Microbiology: Antibiotic stops 'ping-pong'
match
Eric D. Brown
Abstract
As bacteria become resistant to existing drugs, there is a need for antibiotics
with new modes of action. Such a compound has been found, and it works by
binding to an intermediate in the catalytic cycle of its target.
Pathogenic bacteria have developed strains that are resistant to almost all
antibiotics in use today. Particularly worrisome are infections by a large group
of bacteria classified as being Gram-positive, such as staphylococci and
enterococci, which cause pneumonia and other, often fatal, infections. The
problem is highlighted by the emergence of multiply-drug-resistant strains of
these organisms — so-called superbugs — that are resistant to vancomycin, a
drug widely recognized as the last line of defence in many Gram-positive
bacterial infections. Wang and colleagues report the discovery of a new
antibiotic, platensimycin, that has potent antibacterial activity against these
Gram-positive pathogens.
In the past 40 years, only two antibiotics representing new chemical classes
have reached the clinic, namely linezolid (an oxazolidinone) and daptomycin (a
lipopeptide). Most classes of antibiotic were discovered in the 1940s and
1950s, and are directed at a few specific aspects of bacterial physiology —
mainly biosynthesis of the cell wall, and of DNA and proteins. Subsequent
tweaking of these chemical scaffolds has produced most of today's antibiotics.
It is believed that widespread drug resistance among bacterial pathogens is
due to the limited choice of antibiotics that exploit a relatively narrow range of
mechanisms. Wang and colleagues' report of a compound representing a
novel class of antibiotic with activity against Gram-positive bacterial pathogens
is thus particularly exciting, with the added bonus that platensimycin is
effective against multiply-drug-resistant strains of staphylococci and
enterococci.
The report reads like a textbook of modern antibacterial drug discovery,
beginning with a screen of 250,000 extracts from drug-producing
microorganisms. What follows is a series of elegant studies, spanning bacterial
genetics, biochemistry, pharmacology and structural biology, and leading to
the discovery of a small molecule derived from Streptomyces platensis that
targets a seldom-exploited weakness in bacteria: fatty-acid biosynthesis. Fatty
acids —organic acids with long hydrocarbon chains of between 8 and 18
carbon atoms — are the building-blocks of cell membranes and bacterial
surfaces. They are produced through the repetitive action of biosynthetic
machinery that elongates the chains two carbon atoms at a time. The target of
platensimycin is a key enzyme component of this machinery: -ketoacyl-ACP
(acyl carrier protein) synthase, also known as FabF.
The FabF enzyme mediates a reaction that has a fascinating catalytic cycle .
The fatty acid to be elongated is first transferred from ACP to FabF, leaving the
fatty acid bound to the enzyme through an active-site amino acid (cysteine),
affording a transient acyl–enzyme intermediate. The source of extender
carbon atoms is a molecular fragment known as a malonyl group, which is
attached to ACP. The malonyl–ACP substrate is bound by FabF, and then
loses carbon dioxide to produce a reactive two-carbon unit. The reactive unit
attacks the acyl–enzyme intermediate and yields an elongated product that is
released from the enzyme. Enzymologists describe this series of reactions as
'ping-pong'. This loose analogy refers to the way that the first substrate 'pings'
into the active site and the first product 'pongs' out, leaving the enzyme altered,
so that the second substrate does the same as the first, leading to a product
known as -ketoacyl-ACP. There is thus a strict order involving the addition of
fatty acid–ACP and then malonyl–ACP.
Wang et al. provide an account of some terrific detective work that revealed
that platensimycin binds only to the acyl–enzyme intermediate. Such
intermediates are short-lived, typically with lifetimes of the order of
milliseconds, and so are difficult to observe. To overcome this problem, the
researchers created a mimic of the acyl–enzyme intermediate. They prepared
a variant of the FabF enzyme in which the cysteine of the active site was
replaced with the amino acid glutamine. The chemical group that forms the
side chain of glutamine mimics a bound fatty acid. The variant enzyme bound
platensimycin with high affinity, and a high-resolution crystal structure of the
complex of variant FabF with the new antibiotic was obtained. The structure
reveals that formation of the acyl–enzyme intermediate is accompanied by
structural changes that open up the active site, permitting binding of
platensimycin in such a way that it blocks the addition of malonyl–ACP.
Platensimycin is a significant new antibacterial compound with an
extraordinary mechanism, but it is not the first antibiotic known to inhibit
bacterial fatty-acid biosynthesis. Isoniazid and triclosan are synthetic
compounds that also target this pathway. Isoniazid has a clinical niche in
treating tuberculosis in combination with other antibiotics, whereas triclosan
has been widely used in soaps and plastics. In addition, cerulenin and
thiolactomycin are natural products derived from fungi that target the same
specific biosynthetic reaction as platensimycin in bacteria. That neither of
these fungus-derived compounds has found a use in the clinic is testimony to
the high standards required for a successful new antibiotic. Pharmaceutical
companies have generally retreated from the field of antibacterial drugs,
concentrating instead on chronic diseases with perceived product
development and market advantages. It is heartening, therefore, that
platensimycin has been discovered and characterized by workers at
Merck.Wang et al. show that this antibiotic is effective in a mouse model of
infection. The path ahead remains a long one that includes further preclinical
study, and, if these studies are successful, extensive clinical trials for safety
and efficacy in humans. Platensimycin is nevertheless the most potent inhibitor
reported so far for FabF, and thus its discovery is an encouraging one.