This seminar report highlights a select few presentations of cutting-edge research being done in various labs across the Paris Science et Lettre (PSL) network.

1. A Seminar report
on the Chemical
Frontiers of
Living Matter
Seminar Series.
Glen Carter,
M2 Chimie et
Science du
Vivant,
ENS, PSL

2. Chemical Frontiers of Living Matter
Scientific research as a whole has seen
incredible evolution over the past few years
where the three classical divisions of the life
sciences: chemistry, biology and physics, are
seeing their boundaries dissolve entirely in
some cases, permitting the diffusion of
knowledge from once distinct scientific fields
to permeate and react to form new fields and
sub fields which do not fix themselves firmly
into any one of the three classical divisions. In
this evolution we have seen that as the diameter
of our scientific knowledge grows, so too does
the circumference of our ignorance, the
frontiers of science. Of particular interest is the
evolution taking place at the chemistry/biology
interface where fields such as bioorthogonal
chemistry require intelligent design of
biologically inert chemical reactions based on
knowledge of biological systems for imaging
and therapies, we also see the development of
such things as gene therapy, using RNA and
tRNA in genius ways never before imagined to
regulate the very core our biological systems.
Remarkable advancements have also been
made in proteomics, enzymology, imaging of
dynamic cellular processes, medicinal
organometallics and biochemical engineering,
just to name a few. Overall, the interface
between chemistry and biology is very broad
and intricate, but from chemical biology to
biological chemistry, there is great cause to be
hopeful and excited.
The PSL Chemical Frontiers of Living Matter
seminar series covers a great deal of interesting
work and serves as a good cross-sectional view
of the developments at the interface of
chemistry and biology. Here we highlight just
a select few presentations in the series.
Arnaud Gautier (Ecole Normale Superieure)
The work of the Gautier group in the
department of chemistry at ENS focuses on the
development of imaging methods for the
observation and manipulation of biological
processes. They achieve this through their
knowledge in protein engineering, molecular
chemistry and spectroscopic and microscopic
techniques.
Professor Arnaud Gautier started the seminar
series by presenting the latest developments in
fluorescence imaging of biological systems and
presented some of his own research. In general
he spoke about the challenges faced in
observing the complexity of biological systems
and the tools being developed to observe them
dynamically. [1]
The first point professor
Gautier talked about was the use of green
fluorescent proteins (GFPs) as a protein
genetic marker to fluorescently label proteins
in live cells. [2]
It was explained that the
fluorescence occurs due to a fluorophore
synthesised within the GFP after the
‘maturation’ of the flurophore. This is a
dynamic process that involves the folding,
cyclisation, dehydration and aerial oxidation to
occur and highlights the new complexity of
these types of fluorophores over the more
conventionally used fluorophore molecules
which do not generally involve much evolution
of structure. GFPs are acquired from the
jellyfish Aequorea Victoria and they have been
used for genetically encoded fluorescent
labelling to image living proteins which allows
the observation of dynamic processes. It is
possible to induce colour variation which
means that multiple targets can be labelled
simultaneously. Professor Gautier then spoke
about the pros and cons of these fluorescent
probes, mentioning that they are genetically
encodable and that they allow live cell imaging
however they are generally large molecules
with a tendency to oligomerise and
fluorescence maturation can often be quite
slow. Furthermore, these fluorescent probes
have an oxygen dependency for their
maturation and are also not tuneable. These
disadvantages have lead biochemists to try and
come up with solutions to the question: “can
we use synthetic fluorescent probes to
overcome the limitations of conventional
fluorescent probes?” Approximately 30 of such
synthetic fluorescent probes have been
identified each existing somewhere along a
spectrum of colour. These synthetic fluorescent

3. probes have the advantage of having a high
molecular diversity while also retaining target
specificity as these functions exist separately
unlike for genetic fluorescent probes. Here, a
tag gene gives labelling specificity by binding
to the gene of interest and then the synthetic
fluorescent probe binds itself to that tag gene.
It is this separation that gives the freedom of
structure for the fluorescent probes.
