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Magazine
Feature
How to avoid a post-antibiotic age
After decades of warnings, the global spread of antibiotic resistance genes is
becoming more and more threatening. The traditional strategy of semisynthetic
modification of existing or natural antibiotics may fail to keep up with the problem.
Entirely new strategies are now being proposed. Michael Gross reports.
Bacteria and fungi have been
competing for a billion years, resulting in
fungi producing many kinds of chemical
weapons to kill bacteria. Alexander
Fleming’s discovery of penicillin in 1928,
the isolation of the pure compound by
Howard Florey and Ernst Boris Chain in
1940, and the subsequent application
as the first clinical antibiotic gave rise
to the hope that microbial infections
causing death and suffering might
become a thing of the past.
However, during the many millions of
years that fungi spent brewing up new
poisons, bacteria have been evolving
antidotes as well, keeping up an arms
race with fungal competitors. After the
use of antibiotics became widespread
in the second half of the 20th century,
it was only natural to expect that this
new applied selection pressure would
encourage the resurgence and spread
of resistance traits. This predictable
problem is exacerbated by the misuse
of antibiotics, including prescriptions
in cases where they are not needed
as well as the application as growth
promoters in cattle (Curr. Biol. (2013)
23, R1063–R1065).
Warnings about ‘superbugs’ that have
acquired resistance against several
types of drugs have been sounded
since the 1990s. By now, an estimated
700,000 patients a year die from
infections with multiresistant pathogens.
This figure is projected to rise into the
millions very soon, and a post-antibiotic
age of untreatable infections is very
much becoming a possible scenario
(Curr. Biol. (2019) 29, R859–R861).
The existing strategy of developing
new or just slightly tweaked antibiotics
as established drugs become useless
is failing to keep up in the race against
evolution and horizontal gene transfer.
New approaches are needed.
Chemistry and structural biology
The group of Maofu Liao at Harvard
University, USA, applies new
approaches to the development of
antibiotics, starting from the structural
biology of the target molecules. Instead
of screening for substances that kill
bacteria, the group looks for agents
that bind to specific proteins essential
for bacterial functions, elucidates the
mechanism of interaction and then
develops new substances that target
these proteins.
Ideally, according to Liao, several
such agents targeting separate
molecular functions should be exploited
to hinder the development of resistance.
The Harvard group has recently
reported a success in the direction of
this new strategy: two new substances
that attack the ABC transporter MsbA in
bacteria like Escherichia coli in different
ways (Science (2021) 374, 580–585).
ABC (ATP-binding cassette)
transporters are proteins embedded
in the cell membrane that can be
importers or exporters of specific
goods. In the case of Gram-negative
bacteria, the exporters use ATP to
shuttle molecules out of the cytoplasm
and into the periplasm, the space
Resistance: Multidrug-resistant pathogens are threatening our ability to treat infectious diseases.
MRSA (methicillin-resistant Staphylococcus aureus), shown here surrounded by cell debris, was
among the first such germs to gain notoriety. (Photo: NIAID/Flickr (CC BY 2.0).)
Current Biology 31, R1549–R1567, December 20, 2021 R1549
between the cell membrane and the
outer membrane. MsbA, specifically,
transports lipopolysaccharides, which
the bacterium needs to build the outer
membrane.
Liao and colleagues characterised
the complexes of membrane-
embedded MsbA with two of their
inhibitors using cryo-electron
microscopy. They found that the two
agents interacted in different ways.
Tetrahydrobenzothiophene 1 (TBT1)
stimulates the ATPase while blocking
the transport function, thus making
the cell waste energy. In contrast,
G247 inhibits ATPase and thereby
stops transport too. The cryo-EM
images showed the substances
occupying adjacent yet separate sites
in the transmembrane domain of the
transporter. Based on their insights
into the TBT1-induced conformation,
the Harvard researchers have already
formulated one lead compound that
they are planning to develop as a new
antibiotic.
Scaling up the approach, Liao hopes
that researchers starting from the basic
structural biology of the problem will
be able to create drugs to hit multiple
protein targets, and also drugs to hit
multiple sites in one protein. This, he
suggests, can transform antibiotic
discovery into a more systematic,
rational and robust process.
Another popular target for antibiotics
is the bacterial ribosome. While it has
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TBT1
Transport target: Membrane proteins such as ABC transporters are among the targets for new
antibiotics research guided by structural biology. (Image provided by Maofu Liao.)
the same essential shape and function
as the eukaryotic one, ours has evolved
to a much higher structural complexity
(Curr. Biol. (2020) 30, R454–R456), so
local functional sites can often look very
different at the molecular scale. Thus, it
is relatively easy to develop antibiotics
that inhibit bacterial protein synthesis
without affecting our own. Of course,
fungi figured this out long before us,
as many fungal antibiotics target the
bacterial ribosome and have been
valuable tools in ribosome studies.
