Contents
RESEARCH PROFILES
001 Conway Synthesis & Chemical Biology
037 Conway Integrative Biology
097 Conway Molecular Medicine
CONWAY SYNTHESIS & CHEMICAL BIOLOGY
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PROFESSOR MOHAMED AL-RUBEAI
CONWAY SYNTHESIS & CHEMICAL BIOLOGY
IMPROVED CELL LINE DEVELOPMENT
BY A HIGH THROUGHPUT AFFINITY
CAPTURE DISPLAY TECHNIQUE
AND FLOW CYTOMETRY
The project addresses the following
questions:
What is the best method to verify
homogeneity in production cell lines?
How does producers’ homogeneity
confirmed throughout the duration
of the manufacturing process?
Can cell selection be used as a
pressure to increase productivity
of antibody producing cell lines?
How can flow cytometry be used
efficiently to monitor culture
processes and select high producers?
Can cytometric technique be used for
on-line monitoring of cellular growth
and death?
UNCOUPLING OF CELL GROWTH
AND PROLIFERATION TO ENHANCE
PRODUCTIVITY BY METABOLIC
ENGINEERING APPROACH
This project addresses the following
fundamentally important questions
to resolve the underlying physiological
basis for enhancing productivity and
for the development of more efficient
production systems:
To what extent do growth and organelle
biogenesis continue in the absence of
cell cycle progression and cell division?
Can productivity be enhanced even
further? What are the limited
bottlenecks?
What is the relation between nutrient
utilisation and metabolic capability in
arrested cells?
Does bcl-2 over-expression result in
improvement of viability of arrested
cells at high cell density?
OPTIMISATION OF
BIOPHARMACEUTICALS PRODUCTION
FROM MAMMALIAN CELLS USING
CONTINUOUS CHEMOSTAT CULTURE
AT DIFFERENT DILUTION RATES
The use of continuous chemostat culture,
which is widely used in microbial cultures
provides an opportunity to comprehensively
and efficiently survey the limiting factors
of growth and productivity under different
conditions and to estimate the relative
levels of specific key proteins involved
in the control of growth and death in
sub-optimal nutrient levels hopefully
leading to the development of an improved
and stable process. This approach should
readily lead to improvements in the
present state-of-the-art for production
of recombinant products.
The group is also interested in research
in the following areas of cell culture
technology:
In-vitro expansion of chondroprogenitor
cells (adult stem cells).
Bioprocessing of virally transduced
cells for the application of gene therapy.
Development of serum free media.
Development of a scaleable disposable
bioreactor for animal cell culture
Application of systems biology to
understanding the behaviour of
mammalian cells and enhancing their
targeted productivity.
The animal cell technology group, recently
conceived with the support of Science
Foundation Ireland and based in the
Department of Chemical and Biochemical
Engineering and the Conway Institute,
is the first and only such group in Ireland
dedicated to the process engineering
of biotechnological processes involving
animal cells based on a combination of
engineering, analytical, biological and
physiological skills.
The research objectives of the group
concern the provision of design bases
for the more effective and economic
application of intensive production methods
for mammalian cells. In particular, the
intensification of such processes is
dependent upon understanding the
physiological determinants of cell growth
and death, and of product synthesis
and secretion, and also the physical
determinants of culture performance
in the intensified bioreactor environment.
The group approach to cell culture
development and optimisation is to
provide an understanding of the relationship
between gene and protein expression
and growth and productivity. On the basis
of this improved understanding, novel
strategies for optimisation of cell culture
should be possible. These strategies
include the development of methods
to improve cell culture, survival and
proliferation of mammalian cells.
Underlying these efforts is the need for
rapid, reliable techniques for selection of
high producers and monitoring cell viability
and physiology. Underlying the work is
central coherence with existing key research
themes within the Conway Institute (eg.
gene array analysis, proteomics and
cytomics). The programme is focused
exclusively on strategically important
themes in the development of mammalian
cell culture processes for enhanced and
optimised production of biopharmaceuticals.
Mammalian cell culture processes face
numerous challenges related to compressed
product development cycles, capacity
shortages, and the proliferation and
productivity of cell lines and culture
conditions. Exploitation of the advances
in molecular biology will help to resolve
many of the problems associated with
large scale production.