Fluorogenic probes give high contrast without
washing and are the subject of the
Fluorescence-Activating & Absorption-
Shifting Tag (FAST) hybrid approach. [3]
This
method was developed from the 14-kDa
Photoactive yellow Protein (PYP) by directed
evolution. Due to the programmability of yeast
cells, vast libraries were created by first
inducing mutagenesis of pyp genes to create a
library of pyp mutants which then translate into
yeast display libraries of magnitude between
107
– 108
. Library screening was then
conducted in order to sort out the ones to be
kept and those to be discarded. This was done
by Fluorescence Activating Cell Sorting
(FACS) which is capable of screening 50,000
cells per second. One of the major advantages
of FAST binding using HMBR is that it is true
to its acronymous name in being quite fast with
a binding t1/2 = 10 ms. (@20o
C when HMBR =
10 KD). An example of how FAST can be used
was shown in the real-time monitoring of fast
processes that occur in protein synthesis.
Equally fascinating was the use of multicolour
imaging of FAST-tagged proteins where
variants of HMBR that possess a different
colour can be used to target different cellular
organelles and create a sharp contrast. [4] Using
dynamic colour exchange and two colour
cross-correlation, multiple targets can be
differentiated. This allows for three-colour
imaging while only using two detection
channels by image stacking.
To sum up the work presented by professor
Gautier, FAST is a versatile small fluorogenic
protein tag that enables the efficient labelling
of proteins in mammalian cells (including
neurons) and in various other hosts from
microorganisms to zebrafish embryos. FAST
allows the study of rapid processes in near real-
time. There is a high degree of regulation that
can be exerted by the addition or absence of the
fluorogenic ligand. FAST systems hold
significant potential for multiplexed imaging,
super-resolution imaging and biosensing.
Gilles Gasser (Chimie ParisTech).
The Gasser group works within the field of
inorganic chemistry. More specifically in the
areas of inorganic chemical biology, medicinal
inorganic chemistry and medicinal
organometallic chemistry where their aim to
understand, identify and/or influence
biological processes in living cells using metal-
bases compounds requires their expert
knowledge at the interface between inorganic
chemistry, medicinal chemistry, chemical
biology and biology. Current projects include
work on antiparasitic compounds,
radioimaging, anticancer research and
photodynamic therapies.
Professor Gasser first gave us an overview of
currently available metal-based drugs such as
cisplatin the anticancer agent and cardiolite, a
nuclear imaging agent. He briefly explained
how they work in their respective applications
and talked about the advantages of metal-based
drugs, some of them being that the ligands of
these compounds can be exchanged, they
possess a redox activity, catalytic properties,
can be radioisotopes and also have a higher
structural diversity over organic-based drugs.
Professor Gasser then introduced us to his work
on the development of improved immune-PET
imaging agents, demonstrating the design of
improved chelators for 89
Zr and making a good
case for the importance of the work in the
challenges faced in oncological imaging with a
brief overview of the global incidence of
cancer and its effects. Technetium is usually
used as an imaging agent but it has a short half-
life of six hours, which is much less than that
of antibodies so one of the major advantages in
his use of 89
Zr for immune-PET imaging is that
the half-life matches that of the antibodies that
are conjugated to the imaging agent to give

4. selectivity. He also talked about the dangers of
DFO, a hexadentate chelator which is
surprisingly approved for therapeutic use
although it leaves a lot of radioactivity in the
body which tends to localise in bones due to the
high affinity zirconium has for oxygen, of
which there is a lot in bones. In order to prevent
the danger that this treatment poses to bone
marrow, professor Gasser and his team
developed DFO* which is a much more stable
octadentate form of DFO for chelation to
89
Zr4+
. He published a paper on this work in
issue 78 of Chemical Communications in 2014.
