Discovery of antimicrobials by massively parallelized growth assays (Mex)

Abstract

The number of newly approved antimicrobial compounds has been steadily decreasing over the past 50 years emphasizing the need for novel antimicrobial substances. Here we present Mex, a method for the high-throughput discovery of novel antimicrobials, that relies on E. coli self-screening to determine the bioactivity of more than ten thousand naturally occurring peptides. Analysis of thousands of E. coli growth curves using next-generation sequencing enables the identification of more than 1000 previously unknown antimicrobial peptides. Additionally, by incorporating the kinetics of growth inhibition, a first indication of the mode of action is obtained, which has implications for the ultimate usefulness of the peptides in question. The most promising peptides of the screen are chemically synthesized and their activity is determined in standardized susceptibility assays. Ten out of 15 investigated peptides efficiently eradicate bacteria at a minimal inhibitory concentration in the lower µm or upper nm range. This work represents a step-change in the high-throughput discovery of functionally diverse antimicrobials.

Striving for sustainable biosynthesis: discovery, diversification, and production of antimicrobial drugs in Escherichia coli

“…Of the 22 hits chosen for experimental validation, most proved to be active against E. coli , Acinetobacter baumannii and Pseudomonas aeruginosa in the low µM range. Similarly, Koch et al [ 88 ] screened a library of 10 663 naturally occurring peptides with a self-inhibition screen, in which >1000 sequences were active. From these hits, 15 were chemically synthesized and 10 peptides inhibited E. coli at a minimal inhibitory concentration in the upper nM to low µM range.…”