The major themes of the scientific
programme are:
GENOMIC AND PROTEOMIC ANALYSIS
OF CULTURED MAMMALIAN CELLS FOR
BIOPROCESSING
This project addresses the following
fundamentally important questions
using a combination of mammalian
cell bioreaction, molecular cell biology,
genomic and proteomic techniques
and bioinformatics:
How do changes in growth rate and
environmental conditions in batch and
continuous cultures affect gene and
protein expression level and pattern?
What is the relationship between
product expression levels (including
non-expression) and genome pattern?
What are the variations in gene
and protein expression that take place
during various genetic manipulations
(eg. in the apoptotic and cell cycle
pathways)?
How can genetic and proteomic results
from the above be utilised to optimise
productivity of mammalian cell lines
and to minimise development times?
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DR PATRICK CAFFREY
CONWAY SYNTHESIS & CHEMICAL BIOLOGY
DR EOIN CASEY
CONWAY SYNTHESIS & CHEMICAL BIOLOGY
The biofilm engineering group is focused
on the investigation of bacterial biofilms,
with a primary emphasis on interactions
between the physico-chemical
microenvironment and physiology.
Biofilm-related infections of implanted
biomaterials frequently complicate the
treatment of surgical and ICU patients.
The pathogenesis of these infections
generally stems from the ability of
microorganisms to colonise the inert
surfaces of implanted devices. Bacterial
cells embedded in dense polysaccharide
biofilms are inherently resistant to host
immune responses and antimicrobial
chemotherapy. Conventional antibiotic
resistance mechanisms are not sufficient
to explain most cases of antibiotic
resistant biofilm infections. The complexity
of biofilm metabolic behaviour has limited
our understanding of why unwanted
biofilms are particularly resistant to
antimicrobial agents. A promising area
of current research is based on the
hypothesis that slower growth rates
in bacterial biofilms contribute to
increased antimicrobial resistance.
It is widely recognised that biofilms
contain slowly growing and non-growing
cells. It is generally accepted that the
existence of physiological heterogeneity
in biofilms arises mainly as a consequence
of nutrient gradients formed by the
reaction-diffusion mechanism.
Our approach involves a combination
of experimental investigations with
mathematical modelling. We are using
novel scale-down systems to investigate
physiological spatial heterogeneity in
Staphylococcus epidermidis biofilms
and to use these systems to investigate
antibiotic resistance.
CURRENT PROJECTS INCLUDE
Development of a novel drug delivery
system for biofilm associated
infections (Enterprise Ireland funded).
Investigation of the factors that
determine physiological heterogeneity
in biofilms. (Science Foundation
Ireland funded, collaboration with
J O’Gara, Department of Industrial
Microbiology).
Solute gradients in strucurally
heterogeneous biofilms. Enterprise
Ireland funded (collaboration with
C Picioreanu, TU Delft).
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Fig. 1. 16-methyl-16-descarboxyl amphotericin B.
NH2
OO Me
Me
Me
Me
HO
Me
O OOH OH OH
OH
OH 16
OH OH
OH
OH
Many of the antibiotics used in clinical
medicine are derived from natural
products synthesised by bacteria and
fungi. Micro-organisms also synthesise
a number of other important pharma-
ceuticals. These include anti-cancer
drugs such as doxorubicin and epothilone
C, immunosuppressants like cyclosporin
and rapamycin, and the cholesterol–
lowering statins. The need to develop
improved treatments for serious diseases
has intensified interest in biosynthesis
of these compounds. This research group
is interested in genetic manipulation
of bacterial secondary metabolism to
produce useful new compounds. A major
focus is the biosynthesis of polyenes;
highly effective antifungal antibiotics
that disrupt the ergosterol-containing
membranes of fungal cells. Polyenes
have a broad spectrum of activity and
resistance has not emerged as a serious
problem after forty years of clinical use.
The most serious disadvantages of
polyene antibiotics are extreme toxicity
and low water-solubility. However,
the rising incidence of life-threatening
systemic fungal infections is being mirrored
by increased resistance to other classes
of antifungal antibiotics. Engineered
biosynthesis of less toxic polyenes
is clearly a worthwhile objective.
The most important polyene is amphotericin
B, a heptaene produced by Streptomyces
nodosus. The macrolactone core of ampho-
tericin B is assembled from acetate and
propionate units by a modular polyketide
synthase. The late stages involve oxidation
of a methyl branch to a carboxyl group,
glycosylation with an aminodeoxyhexose
sugar, mycosamine, and hydroxylation.