[1]
In this publication he reported a remarkably
improved stability of the DFO* complex in
vitro as compared to DFO in transchelation
experiments. This result along with testing the
cell internalisation and receptor saturation led
them to conclude that the DFO* complex
ultimately resulted in less bone accumulation
of 89
Zr. [5]
Next, we were given an introduction to peptide
nucleic acids (PNAs) which have several
advantages over DNA in bioconjugation for
use in radioimagery. [6]
The basic principle of
the pre-targeting approach involves the binding
of a radionuclide/chelator through the coupling
of two complementary oligonucleotides, one of
which is bound to a non-radioactive
monoclonal antibody.[7]
The aim then is the
imaging and/or destruction of targeted cells by
radiation. They designed and synthesised some
of these bioconjugate radiotracers and found
some promising potential for in vivo imaging.[8]
The Gasser group is continuing work on this
and have identified the promising potential of
PNA bioconjugates, yet much more work is
required to bring this technology to application
and fully understand the dynamics involved in
the function.
The Gasser group is also working on
photodynamic therapy (PDT) photosensitisers
for potential uses in many forms of oncological
therapies as well as the potential to treat
infections such as sinusitis. [9]
The general
concept of PDT is to use photosensitisers,
(which are mostly porphyrin-based), to
generate free radicals and singlet oxygen from
tissue oxygen upon photoexcitation of the
photosensitiser, which then cause cellular
toxicity. However, due to a number of
limitations with porphyrin-based agents the
Gasser group looked at using ruthenium (II)
polypyridyl complexes as alternative PDT
agents. [10]
A number of advantages of Ru(II)
over conventional porphyrins were cited, such
as the lack of photobleaching, the ease of
synthesis, high water solubility and the inert,
non-toxic and economic advantages. Through
their latest work they came to conclude that
using a combination of cell cycle inhibitors and
PS targeting there existed great potential for the
Ru(II) polypyridyl complexes developed for
PDT. [11]
Furthering this research they then
developed a number of two-photon
photosensitisers also based on a Ru(II) core.
From this they were able to demonstrate the
killing of cancer and bacterial cells using low
irradiation doses opening up questions about
further optimisation and development.
Finally, Professor Gasser ran through some of
his work on developing new organometallic
antischistosomal drug candidates. These are
fascinating antiparasicitic agents that the group
are developing for a range of parasitic diseases,
schistosomiasis in particular which is caused
by trematodes and exists currently as a major
health problem worldwide that results in the
death of ~280,000 people per annum and
greater than 207 million are infected. [8,9]
With
this overview and the fact that current
treatments of praziquantel (PZQ) are not active
against the juvenile stages of the parasites, the
cause for the development of more effective
treatments was made clear. The Gasser group
synthesised a number of chromium-PZQ
derivatives [10,11]
and investigated the
mechanism of action of PZQ.
Professor Gasser presented a large amount of
diverse, high-quality research and
demonstrated that there is an astonishing
amount of potential in the field of medicinal
organometallic chemistry.

5. Djemel Hamdane (College de France)
Dr. Hamdane’s work revolves around the
mechanisms of enzymes and the use of a
plethora of advanced biophysical tools for the
investigation of how redox enzymes function.
He presented a seminar looking closely at
tRNAs, their history, constitution and the
current research being done on tRNA
enzymatic systems.
Prior to 1951 not much was known about the
ribosome or indeed about genetic information
for the construction of peptides and proteins,
[11]
but this changed between 1951 – 1965
when discoveries were made which identified
three different species of RNA : messenger
RNA (mRNA), [12]
the carrier of genetic
information, transport RNA (tRNA), [13]
responsible for the transport of amino acids to
the ribosome and a physical link between
mRNA and the protein, and finally ribosomal
RNA (rRNA) [14]
which constitutes roughly
60% of the mass of ribosomes and is further
divided into two subunits: the large subunit
(LSU) and the small subunit (SSU), where
LSU rRNA acts as a ribozyme and catalyses
peptide-bond formation. [15]
Between 1965 –
1967 the complete structure of a nucleotide
sequence had been solved [16]
and this lead to
numerous further discoveries such as the
modification of RNA by enzymes. This would
result in the ability of researchers to make
custom RNA modifications, which to date
there are greater than 120 modifications
reported with tRNAs being the most heavily
modified.
After giving this historical background and the
incremental advances made to the
understanding of protein synthesis, Dr.
