Molecular networking-based strategies in mass spectrometry coupled with in silico dereplication of peptidic natural products and gene cluster analysis

Abstract

Peptidic natural products (PNPs) are valuable sources for drug development as they are often associated with desirable bioactivities. Chemoenzymatic approaches coupled with description of structure-activity relationships have enabled the production of analogs to PNPs such as daptomycin and vancomycin which exhibit optimized bioactivities. The natural promiscuity of biosynthetic enzymes allows the producer organism to generate various analogs potentially serving as multiple hits for one target or to diversify the bioactivity of a given natural product. Thus, approaches that allow rapid discovery of novel peptide natural products by mining their presence in crude extracts while providing insights into promiscuity of biosynthetic enzymes are sought out by natural product biochemists and chemists. In this chapter, we describe how two different molecular networking-based approaches combined with in silico tools can be used to dereplicate PNPs from untargeted mass spectrometry data acquired on crude extracts and how to propagate annotations to structurally related molecules. We further describe steps to gain knowledge of enzyme promiscuity by combining molecular networking analysis with gene cluster analysis.

Keywords: Biosynthetic gene clusters; GNPS; MIBiG; Mass spectrometry; Metabolomics; Molecular networking; Peptidic natural products.