Metabolic suppression identifies new antibacterial inhibitors under nutrient limitation

Abstract

Characterizing novel drugs and chemical probes of biological systems is hindered by difficulties in identifying the mechanism of action (MOA) of biologically active molecules. Here we present a metabolite suppression approach to explore the MOA of antibacterial compounds under nutrient restriction. We assembled an array of metabolites that can be screened for suppressors of inhibitory molecules. Further, we identified inhibitors of E. coli growth under nutrient limitation and charted their interactions with our metabolite array. This strategy led to the discovery and characterization of three novel antibacterial compounds, MAC168425, MAC173979 and MAC13772. We showed that MAC168425 interferes with glycine metabolism, MAC173979 is a time-dependent inhibitor of p-aminobenzoic acid biosynthesis and MAC13772 inhibits biotin biosynthesis. We conclude that metabolite suppression profiling is an effective approach to focus MOA studies on compounds impairing metabolic capabilities. Such bioactives can serve as chemical probes of bacterial physiology and as leads for antibacterial drug development.

Target-Based Identification of Whole-Cell Active Inhibitors of Biotin Biosynthesis in Mycobacterium tuberculosis

“…None of the hits showed activity in the BioD counter-screen (IC 50 > 20 μM). Since BioA is a PLP-dependent aminotransferase and because previous BioA inhibitors have been shown to covalently bind the PLP cofactor, we evaluated all compounds against aspartate transaminase (AST), a ubiquitous and functionally related PLP-dependent enzyme, in order to assess potential enzyme selectivity (AID#743184; Dai, et al, 2014; Sandmark, et al, 2002; Shi, et al, 2011; Zlitni, et al, 2013). All of the hits were inactive against AST suggesting they possess a useful level of selectivity.…”

Essential genome of Pseudomonas aeruginosa in cystic fibrosis sputum

“…These include several cofactors such as biotin, pantothenate, and riboflavin, as well as the electron carriers flavin mononucleotide and flavin adenine dinucleotide. These unavailable nutrients are particularly interesting from a therapeutic perspective, because bacteria-specific pathways for biosynthesis of these metabolites may represent novel therapeutic targets (31,32). Thus, although CF sputum is an amino acid-rich environment our comparative Tn-seq approach reveals that it is relatively cofactor-poor.…”

Pterin–sulfa conjugates as dihydropteroate synthase inhibitors and antibacterial agents

“…Under these conditions, most conjugates showed appreciable antibacterial activity, with the exception of the sulfanilamide and dapsone hybrids ( 21, 22 ) mirroring the weaker direct activity of the corresponding parent sulfonamides. 24 The sulfamethoxazole hybrid ( 15 ) showed the most potency with a MIC of 10.9 µM. Overall the minimal inhibitory concentration activities for the conjugates were usually around 10 times weaker than for the corresponding parent sulfonamides (compound 15 10.9 µM, vs sulfamethoxazole 0.8 µM).…”