David's New Book

Monday, May 15, 2017

A Giant Step Forward for Antibiotics for Gram-negatives


Last week, a remarkable paper was published in Nature (subscription required – sorry). The paper is remarkable because it takes a simple, practical and elegant approach to understanding how drugs penetrate Gram-negative bacteria.  This problem has confounded antibiotic discovery for decades.  The penetration problem has recently been highlighted by the Pew Charitable Trust Roadmap for antibiotic discovery and by the proposed OMEGA project. The problem has been so challenging that many scientists, including yours truly, did not believe that there were universal rules that one could follow to achieve penetration of antibiotics into Gram-negatives. While we may not be 100% wrong, it is now clear that there are a few important such rules for E. coli, an important Gram negative pathogen.
 
Richter et. al. from the Department of Chemistry and the Institute for Genomic Biology at the University of Illinois used a very sensitive method (tandem mass spectrometry) to actually measure the penetration of various molecules into E. coli. They then studied a collection of 100 molecules including antibiotics with known activity against E. coli and those that were active against Gram positive bacteria but not against Gram negatives. Based on these data, the authors were able to show a strong correlation with the presence of a positive charge at neutral pH or primary amine. They also realized that even though a positive charge might be required, it was not sufficient since not all such molecules were able to penetrate E. coli.

To further explore the requirements for penetration, the authors carried out a search of compounds with primary amines for 297 different molecular characteristics. Those characteristics that were associated with penetration could be identified.  The authors then went further and measured the penetration of compounds where specific characteristics differed – one at a time. In this way, they showed that rigid compounds penetrated better than flexible ones and that flat compounds were better than globular compounds. Using this information, they were then able to take a natural product that was active against Gram positive bacteria, and by altering it chemically along the lines of their predictive model, they were able to create a new compound with activity against both Gram positive and Gram negative bacteria.

What is surprising to many of us is that the data provided by the authors differs considerably from the conclusions we had surmised based entirely on retrospective analyses of marketed antibiotics. The great thing about science is that progress means change and with progress more questions always arise. Its perpetual.

So, Hermione, there are at least some rules after all. While the paper by Richter and coworkers is a breakthrough – no question about that – it is not going to be the whole story. And the authors clearly recognize this. How about Klebsiella?  It is closely related to E. coli. What about E. coli that are resistant already either via increasing their ability to efflux compounds out of the cell or by limiting the ingress of compounds? Then there is the problem of Pseudomonas – a pathogen with not only the ability to radically limit ingress of molecules compared to E. coli, but also one that more readily pumps them back out again. What about Acinetobacter? – a complete unknown here. Will these rules apply to all Gram negatives or are they specific to E. coli?

Richter and coworkers have shown us a way forward. We now have to fill in the rest of the blanks.