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.
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