Dereplication of microbial metabolites through database search of mass spectra

Hosein Mohimani, Алексей Александрович Гуревич, Александр Юрьевич Шлемов, Алла Александровна Михеенко, Антон Иванович Коробейников, Liu Cao, Егор Щербин, Louis-Felix Nothias, P. C. Dorrestein, Павел Аркадьевич Певзнер

Research output

18 Citations (Scopus)

Abstract

Natural products have traditionally been rich sources for drug discovery. In order to clear the road toward the discovery of unknown natural products, biologists need dereplication strategies that identify known ones. Here we report DEREPLICATOR+, an algorithm that improves on the previous approaches for identifying peptidic natural products, and extends them for identification of polyketides, terpenes, benzenoids, alkaloids, flavonoids, and other classes of natural products. We show that DEREPLICATOR+ can search all spectra in the recently launched Global Natural Products Social molecular network and identify an order of magnitude more natural products than previous dereplication efforts. We further demonstrate that DEREPLICATOR+ enables cross-validation of genome-mining and peptidogenomics/glycogenomics results.

Original languageEnglish
Article number4035
Number of pages12
JournalNature Communications
Volume9
Issue number1
DOIs
Publication statusPublished - 1 Dec 2018

Fingerprint

metabolites
Metabolites
Biological Products
mass spectra
Databases
products
terpenes
Polyketides
alkaloids
genome
Terpenes
Drug Discovery
roads
Alkaloids
Flavonoids
Social Support
drugs
Genes
Genome

Scopus subject areas

  • Physics and Astronomy(all)
  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Mohimani, H., Гуревич, А. А., Шлемов, А. Ю., Михеенко, А. А., Коробейников, А. И., Cao, L., ... Певзнер, П. А. (2018). Dereplication of microbial metabolites through database search of mass spectra. Nature Communications, 9(1), [4035]. https://doi.org/10.1038/s41467-018-06082-8
Mohimani, Hosein ; Гуревич, Алексей Александрович ; Шлемов, Александр Юрьевич ; Михеенко, Алла Александровна ; Коробейников, Антон Иванович ; Cao, Liu ; Щербин, Егор ; Nothias, Louis-Felix ; Dorrestein, P. C. ; Певзнер, Павел Аркадьевич. / Dereplication of microbial metabolites through database search of mass spectra. In: Nature Communications. 2018 ; Vol. 9, No. 1.
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abstract = "Natural products have traditionally been rich sources for drug discovery. In order to clear the road toward the discovery of unknown natural products, biologists need dereplication strategies that identify known ones. Here we report DEREPLICATOR+, an algorithm that improves on the previous approaches for identifying peptidic natural products, and extends them for identification of polyketides, terpenes, benzenoids, alkaloids, flavonoids, and other classes of natural products. We show that DEREPLICATOR+ can search all spectra in the recently launched Global Natural Products Social molecular network and identify an order of magnitude more natural products than previous dereplication efforts. We further demonstrate that DEREPLICATOR+ enables cross-validation of genome-mining and peptidogenomics/glycogenomics results.",
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Mohimani, H, Гуревич, АА, Шлемов, АЮ, Михеенко, АА, Коробейников, АИ, Cao, L, Щербин, Е, Nothias, L-F, Dorrestein, PC & Певзнер, ПА 2018, 'Dereplication of microbial metabolites through database search of mass spectra', Nature Communications, vol. 9, no. 1, 4035. https://doi.org/10.1038/s41467-018-06082-8

Dereplication of microbial metabolites through database search of mass spectra. / Mohimani, Hosein; Гуревич, Алексей Александрович; Шлемов, Александр Юрьевич; Михеенко, Алла Александровна; Коробейников, Антон Иванович; Cao, Liu; Щербин, Егор; Nothias, Louis-Felix; Dorrestein, P. C.; Певзнер, Павел Аркадьевич.

In: Nature Communications, Vol. 9, No. 1, 4035, 01.12.2018.

Research output

TY - JOUR

T1 - Dereplication of microbial metabolites through database search of mass spectra

AU - Mohimani, Hosein

AU - Гуревич, Алексей Александрович

AU - Шлемов, Александр Юрьевич

AU - Михеенко, Алла Александровна

AU - Коробейников, Антон Иванович

AU - Cao, Liu

AU - Щербин, Егор

AU - Nothias, Louis-Felix

AU - Dorrestein, P. C.

AU - Певзнер, Павел Аркадьевич

PY - 2018/12/1

Y1 - 2018/12/1

N2 - Natural products have traditionally been rich sources for drug discovery. In order to clear the road toward the discovery of unknown natural products, biologists need dereplication strategies that identify known ones. Here we report DEREPLICATOR+, an algorithm that improves on the previous approaches for identifying peptidic natural products, and extends them for identification of polyketides, terpenes, benzenoids, alkaloids, flavonoids, and other classes of natural products. We show that DEREPLICATOR+ can search all spectra in the recently launched Global Natural Products Social molecular network and identify an order of magnitude more natural products than previous dereplication efforts. We further demonstrate that DEREPLICATOR+ enables cross-validation of genome-mining and peptidogenomics/glycogenomics results.

AB - Natural products have traditionally been rich sources for drug discovery. In order to clear the road toward the discovery of unknown natural products, biologists need dereplication strategies that identify known ones. Here we report DEREPLICATOR+, an algorithm that improves on the previous approaches for identifying peptidic natural products, and extends them for identification of polyketides, terpenes, benzenoids, alkaloids, flavonoids, and other classes of natural products. We show that DEREPLICATOR+ can search all spectra in the recently launched Global Natural Products Social molecular network and identify an order of magnitude more natural products than previous dereplication efforts. We further demonstrate that DEREPLICATOR+ enables cross-validation of genome-mining and peptidogenomics/glycogenomics results.

KW - BIOSYNTHESIS

KW - COLLISIONALLY ACTIVATED DISSOCIATION

KW - DRUG DISCOVERY

KW - GENE CLUSTERS

KW - MOLECULAR NETWORKING

KW - PEPTIDIC NATURAL-PRODUCTS

KW - PROTEIN IDENTIFICATION

KW - SPECTROMETRY DATA

KW - STREPTOMYCES-ROSEOSPORUS

KW - STRUCTURE ELUCIDATION

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UR - http://www.mendeley.com/research/dereplication-microbial-metabolites-through-database-search-mass-spectra

U2 - 10.1038/s41467-018-06082-8

DO - 10.1038/s41467-018-06082-8

M3 - Article

C2 - 30279420

VL - 9

JO - Nature Communications

JF - Nature Communications

SN - 2041-1723

IS - 1

M1 - 4035

ER -

Mohimani H, Гуревич АА, Шлемов АЮ, Михеенко АА, Коробейников АИ, Cao L et al. Dereplication of microbial metabolites through database search of mass spectra. Nature Communications. 2018 Dec 1;9(1). 4035. https://doi.org/10.1038/s41467-018-06082-8