Hamdane introduced the world of RNA
modifications. He showed how rapidly the field
was advancing and how new modifications can
result in new chemistries. One such example
was made in showing how the decoding
capacity of tRNAs could be expanded by
modification of position 34 and the
identification of the crystal structure of archaeal
tRNA.[15]
They created novel modifications at
the wobble position in order to do this. Accurate
protein synthesis depends on the ability of the
ribosome select cognate tRNA by the
complement of its anticodon to the mRNA
codon, while rejecting near and non-cognate
tRNA. Watson-crick base pairing at the first
and second positions of the codon-anticodon
helix occurs due to interaction with the
ribosome, but the third codon, the wobble
position, allows for a number of non-canonical
interactions. Exploiting this property is how
much of the decoding of codons is done and
also defects at this wobble base in
mitochondrial tRNAs has been associated with
a number of human dieseaes, so this presents
itself as an opportunity to intervene.
Philippe NGHE (ESPCI)
The seminar of Dr. Nghe took us down a much
more philosophical and existential perspective
of research within the field of biochemistry.
His team studies biochemical interaction
networks using biophysics and biochemical
engineering where they aim to solve the many
unanswered questions in biological evolution
under constraints from functional interactions
between genes and how evolution could begin
self-replicating reaction networks in vitro. The
aim of the Nghe group can be summarised in
two question; What are the conditions for
molecular systems to build up in complexity ?
and how can we control and evolve gene
networks?
Dr. Nghe began his presentation by asking
“what are the properties that make chemistry
evolvable ?” and running through definitions of
chemical evolution according to ‘Darwinian
chemistries’. This gave a realisation of the
profound complexity of life and the unlikely
circumstances that were required for the
genesis of biological life. What followed were
more questions on how complex systems
require mechanisms that themselves require the
complex systems in what was described as a
“chicken and egg” problem. By looking for
mechanisms that do not require growth and
division control, coupling between
compartments in systems and the molecules

6. those systems contain and a synchronisation
between those molecules, all of which lead to
the investigation of transient compartmentation
which describes a system in atmospheric
aerosol droplets where spontaneous
compartmentalisation and then incubation in
microcompartments can occur, leading to
selection of those compartments with the best
conditions to evolve into more complex
systems such as lipid vesicles and then fuse and
form more complex systems again. Based on
this principle and using model protocells, Dr.
Nghe and his team designed microfluidic
devices capable of creating this
compartmentalisation in microfluidic droplets
and further compare the dynamics of these
compartments with and without an artificial
selection. This design is an attempt to model
the before mentioned system of chemical
evolution and evolution dynamics and lead the
team to conclude that transient
compartmentalisation was sufficient to ensure
the genetic stability and survival of replicating
molecules. [20]
Next, Dr. Nghe brought us through some work
investigating the conditions required for self-
replication and natural selection by chemical
systems. [21]
These are some of the
requirements for the origins of life as such
systems need to be able to maintain and evolve
biological information. They were interested in
finding answers to how self-replicating RNA
could possess a mutation rate low enough to be
able to retain their own molecular information
while also being able to mutate enough to
compete against molecular parasites. They
theorised that networks of interacting
molecules were likely to develop and sustain
life-like behaviour. They began experimenting
through the use of compositional genomes
where the genotype is coded in the relative
fraction of each species, instead of a sequence.
The change over time that they would observe
became inheritable information due to multiple
growth attractors. Shown in the presentation
were mixtures of RNA fragments that
spontaneously self-assemble into self-
replicating ribozymes from cooperative
catalytic cycles and networks. They observed
the evolvable nature of networks through in
vitro selection and noted that specific three-
membered networks grow faster than
autocatalytic cycles, meaning that RNA
populations possess an intrinsic ability to
evolve greater complexity through their
cooperation networks. Their research
demonstrated the advantages of high
cooperativity for growth dynamics at the
molecular stages of life.