The groups of Yury Polikanov at
the University of Illinois at Chicago
and Andrew Myers at Harvard, both
USA, have now established how
bacteria develop resistance against
the antibiotic clindamycin and similar
drugs, and how this resistance can be
overcome (Nature (2021) 599, 507–512).
The resistance relies on the
methylation of one particular nucleotide
in the ribosomal RNA. Polikanov’s
group had already shown in previous
work that this modification displaces
a water molecule that is essential for
the activity of the antibiotic. There are
several known methylation enzymes
that can convey this kind of protection
to the ribosome. These enzymes give
rise to macrolide, lincosamide and
streptogramin B (MLSB) cross-resistance,
R1550 Current Biology 31, R1549–R1567, December 20, 2021
G247
which has been highlighted in the 2019
CDC report on antibiotic resistance
as one of the most urgent problems in
this field. And yet finding an inhibitor
for that enzyme wouldn’t solve the
problem, as many others are ready to
replace it.
Polikanov, Myers and colleagues
now describe substantial chemical
modifications on the structure
of clindamycin, leading to a new
candidate called iboxamycin, which
is just as effective as a ribosome
inhibitor without being affected by the
methylation. A crystal structure of the
ribosome with iboxamycin bound now
shows the surprising explanation: the
agent just pushes the troublesome
methylated nucleotide aside by two
angstroms.
Data driven
The first antibiotics were discovered
by luck, such as penicillin, then
by screening natural products. In
comparison with the early days,
science today has a vast range of
additional tools that can be used to
address the problem of resistance,
including computational tools and
supercomputers that can predict the
effectiveness of new molecules based
on simulations.
Magazine
Gerhard König from the Max
Planck Institute for Coal Research in
Mülheim, Germany, with colleagues,
including ribosome structure pioneer
Ada Yonath at the Weizmann
Institute in Israel, have unleashed
a supercomputer on the class of
macrolid antibiotics derived from the
natural substance erythromycin, a
classic antibiotic first isolated in 1952
from the bacterium Saccharopolyspora
erythraea (Proc. Natl. Acad. Sci. USA
(2021) 118, e2113632118).
The researchers chose requirements
that the substance had to meet,
including synthetic accessibility,
solubility in water, cell permeability,
binding affinity and absence of toxicity.
Starting from the existing antibiotic
clarithromycin, the researchers let the
supercomputer screen new derivatives
on the basis of these criteria and
obtained a shortlist of three compounds
that they then synthesised and
tested in laboratory experiments. The
experimental results, in turn, enabled
them to assess the computational
method and improve the criteria.
Information technology can also
help us to understand how resistance
genes spread among bacteria.
Horizontal gene transfer is common
and will be particularly encouraged
by selective pressure, for which the
use and misuse of antibiotics provides
a beautiful, if unfortunate, example.
The global presence of antibiotics in
the environment resulting from their
massive use in areas where they don’t
save human lives, such as agriculture,
has also led to a global boost for the
matching resistance genes.
Until now, researchers had no way of
predicting which bacteria would engage
in gene transfer at what time. The group
of Ilana Brito at Cornell University at
Ithaca, USA, has now applied machine
learning to develop methods to model
and predict these transfers (Sci. Adv.
(2021) 7, eabj5056). The new method
turned out to be especially successful
with bacteria that live in contact with
humans, and with medically relevant
genes, such as those for resistance
traits.
To determine which resistance genes
are present in a real-world environment,
new methods in metagenomics
can yield substantial amounts of
information. An example is wastewater
sampling, an area that has recently seen
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Magazine

a dramatic boost in interest due to its

ability to detect COVID-19 earlier than
clinical testing (Curr. Biol. (2021) 31,
R267–R269).
Wastewater monitoring for resistance
traits can detect, for instance, which
ones are present in a given hospital
and thus enable doctors to choose
their treatments wisely. In a recent
review of the global surveillance for
resistance traits in wastewater systems,
Amy Pruden from Virginia Tech at
Blacksburg, USA, and colleagues argue
that its application has been lagging so
far but has benefited from the interest
in monitoring for COVID-19 (Curr.
Opin. Microbiol. (2021) 64, 91–99).
