Comprehensive prediction of secondary metabolite structure and biological activity from microbial genome sequences.

Novel antibiotics are urgently needed to address the looming global crisis of antibiotic resistance. Historically, the primary source of clinically used antibiotics has been microbial secondary metabolism. Microbial genome sequencing has revealed a plethora of uncharacterized natural antibiotics that remain to be discovered. However, the isolation of these molecules is hindered by the challenge of linking sequence information to the chemical structures of the encoded molecules. Here, we present PRISM 4, a comprehensive platform for prediction of the chemical structures of genomically encoded antibiotics, including all classes of bacterial antibiotics currently in clinical use. The accuracy of chemical structure prediction enables the development of machine-learning methods to predict the likely biological activity of encoded molecules. We apply PRISM 4 to chart secondary metabolite biosynthesis in a collection of over 10,000 bacterial genomes from both cultured isolates and metagenomic datasets, revealing thousands of encoded antibiotics. PRISM 4 is freely available as an interactive web application at http://prism.adapsyn.com .

Targeting Two-Component Systems Uncovers a Small-Molecule Inhibitor of Salmonella Virulence.

Salmonella serovars are leading causes of gastrointestinal disease and have become increasingly resistant to fluoroquinolone and cephalosporin antibiotics. Overcoming this healthcare crisis requires new approaches in antibiotic discovery and the identification of unique bacterial targets. In this work, we describe a chemical genomics approach to identify inhibitors of Salmonella virulence. From a cell-based, promoter reporter screen of ∼50,000 small molecules, we identified dephostatin as a non-antibiotic compound that inhibits intracellular virulence factors and polymyxin resistance genes. Dephostatin disrupts signaling through both the SsrA-SsrB and PmrB-PmrA two-component regulatory systems and restores sensitivity to the last-resort antibiotic, colistin. Cell-based experiments and mouse models of infection demonstrate that dephostatin attenuates Salmonella virulence in vitro and in vivo, suggesting that perturbing regulatory networks is a promising strategy for the development of anti-infectives.

Enantiopure Phospha[1]ferrocenophanes: Textbook Examples of Through-Space Nuclear Spin-Spin Coupling.

Three enantiopure phospha[1]ferrocenophanes (2R ) equipped with either a phenyl, an isopropyl, or a tert-butyl group at the bridging phosphorus atom were synthesized by a salt-metathesis approach in isolated yields between 52 and 63 %. The chirality in these strained sandwich compounds stems from the planar-chiral ferrocene moiety, which is symmetrically equipped with two iPr groups adjacent to phosphorus. Surprisingly, all three phospha[1]ferrocenophanes show an uncommon through-space nuclear 1 H-31 P coupling. As a result of the embedded symmetry, these new compounds are ideal examples to differentiate between through-space and through-bond coupling mechanisms in NMR spectroscopy.