Nucleophilic 1,4-Additions for Natural Product Discovery
Open accessAbstract
Natural products remain an important source of drug candidates, but the difficulties inherent to traditional isolation, coupled with unacceptably high rates of compound rediscovery, limit the pace of natural product detection. Here we describe a reactivity-based screening method to rapidly identify exported bacterial metabolites that contain dehydrated amino acids (i.e., carbonyl- or imine-activated alkenes), a common motif in several classes of natural products. Our strategy entails the use of a commercially available thiol, dithiothreitol, for the covalent labeling of activated alkenes by nucleophilic 1,4-addition. Modification is easily discerned by comparing mass spectra of reacted and unreacted cell surface extracts. When combined with bioinformatic analysis of putative natural product gene clusters, targeted screening and isolation can be performed on a prioritized list of strains. Moreover, known compounds are easily dereplicated, effectively eliminating superfluous isolation and characterization. As a proof of principle, this labeling method was used to identify known natural products belonging to the thiopeptide, lanthipeptide, and linaridin classes. Further, upon screening a panel of only 23 actinomycetes, we discovered and characterized a novel thiopeptide antibiotic, cyclothiazomycin C.
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Numerous thiol containing chemical probes have been utilized to detect these functional groups in a targeted fashion.
“Over the years, mimicking this unique reactivity has turned into a strategy to detect these functional groups in a targeted fashion, for this purpose numerous thiol containing chemical probes (e.g., glutathione, mercaptoethanol, 4-chlorothiophenol),122–124 have been utilized.”
From Connecting metabolome and phenotype: recent advances in functional metabolomics tools for the identification of bioactive natural products (2024) · cites this paper as [124]
The Results and Discussion (‘Rationale and overview of a new natural product discovery method’; page not provided) describe using the thiol probe dithiothreitol to detect dehydrated amino acid–containing natural products. The paper supports the targeted-detection strategy, but it does not establish the use of numerous probes or the listed examples—glutathione, mercaptoethanol, and 4-chlorothiophenol. (LLM, conf=0.86)
Experimental — accuracy not yet measuredThe practice of labeling functional groups in uncharacterized NP mixtures using a non-targeted metabolomics approach is uncommon in NP discovery, and there are currently only a few existing examples.
“Although these approaches have been in certain cases efficiently applied for NP discovery, the practice of labeling functional groups in uncharacterized NP mixtures using a non-targeted metabolomics approach is uncommon in NP discovery, and there are currently only a few existing examples.124–128”
From Connecting metabolome and phenotype: recent advances in functional metabolomics tools for the identification of bioactive natural products (2024) · cites this paper as [124]
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- Authors
- Cox, C. L., Tietz, J. I., Sokolowski, K., Melby, J. O., Doroghazi, J. R., & Mitchell, D. A.
- Affiliations
- University of Illinois Urbana-Champaign (US)
- Corresponding author
- Mitchell, Douglas A.
- Venue
- ACS Chemical Biology
- Publisher
- American Chemical Society (ACS)
- Published
- 2014-06-17
- Volume
- 9
- Issue
- 9
- Pages
- 2014-2022
- ISSN
- 1554-8929 (ISSN-L)
- 1554-8937
- PMC
- PMC4168802
- OpenAlex
- W1978333914
- Cited by
- 63
- References
- 54
- Citations by year
- 2026: 2 · 2025: 2 · 2024: 5 · 2022: 4 · 2021: 10 · 2020: 10 · 2019: 11 · 2018: 5 · 2017: 5 · 2016: 5 · 2015: 4
- FWCI
- 3.40
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- ACS Chemical Biology (publishedVersion, other-oa)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health (1dp2od008463-01)
- National Center for Research Resources (S10 RR027109 A, S10RR027109)
- Topics
- Health Sciences › Medicine › Pharmacology › Microbial Natural Products and Biosynthesis
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chemical Synthesis and Analysis
- Keywords
- natural product discovery, activated alkenes, dereplication, thiopeptides, lanthipeptides, actinomycetes, covalent labeling
- MeSH terms
- Amino Acids, Anti-Bacterial Agents, Bacteriocins, Biological Products, Dithiothreitol, Drug Evaluation, Preclinical, Ethylamines, Multigene Family, Peptides, Cyclic, Mass Spectrometry, Thiazoles, Thiostrepton, Reproducibility of Results, Molecular Structure, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Computational Biology, Actinobacteria, Drug Discovery
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