“Methodologies for tracking AMR
[antimicrobial resistance], including
metagenomics, are rapidly advancing,
but need to be standardized and made
modular for access by LMICs [low-
and middle-income countries], while
also developing systems for sample Virulent: Drugs specifically suppressing virulence factors instead of eradicating the bacteria have
archiving and data sharing,” the authors been tried on Salmonella enterica serovar Typhimurium, among other pathogens. Here, Salmo-
write. nella cells (yellow) invade a human gut epithelial cell (blue). (Photo: NIAID/Flickr (CC BY 2.0).)

Alternative approaches
A radical idea that has gained ground
in the last two decades is not to kill
the bacteria but just stop them from
killing us instead. There are examples
of bacterial species that occur in
perfectly peaceful strains in nature, with
only certain strains carrying a virulence
factor that causes us problems. One of
the most prominent examples is Vibrio
cholerae, which depends on a specific
bacteriophage to complete its virulence
factor, the cholera toxin.
The idea of developing anti-virulence
drugs is to find such factors that, for
a given pathogen, are essential to its
disease-causing effects but not to its
survival. The presence of antibiotics
triggers an SOS mutagenic response
in bacteria that improves their chances
of evolving resistance. The hope is that
less than life-threatening interventions
will not trigger this response and will
be at a much lower risk of producing
or selecting for resistance traits.
However, whether this plan works has
to be established on a case-by-case
basis.
One promising target for such drugs
is the folding helper protein DsbA of
several Gram-negative pathogens
including Salmonella enterica serovar
Typhimurium and uropathogenic E. coli.
This enzyme catalyses the formation
of disulfide bonds that are essential for
the structural and functional integrity
of several virulence factors. For
instance, in Salmonella it is required
for the folding of RcsC, a mediator of
biofilm formation, and thus a key cause
of chronic infections, such as in the
gallbladder.
Rabeb Dhouib from the Queensland
University of Technology at Herston,
Australia, and colleagues tested the
evolutionary robustness of anti-virulence
drugs targeting several DsbA enzymes
using in vitro systems mimicking
certain aspects of the physiological
environment that the bacteria face,
particularly nutrient deprivation
inside macrophages (FASEB Bioadv.
(2021) 3, 231–242). Using several
small-molecule inhibitors originally
developed against the prototype DsbA
enzyme of the classic laboratory strain
E. coli K12, the authors were able to
suppress Salmonella virulence factors
in laboratory culture conditions without
affecting bacterial growth.
In their physiologically inspired model
system, by contrast, the inhibitors
slowed down growth as well as
blocked the virulence factors. Thus,
the inhibitors could be described as
having both anti-virulence and antibiotic
activity. The treatment did not result
in the evolution of any more resistant
variants, whereas a parallel experiment
with conventional antibiotics did.
Although the substances used in
this study are too toxic to be useful as
drug candidates, the authors conclude
that their findings “support the case for
further development of DsbA inhibitors
as a novel and effective strategy to
control multidrug-resistant Gram-
negative bacteria”.
Other examples of non-lethal
weapons developed against bacteria
in recent years include extracellular
siderophore (iron-scavenging)
quenching in Pseudomonas aeruginosa
as well as quorum sensing in the same
species. Results suggest that the
approach is not evolution-proof but
may, under the right circumstances,
be relatively safe from pathogens
evolving countermeasures. Collective
phenomena like quorum sensing
(Curr. Biol. (2017) 27, R1293–R1296)
and biofilm formation are often a key
element of pathogen invasion and will
surely provide further targets for such
interventions.
One fundamental problem with
anti-virulence drugs is that they have
to be developed specifically for each
pathogen and each host environment,
as bacteria may need different virulence
factors for invading different organs.
Therefore, nobody is expecting these

Current Biology 31, R1549–R1567, December 20, 2021 R1551

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drugs, of which only a few are currently
approved or in development, to replace
conventional antibiotics, but they could
help to take the strain in cases of
specific infectious diseases where the
antibiotic options are running out.
Another potential escape from the
problems of pitching drugs against
evolving targets is to have the cure
evolve along with the target. This is
one of the hopes associated with the
use of bacteriophages (phages) against
pathogens. When bacteria evolve to
cope with phage attacks, phages can in
turn also up their game.
The idea of phage therapy is even
older than the medical use of antibiotics
(Curr. Biol. (2014) 24, R541–R544).
While there is no shortage of anecdotal
success stories through the ages, the
pharmaceutical industry has steered
clear of the idea. Among the problems
of the approach that may have scared
away big pharma is the very nature
of working with an evolving biological
entity, which is thus hard to patent and
to produce with a reliable composition
and quality.
