Increased diversity of peptidic natural products revealed by modification-tolerant database search of mass spectra

Abstract

Peptidic natural products (PNPs) include many antibiotics and other bioactive compounds. While the recent launch of the Global Natural Product Social (GNPS) molecular networking infrastructure is transforming PNP discovery into a high-throughput technology, PNP identification algorithms are needed to realize the potential of the GNPS project. GNPS relies on the assumption that each connected component of a molecular network (representing related metabolites) illuminates the “dark matter of metabolomics” as long as it contains a known metabolite present in a database. We reveal a surprising diversity of PNPs produced by related bacteria and show that, contrary to the “comparative metabolomics” assumption, two related bacteria are unlikely to produce identical PNPs (even though they are likely to produce similar PNPs). Since this observation undermines the utility of GNPS, we developed a PNP identification tool VarQuest that illuminates the connected components in a molecular network even if they do not contain known PNPs and only contain their variants. VarQuest revealed an order of magnitude more PNP variants than all previous PNP discovery efforts and demonstrated that GNPS already contains spectra from 41% of currently known PNP families. The enormous diversity of PNPs suggests that biosynthetic gene clusters in various microorganisms constantly evolve to generate a unique spectrum of PNP variants that differ from PNPs in other species.

Thinking Outside the Box—Novel Antibacterials To Tackle the Resistance Crisis

“…[17,18] Target-based whole-cell screenings include comparative profiling of,f or example,g enetically modified versus wildtype bacterial strains or the rescue of an antibiotic effect upon external supplementation, for example,o fametabolite. [105][106][107][108][109] Numerous HTS campaigns have been performed in various genetically modified E. coli reporter strains.…”

“…Bioinformatic approaches aim to take advantage of these huge data sets to identify new antibacterial compounds and potential new targets or to help clarify the mode of action of new compounds. [105][106][107][108][109]…”

Über bisherige Denkweisen hinaus – neue Wirkstoffe zur Überwindung der Antibiotika‐Krise

“…Bioinformatische Methoden haben das Ziel, diese großen Datensätze zu nutzen, um neue antibakterielle Verbindungen und potentielle neue zelluläre Targets zu identifizieren oder den Wirkmechanismus von neuen Verbindungen aufzuklären. [105][106][107][108][109]…”

Molecular networking as a dereplication strategy for monitoring metabolites of natural product treated cancer cells

“…Conventionally, spectra of a natural product obtained by liquid chromatography–mass spectrometry, nuclear magnetic resonance and infrared spectroscopy are interpreted based on prior knowledge, or at least “postulation” to the chemical structures of the analyte compounds . Recently, a dereplication strategy utilizing Global Natural Product Social (GNPS) molecular networking has been proposed to leverage the structural features of known compounds to decrypt the tandem mass spectra of unknown compounds . Specifically, cosine similarities among each pair of tandem mass spectra of individual specialized metabolites are calculated, of which the compounds with similar chemical structures are prone to cluster together .…”

“…13 Recently, a dereplication strategy utilizing Global Natural Product Social (GNPS) molecular networking has been proposed to leverage the structural features of known compounds to decrypt the tandem mass spectra of unknown compounds. [14][15][16][17] Specifically, cosine similarities among each pair of tandem mass spectra of individual specialized metabolites are calculated, of which the compounds with similar chemical structures are prone to cluster together. 17,18 This method provides an ability to rapidly categorize hundreds or thousands of specialized metabolomes collected from various organisms based on their chemical structures.…”