Concluding remarks
The Chemical Frontiers of Living Matter
seminar series ran from mid-September to the
end of December and covered a diverse range
of the latest research in many fields, from
chemical biology to biological chemistry,
inorganic to organic and ranging from
medicinal and diagnostic applications, to the
more pure and philosophical. Overall the series
was truly impressive and did well to bring the
most interesting research in many fields of life
science and instil great hope and optimism to
forward-looking scientists. However, just
eleven seminar presentations cannot fully cover
the full breath of astounding work being done
within the 181 laboratories under PSL, so it
would be interesting to see the introduction of
even more areas of research with the invitation
of researchers such as Daniel Scherman of
Chimie ParisTech who is doing interesting
work in genetic pharmacology for which he
recently won an academy of sciences prize, or
perhaps Edith Heard of the Institut Curie for her
work in epigenetics and developmental biology
for which she won the INSERM grand prix.
Overall, the seminar series was a wonderful
exhibition of the profound and exciting research
being done across the many laboratories of PSL
and promotes a great deal of optimism for any
scientist looking forward.

7. References
(1) Lavis, L. D.; Raines, R. T. Bright
Ideas for Chemical Biology. ACS Chem.
Biol. 2008, 3 (3), 142–155 DOI:
10.1021/cb700248m.
(2) Li, C.; Tebo, A. G.; Gautier, A.
Fluorogenic Labeling Strategies for
Biological Imaging. Int. J. Mol. Sci. 2017,
18 (7), 1473 DOI: 10.3390/ijms18071473.
(3) Plamont, M.-A.; Billon-Denis, E.;
Maurin, S.; Gauron, C.; Pimenta, F. M.;
Specht, C. G.; Shi, J.; Quérard, J.; Pan, B.;
Rossignol, J.; et al. Small fluorescence-
activating and absorption-shifting tag for
tunable protein imaging in vivo. Proc.
Natl. Acad. Sci. 2016, 113 (3), 497–502
DOI: 10.1073/pnas.1513094113.
(4) Li, C.; Plamont, M.-A.;
Sladitschek, H. L.; Rodrigues, V.; Aujard,
I.; Neveu, P.; Saux, T. L.; Jullien, L.;
Gautier, A. Dynamic multicolor protein
labeling in living cells. Chem. Sci. 2017, 8
(8), 5598–5605 DOI:
10.1039/C7SC01364G.
(5) Patra, M.; Bauman, A.; Mari, C.;
Fischer, C. A.; Blacque, O.; Häussinger,
D.; Gasser, G.; Mindt, T. L. An
octadentate bifunctional chelating agent
for the development of stable zirconium-
89 based molecular imaging probes. Chem.
Commun. 2014, 50 (78), 11523–11525
DOI: 10.1039/C4CC05558F.
(6) Vugts, D. J.; Klaver, C.; Sewing,
C.; Poot, A. J.; Adamzek, K.; Huegli, S.;
Mari, C.; Visser, G. W. M.; Valverde, I.
E.; Gasser, G.; et al. Comparison of the
octadentate bifunctional chelator DFO*-
<Emphasis
Type=“Italic”>p</Emphasis>Phe-NCS
and the clinically used hexadentate
bifunctional chelator DFO-<Emphasis
Type=“Italic”>p</Emphasis>Phe-NCS for
<Superscript>89</Superscript>Zr-
immuno-PET. Eur. J. Nucl. Med. Mol.
Imaging 2017, 44 (2), 286–295 DOI:
10.1007/s00259-016-3499-x.
(7) Reilly, R. M. Monoclonal Antibody
and Peptide-Targeted Radiotherapy of
Cancer; John Wiley & Sons, 2010.
(8) Leonidova, A.; Foerster, C.;
Zarschler, K.; Schubert, M.; Pietzsch, H.-
J.; Steinbach, J.; Bergmann, R.; Metzler-
Nolte, N.; Stephan, H.; Gasser, G. In vivo
demonstration of an active tumor
pretargeting approach with peptide nucleic
acid bioconjugates as complementary
system. Chem. Sci. 2015, 6 (10), 5601–
5616 DOI: 10.1039/C5SC00951K.
(9) Pierroz, V.; Rubbiani, R.; Gentili,
C.; Patra, M.; Mari, C.; Gasser, G.; Ferrari,
S. Dual mode of cell death upon the photo-
irradiation of a RuII polypyridyl complex
in interphase or mitosis †Electronic
supplementary information (ESI)
available. See DOI: 10.1039/c6sc00387g
Click here for additional data file. Click
here for additional data file. Click here for
additional data file. Click here for
additional data file. Chem. Sci. 2016, 7 (9),
6115–6124 DOI: 10.1039/c6sc00387g.
