A metabolomics guided exploration of marine natural product chemical space

Abstract

Introduction: Natural products from culture collections have enormous impact in advancing discovery programs for metabolites of biotechnological importance. These discovery efforts rely on the metabolomic characterization of strain collections.

Objective: Many emerging approaches compare metabolomic profiles of such collections, but few enable the analysis and prioritization of thousands of samples from diverse organisms while delivering chemistry specific read outs.

Method: In this work we utilize untargeted LC-MS/MS based metabolomics together with molecular networking to.

Result: This approach annotated 76 molecular families (a spectral match rate of 28 %), including clinically and biotechnologically important molecules such as valinomycin, actinomycin D, and desferrioxamine E. Targeting a molecular family produced primarily by one microorganism led to the isolation and structure elucidation of two new molecules designated maridric acids A and B.

Conclusion: Molecular networking guided exploration of large culture collections allows for rapid dereplication of know molecules and can highlight producers of uniques metabolites. These methods, together with large culture collections and growing databases, allow for data driven strain prioritization with a focus on novel chemistries.

Keywords: Marine natural products; Mass spectrometry; Metabolomics; Molecular networking.

Fig. 1

Here we show global relationships among samples through three extractions Acetonitrile/Methanol, ethyl acetate/methanol, and butanol (green, purple, and red, respectively) in PCoA space. a Media controls in grey cluster together with their corresponding extracts. The compound level inventory is displayed in the molecular network b with families containing compounds of interest boxed and the nodes with library annotations highlighted in yellow. The most notable include: valinomycin (1), nonactins (2), glucopericidin (3), actinomycin D (4), alteramide A and B (5), lobophorin (6), acyl and amphipathic (des)ferrioxamines (7), echinomycin (8), streptorubin and undecylprodiginine (9), piericidin A1 (10), antipain (11), stendomycin (12), surfactins (13), nodularin (14), wortmannin (15), ethanolaomines (16), various lipid families (17), formate clusters (18) and maridric acids (19). Chemistries observed in a single microorganism are orange, while those observed in multiple microorganisms are blue. Molecular overlap of each extraction method is displayed in a proportional Euler diagram (c). The merged rarefaction curves (d) of each extraction method shows the observed chemistries gained by additional sampling from each extraction, while the frequency analysis (e) of each metabolite shows that there is a large low abundance diversity throughout the sample set and that spectral networking is able to putatively identify metabolites at all levels of abundance (Color figure online)

Fig. 2

The molecular family (a) containing new chemistries maridric acids A and B (b) is composed mainly of nodes derived from a single marine organism (orange). Nodes are labeled with their parent mass and thicker edges between nodes indicate higher spectral similarity score. The four nodes with spectra shown are highlighted with colored borders and the newly identified compounds are labeled in bold. MS/MS spectra (c) of four nodes show the polymeric nature of this molecular family (Color figure online)