Research into phage therapy was
popular in the Soviet Union, but ever
since its demise the field has remained
stuck in the role of the interesting
alternative that we should perhaps also
consider. Still, some academic research
groups keep the idea alive. In a recent
effort, the group of Stefano Pagliara at
the University of Exeter, UK, described
a laboratory test system designed
to mimic the conditions under which
therapeutic phages would encounter
their bacterial targets inside their
human hosts (PLoS Biol. (2021) 19,
e3001406). The researchers used this
system to study how E. coli responds
to phage attack in a human-like
environment.
Nothing will replace antibiotics
anytime soon, so if we want to continue
to enjoy their protection from infectious
disease we will have to use them much
more responsibly and come up with
fundamentally new ways out of the race
against evolution. A broad and well-
populated spectrum of antimicrobial
treatments that could be used
combinatorially may be the best chance
of keeping up with the evolving threat.
Michael Gross is a science writer based at
Oxford. He can be contacted via his web page
at www.michaelgross.co.uk
R1552 Current Biology 31, R1549–R1567, December 20, 2021
Q&A
Ila Fiete
Interviewed by Maxine
Herman-Oakley Mills
Ila Fiete is Professor of Brain and
Cognitive Sciences at Massachusetts
Institute of Technology, an Associate
Member of the McGovern Institute,
and the Director of the K. Lisa
Yang Integrative Computational
Neuroscience Center. Before joining
MIT in 2018, Ila worked at the
University of Texas at Austin, where
she first started her group and
joined the faculty as an Assistant
Professor, working in the Center for
Learning and Memory as well as
the Department of Neuroscience.
Prior to UT Austin, Ila completed
her postdoctoral training first at
the Kavli Institute for Theoretical
Physics at the University of California,
Santa Barbara and then as a Broad
Fellow at the California Institute of
Technology. Ila has a PhD from the
Department of Physics at Harvard,
though her research already
involved work in neuroscience with
Sebastian Seung at this time, and
she completed her undergraduate
work at the University of Michigan
in Ann Arbor, studying physics and
mathematics, as well as philosophy.
Before this, Ila studied primarily in
various places in Mumbai (formerly
Bombay) in India where she grew up,
spending much of her elementary,
middle, and high school years going
back and forth between Mumbai
and Princeton and Berkeley, both
in the US, as a result of her father’s
work. Her group is interested in
trying to understand the microscopic
cellular and synaptic dynamics,
principles, and processes that give
rise to the rich behaviors of memory
and cognition in the brain, trying to
determine how interesting functions
and memory emerge from these very
low-level interactions. Over the last
decade and a half the group has
studied spatial navigation circuits,
which provide a unique insight
into cognitive computations while
also allowing the team to address
questions at the cellular and circuit
levels.
Magazine
What turned you on to physics
and biology in the first place? Of
all the sciences, I was always most
intrigued by biology, even as a child.
I didn’t study biology seriously during
my undergraduate work or even at
the beginning of graduate school
because I didn’t know if there was
a path in biology that involved more
computational and mathematical
approaches. I felt like my drive to be
a scientist was to do more analytical
or theoretical work and, as I did not
have exposure to any theoretical work
in biology, I had no idea that this was
a possible option. So I continued in
math and physics. When I went to
graduate school to study physics, I
hoped that there might be a path into
biophysics. Quite accidentally, as I
was looking around for something
to do in biology, I ended up taking
a class at MIT taught by Sebastian
Seung. It was a computational
systems biology class that surveyed
many different topics but approached
them in a computational way, aiming
to understand things like gene–protein
interactions, regulation systems,
molecular binding kinetics, and cell-
molecular circuits, as well as a little
bit of neuroscience at the end. I really
enjoyed that class. It was finally the
exact space that I wanted to work
in and I thought Sebastian was an
amazing person and teacher, so I
asked to join his group, not knowing
much of anything about neuroscience.
So your time in Sebastian’s group
really helped to decide the future
direction of your studies? Yes,
very much so. Sebastian is actually
a physicist — a theoretical physicist
by training. That’s probably in
part why the way he taught that
class resonated with me: we had a
common background, though by that
point he had already moved fully into
working on statistical learning theory
and computational neuroscience. So,
in joining his group, I had essentially
made the decision — though without
knowing exactly what that meant at
the time — that I would be working
in computational neuroscience as
well. It was a fascinating field and it
gripped me immediately. Ever since
then, I haven’t looked back; this was
where I learned about neurons and
computational neuroscience for the