(10) Mari, C.; Pierroz, V.; Ferrari, S.;
Gasser, G. Combination of Ru(II)
complexes and light: new frontiers in
cancer therapy. Chem. Sci. 2015, 6 (5),
2660–2686 DOI: 10.1039/C4SC03759F.
(11) Dolmans, D. E. J. G. J.; Fukumura,
D.; Jain, R. K. Photodynamic therapy for
cancer. Nat. Rev. Cancer 2003, 3 (5), 380–
387 DOI: 10.1038/nrc1071.
(12) Patra, M.; Ingram, K.; Leonidova,
A.; Pierroz, V.; Ferrari, S.; Robertson, M.
N.; Todd, M. H.; Keiser, J.; Gasser, G. In
Vitro Metabolic Profile and in Vivo
Antischistosomal Activity Studies of (η6-
Praziquantel)Cr(CO)3 Derivatives. J. Med.
Chem. 2013, 56 (22), 9192–9198 DOI:
10.1021/jm401287m.
(13) Sayed, A. A.; Simeonov, A.;
Thomas, C. J.; Inglese, J.; Austin, C. P.;
Williams, D. L. Identification of
oxadiazoles as new drug leads for the
control of schistosomiasis. Nat. Med.
2008, 14 (4), 407–412 DOI:
10.1038/nm1737.
(14) Liu, R.; Dong, H.-F.; Guo, Y.;
Zhao, Q.-P.; Jiang, M.-S. Efficacy of
praziquantel and artemisinin derivatives
for the treatment and prevention of human
schistosomiasis: a systematic review and

8. meta-analysis. Parasit. Vectors 2011, 4,
201 DOI: 10.1186/1756-3305-4-201.
(15) Allen, F. W. The Biochemistry of
the Nucleic Acids, Purines, and
Pyrimidines. Annu. Rev. Biochem. 1941,
10 (1), 221–244 DOI:
10.1146/annurev.bi.10.070141.001253.
(16) Lamfrom, H. Factors determining
the specificity of hemoglobin synthesized
in a cell-free system. J. Mol. Biol. 1961, 3
(3), 241–252 DOI: 10.1016/S0022-
2836(61)80064-8.
(17) Rich, A.; RajBhandary, U. L.
Transfer RNA: Molecular Structure,
Sequence, and Properties. Annu. Rev.
Biochem. 1976, 45 (1), 805–860 DOI:
10.1146/annurev.bi.45.070176.004105.
(18) Woese, C. R. Interpreting the
universal phylogenetic tree. Proc. Natl.
Acad. Sci. U. S. A. 2000, 97 (15), 8392–
8396.
(19) Yasukawa, T.; Suzuki, T.; Ishii, N.;
Ohta, S.; Watanabe, K. Wobble
modification defect in tRNA disturbs
codon-anticodon interaction in a
mitochondrial disease. EMBO J. 2001, 20
(17), 4794–4802 DOI:
10.1093/emboj/20.17.4794.
(20) Voorhees, R. M.; Mandal, D.;
Neubauer, C.; Köhrer, C.; RajBhandary,
U. L.; Ramakrishnan, V. The structural
basis for specific decoding of AUA by
isoleucine tRNA on the ribosome. Nat.
Struct. Mol. Biol. 2013, 20 (5), 641–643
DOI: 10.1038/nsmb.2545.
(21) Vaidya, N.; Manapat, M. L.; Chen,
I. A.; Xulvi-Brunet, R.; Hayden, E. J.;
Lehman, N. Spontaneous network
formation among cooperative RNA
replicators. Nature 2012, 491 (7422), 72
DOI: 10.1038/nature11549.