk, Ivan, Zhang, Zheng, Sarvepalli, Abi, Leyssen, Pieter +6 more·2018·Journal of Natural Products
DOI 10.1021/acs.jnatprod.7b00737
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Abstract

It is a common problem in natural product therapeutic lead discovery programs that despite good bioassay results in the initial extract, the active compound(s) may not be isolated during subsequent bioassay-guided purification. Herein, we present the concept of bioactive molecular networking to find candidate active molecules directly from fractionated bioactive extracts. By employing tandem mass spectrometry, it is possible to accelerate the dereplication of molecules using molecular networking prior to subsequent isolation of the compounds, and it is also possible to expose potentially bioactive molecules using bioactivity score prediction. Indeed, bioactivity score prediction can be calculated with the relative abundance of a molecule in fractions and the bioactivity level of each fraction. For that reason, we have developed a bioinformatic workflow able to map bioactivity score in molecular networks and applied it for discovery of antiviral compounds from a previously investigated extract of Euphorbia dendroides where the bioactive candidate molecules were not discovered following a classical bioassay-guided fractionation procedure. It can be expected that this approach will be implemented as a systematic strategy, not only in current and future bioactive lead discovery from natural extract collections but also for the reinvestigation of the untapped reservoir of bioactive analogues in previous bioassay-guided fractionation efforts.

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  • Bioactivity-based molecular networking approaches have been successful in guiding the isolation of novel compounds with specific activity, such as antibacterial or antiviral activity.

    “These approaches have been successful in guiding the isolation of novel compounds with specific activity (e.g., antibacterial or antiviral).”

    From Connecting metabolome and phenotype: recent advances in functional metabolomics tools for the identification of bioactive natural products (2024) · cites this paper as [32]

    The results (p. 5) report that bioactive molecular networking guided the isolation of four new compounds, two of which selectively inhibited chikungunya virus replication. This supports the antiviral example, but our copy does not show that the approach guided isolation of antibacterial compounds. (LLM, conf=0.84)

    Experimental — accuracy not yet measured

  • Synergistic or antagonistic activity between two or more natural products presents a challenge as the assumption of response of bioactivity and molecule concentration may be broken.

    “Synergistic or antagonistic activity between two or more natural products presents a challenge as the assumption of response of bioactivity and molecule concentration may be broken.32”

    From Connecting metabolome and phenotype: recent advances in functional metabolomics tools for the identification of bioactive natural products (2024) · cites this paper as [32]

    The introduction (p. 1) identifies synergistic effects between multiple compounds as a reason bioassay-guided fractionation can fail. The paper defines its bioactivity score as a correlation between a molecule’s abundance and a fraction’s activity (p. 4), but our copy does not say that synergy breaks that relationship or identify antagonism as a challenge. (LLM, conf=0.82)

    Experimental — accuracy not yet measured

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Authors
Nothias, L.-F., Nothias-Esposito, M., da Silva, R., Wang, M., Protsyuk, I., Zhang, Z., Sarvepalli, A., Leyssen, P., Touboul, D., Costa, J., Paolini, J., Alexandrov, T., Litaudon, M., & Dorrestein, P. C.
Affiliations
  • University of California, San Diego , , , ,
  • Université Paris-Sud , , , ,
  • University of California San Diego (US)
  • European Molecular Biology Laboratory (ES)
  • Rega Institute for Medical Research (BE)
  • Université Paris-Sud (FR)
  • Centre National de la Recherche Scientifique (FR)
Corresponding author
Dorrestein, Pieter C.
ORCID
Venue
Journal of Natural Products
Publisher
American Chemical Society (ACS)
Published
2018-03-02
Volume
81
Issue
4
Pages
758-767
ISSN
  • 0163-3864 (ISSN-L)
  • 1520-6025
DOI
10.1021/acs.jnatprod.7b00737
OpenAlex
W2790225116
Cited by
433
References
66
Citations by year
2026: 64 · 2025: 70 · 2024: 62 · 2023: 43 · 2022: 58 · 2021: 42 · 2020: 44 · 2019: 39 · 2018: 11
FWCI
14.79
Type
journal article
Language
en
Open access
Licence
Locations
  • Journal of Natural Products (publishedVersion, other-oa)
  • PubMed (publishedVersion)
  • Lirias (KU Leuven) (submittedVersion, other-oa)
  • HAL (submittedVersion)
Funders
  • H2020 Marie Sklodowska-Curie Actions (704786)
  • H2020 Health (634402)
  • Agence Nationale de la Recherche (ANR-10-LABX-25-01, ANR-16-CE29-0002-01)
Topics
  • Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
  • Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
Keywords
dereplication, bioassay-guided fractionation, lead compound identification, natural products, tandem mass spectrometry, antiviral agents, Euphorbia dendroides, bioactive compound isolation
MeSH terms
Biological Assay, Biological Products, Plant Extracts, Euphorbia, Tandem Mass Spectrometry, Drug Discovery

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