Targeting Reactive Carbonyls for Identifying Natural Products and Their Biosynthetic Origins

J Am Chem Soc. 2016 Nov 23;138(46):15157-15166. doi: 10.1021/jacs.6b06848. Epub 2016 Nov 14.


Natural products (NPs) serve important roles as drug candidates and as tools for chemical biology. However, traditional NP discovery, largely based on bioassay-guided approaches, is biased toward abundant compounds and rediscovery rates are high. Orthogonal methods to facilitate discovery of new NPs are thus needed, and herein we describe an isotope tag-based expansion of reactivity-based NP screening to address these shortcomings. Reactivity-based screening is a directed discovery approach in which a specific reactive handle on the NP is targeted by a chemoselective probe to enable its detection by mass spectrometry. In this study, we have developed an aminooxy-containing probe to guide the discovery of aldehyde- and ketone-containing NPs. To facilitate the detection of labeling events, the probe was dibrominated, imparting a unique isotopic signature to distinguish labeled metabolites from spectral noise. As a proof of concept, the probe was then utilized to screen a collection of bacterial extracts, leading to the identification of a new analogue of antipain, deimino-antipain. The bacterial producer of deimino-antipain was sequenced and the responsible biosynthetic gene cluster was identified by bioinformatic analysis and heterologous expression. These data reveal the previously undetermined genetic basis for a well-known family of aldehyde-containing, peptidic protease inhibitors, including antipain, chymostatin, leupeptin, elastatinal, and microbial alkaline protease inhibitor, which have been widely used for over 40 years.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aldehydes / chemistry*
  • Aldehydes / metabolism
  • Biological Products / analysis*
  • Biological Products / metabolism*
  • Computational Biology
  • Ketones / chemistry*
  • Ketones / metabolism
  • Molecular Structure
  • Streptomyces / chemistry*
  • Streptomyces / isolation & purification
  • Streptomyces / metabolism


  • Aldehydes
  • Biological Products
  • Ketones