Chemistry & Biology

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Antibacterial Drug Discovery: Doing It Right

Martin Gengenbacher1 and Thomas Dick2,*
1Tuberculosis Research Laboratory, Department of Microbiology, Yong Loo Lin School of Medicine, National University Health System,
National University of Singapore, Singapore 117545, Republic of Singapore
2Antibacterial Drug Discovery Laboratory, Department of Microbiology, Yong Loo Lin School of Medicine, National University Health System,
National University of Singapore, Singapore 117545, Republic of Singapore
*Correspondence: thomas_dick@nuhs.edu.sg
http://dx.doi.org/10.1016/j.chembiol.2014.12.005

Antibacterial drug discovery needs to develop new strategies to identify attractive hit-target couples for more
effective lead finding and optimization. In this issue of Chemistry & Biology, Park and coworkers describe
a novel target-based whole cell combination screening approach resulting in the identification of new inhibitors of biotin biosynthesis in Mycobacterium tuberculosis.
Resistance of bacteria against antibiotics
is on the rise, and the situation is likely
to get much worse in the future while
the drug development pipelines are thin
(ONeill, 2014). Multiple reasons exist
why we are not generating new drug
candidates. Yes, the pharmaceutical industry has largely left the arena and,
yes, there is limited funding for drug discovery in academic settings. However,
an often overlooked reason is that we
dont really know how to make new antibiotics in a rational way. After the golden
era of antibiotic discovery in the middle
of the last century, during which most
of our antibiotic classes were discovered
empirically by whole cell screens, the
area became rather quiet. A new push
triggered by the genome revolution
(now its easy: we do biochemical
screens on genetically essential, isolated
targets) fizzled out because it did not
deliver candidates, often not even whole
cell active hits (Payne et al., 2007). And if
some hits showed whole cell activity,
was this achieved by engaging the presumed target? As a result, the field
largely moved back to empirical whole
cell approaches. Those do work, as
once again demonstrated by the new
tuberculosis drug, bedaquiline (Andries
et al., 2005). However, black-box whole
cell approaches must manage lead
finding and optimization without a target
and, thus, cannot leverage modern
structure-based design tools. As a result,
such approaches are not efficient and
are plagued by very high attrition rates
(Dick and Young 2011). Moreover, targets identified along the way might not
be useful for drug design because of
their complexity (Rao et al., 2013). Worse

still, the advanced lead compound might

lack animal efficacy, because the unknown target may only be required by
the bacterium in vitro but not during
infection (Pethe et al., 2010). Taken
together, there is a realization for a
need to reconnect modern genome
biology with drug discovery, to integrate
and combine target and whole cell
approaches (Dick and Young, 2011).
One example is the development of
target-based whole cell approaches.
Underexpression of a gene of interest
sensitizes the bacterium for inhibitors
of the particular target or pathway and
allows simultaneous identification of
whole cell active hits along the associated target (Kana et al., 2014).
Now Park et al. (2015) report a new
version of a target-based whole cell
approach for Mycobacterium tuberculosis. They carried out a biochemical
screen on an isolated target, the aminotransferase BioA involved in biosynthesis
of the essential cofactor biotin, and
subsequently identified the hits that
exert their antimicrobial whole cell activity via this target by pathway assays.
This exciting strategy delivered a set
of distinct hitsBioA couples which
can now undergo structure-based lead
finding.
What makes this work remarkable is
that it not only describes a conceptually
novel approach, biochemical targetbased screen followed by pathway
screen of the hits, but it also provides a
thorough and thoughtful integration of
the other why we failed aspects that
we have learned over the past decade.
For example, in terms of target selection criteria, the authors didnt simply

select an in vitro genetically essential,

epidemiologically conserved, druggable, and assayable target. BioA
had been shown genetically to be essential and vulnerable in vivo. Chemical
(pharmacological) vulnerability had been
demonstrated in vitro. Furthermore, the
authors developed an elegant fluorescence displacement screening assay
and addressed the issue around limited
chemical diversity in the screening
libraries by including diversity-orientedsynthesis scaffolds. The hits that showed
both an activity against the enzyme and
with whole cell activity were then counter
screened in two whole cell assays to
filter out compounds whose whole cell
activity was off target. The first assay
was based on chemical complementation, i.e., adding biotin to the medium
and identifying those (on target) hits
whose whole cell activity is biotin
dependent. The second assay made use
of a BioA underexpression, i.e., BioA
depleted, and therefore hypersensitized
bacilli. Interestingly, the employment
of an underexpressor strain allowed
the identification of weak whole cell
BioA on-target hits that would have
been missed otherwise. After providing
biochemical, metabolic, and genetic
on-target evidence, binding of the corresponding hits was biophysically demonstrated via X-ray co-structure determination, which provides at the same time
the foundation for structure-based hitto-lead projects.
In summary, Park et al. (2015) describe
the identification of new inhibitors for an
essential enzyme in biotin biosynthesis
in Mycobacterium tuberculosis. This discovery is an impactful achievement

Chemistry & Biology 22, January 22, 2015 2015 Elsevier Ltd All rights reserved 5

Chemistry & Biology

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in itself in the field of tuberculosis

drug discovery. The novel, thorough,
and thoughtful approach the authors
took is impressive and represents a case
study showing that we are slowly figuring
out the science of rational antibiotics
discovery.

J., Timmerman, P., Zhu, M., Lee, E., et al. (2005).

Science 307, 223227.

Barry, C., et al. (2015). Chem. Biol. 22, this issue,

7686.

Dick, T., and Young, D. (2011). Future Microbiol. 6,

603604.

Payne, D.J., Gwynn, M.N., Holmes, D.J., and

Pompliano, D.L. (2007). Nat. Rev. Drug Discov. 6,
2940.

Kana, B.D., Karakousis, P.C., Parish, T., and Dick,

T. (2014). Tuberculosis (Edinb.) 94, 551556.

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6 Chemistry & Biology 22, January 22, 2015 2015 Elsevier Ltd All rights reserved

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