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New rules for Gram-negative antibiotics

Properties that allow compounds to get into and stay in Gram-negative bacteria could guide antibiotic discovery

by Stu Borman
May 10, 2017 | A version of this story appeared in Volume 95, Issue 20

In the fight against pathogenic bacteria, Gram-negative bacteria such as Escherichia coli and Pseudomonas aeruginosa are particularly challenging foes.

By linking an amine group (red) to a ring-expanded analog of deoxynybomycin (left), researchers converted the Gram-positive-active agent into one that also works on Gram-negative bacteria.

These microbes don’t respond to many common antibiotics, and no new drug active against Gram-negative bacteria has been approved in nearly a half-century. Part of the difficulty in developing such antibiotics is that molecules have a hard time slipping inside Gram-negative bacteria. The bacteria have two cell membranes, and compounds must also navigate porin protein channels to enter.

A new study outlines a systematic approach to ferreting out properties compounds must have to penetrate and accumulate in Gram-negative bacteria. The authors demonstrated the power of the approach by converting an antibiotic that previously couldn’t enter Gram-negative bacteria into one that can.

Paul J. Hergenrother and coworkers at the University of Illinois, Urbana-Champaign used liquid chromatography and tandem mass spectrometry to assess the ability of compounds to enter and remain in E. coli (Nature 2017, DOI: 10.1038/nature22308). The researchers analyzed the accumulation of more than 180 compounds from a library of modified natural products they had synthesized.

A computational analysis of common properties of compounds that accumulated determined that the molecules must have an unhindered amine group and should be rigid and flattish, instead of floppy and spherical. The properties of some existing Gram-negative medications are consistent with these findings.

The team demonstrated the power of the findings by linking an amine group to a ring-expanded analog of deoxynybomycin, a rigid and flat antibacterial agent. This simple addition converted the molecule from a Gram-positive-only agent to one that also shows efficacy against Gram-negative bacteria.

Kim Lewis, director of the Antimicrobial Discovery Center at Northeastern University, comments that additional work is still needed to determine a complete list of properties. But the study “is a genuine breakthrough,” he says. “It opens up a new field—the search for comprehensive rules of compound accumulation in Gram-negative bacteria.” Until now, Lewis says, researchers have debated whether such rules even existed, although simpler parameters favoring accumulation, such as low molecular weight and high polarity, were known from previous studies.

The new findings come at a time when scientists have been focusing intently on Gram-negative drug discovery. The Pew Charitable Trusts and the National Institute of Allergy & Infectious Diseases held a conference on the problem in February, and the National Institutes of Health has a call out for grant proposals on tools to advance the discovery of therapeutics for antimicrobial-resistant Gram-negative bacteria.

Derek Tan of Memorial Sloan-Kettering Cancer Center, whose group previously developed a related technique to identify structural properties conducive to bacterial entry, comments that the new study extends this type of strategy to a higher level. “It’s a major advance and just the beginning,” he says. “There is much more to be done in this field.” For example, the aminated deoxynybomycin was not active in P. aeruginosa—suggesting the importance of further expanding the approach by analyzing traits controlling the ability of more molecules to accumulate in multiple Gram-negative species, Tan says.


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