We have characterised the amphotericin
biosynthetic gene cluster and developed
methods for genetic manipulation of
S. nodosus. Analysis of the polyketide
synthase sequence has given insights
into how these enzymes determine the
stereochemistry of chiral centres during
assembly of polyketide carbon chains.
Targeted gene replacements have yielded
several amphotericin analogues.
To date, the most promising of these
is 16-descarboxyl-16-methyl amphotericin
B, which is expected to show a reduction
in toxicity similar to that of the semi-
synthetic derivative amphotericin
B methyl ester.
Most of the engineered strains produce
10 to 50 mg of novel polyene per litre
of culture. Future work aims to maximise
these yields to produce large quantities
for therapeutic testing. In addition to
its antifungal action, amphotericin B also
has some activity against prion diseases,
enveloped viruses and Leishmania parasites.
The new amphotericin analogues will also
be tested for improvements in these
biological activities.
Additional projects include development
of methods for genetic manipulation of
other antibiotic-producing bacteria and
engineering glycosylation of bioactive
natural products.
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PROFESSOR PAUL ENGEL
CONWAY SYNTHESIS & CHEMICAL BIOLOGY
Research carried out by my group focuseson various aspects of enzymes, especiallythose involved in oxidising amino acidsand fatty acids, aiming at a molecularunderstanding of how they work. Typicallythis involves obtaining the enzymes in ahighly purified state, usually after cloningthe gene into a suitable host organismin order to achieve high levels of theenzyme protein.
Some of the work involves studyingthe enzyme mechanisms, seeking thestructural basis of their catalytic activityand in particular aiming for a betterunderstanding of how different proteinsubunits work together to providesophisticated regulation of activity– eg. in the allosteric control ofglutamate dehydrogenase.
Other work, in part supported throughEnterprise Ireland’s advanced technologyresearch programme, is focused onpractical applications. Modern genetechnology makes it possible to alterand adapt enzymes, in search of usefulnew properties. The chemical industryneeds good catalysts, and specifically itneeds ‘chiral’ catalysts that can distinguishbetween left and right-handed versionsof chemical molecules. Enzymes are idealin this regard: they are extremely potentcatalysts and they normally give 100%discrimination between left and right.The snag in the past has been that theywere too expensive, too fragile and oftenworked only on the wrong compounds– ie. biological compounds that mightnot match the chemist’s requirements.This line of research is now producingbiocatalysts that are cheap, robust andabove all can now work on a wider andmore attractive range of chemical targets.This is primarily aimed at producingbuilding blocks for the drug industry.
A third strand of this group’s researchaims to discover the various ways in which
genetic defects in three different enzymescause disease. The enzyme MCAD (mediumchain acyl CoA dehydrogenase) works inthe breakdown of fats to harness energy. Itis one of a set with overlapping function andbecause of this we can function for most ofthe time with defective MCAD. This makes itinto a hidden weakness which emerges attimes of stress (infection, fasting etc.) andso MCAD deficiency is associated with ‘cotdeath’ (SIDS). It seems that many ofthe MCAD defects relate to the molecule’sinability to fold up into the right shape.Another enzyme under study is G6PD(glucose 6-phosphate dehydro-genase),defective in over 400 million peopleworldwide. The disease mainly affectsred blood cells, causing anaemia, and is soprevalent because it coincidentally protectsagainst malaria! Most of the diseasemutations affect the long-term stabilityof the enzyme in the red cell which cannotreplace damaged enzyme molecules.
The third disease-related enzyme understudy is IMPDH1. A defect in this enzymeis responsible for progressive blindness inone of the forms of retinitis pigmentosa.This particular form RP10 shows ‘negativedominant’ inheritance, so that gettingthe ‘bad’ gene from one parent only issufficient to cause blindness. The researchis aimed at understanding how this happens,with perhaps a chance of finding waysto slow or prevent loss of sight.
Finally, another aspect of the group’sresearch focuses on ‘extremophiles’;organisms that live in what, to us, seemvery hostile environments (ie hot, cold,salty). The enzymes of these organismshave to be able to survive the conditions,otherwise the organisms themselves woulddie Looking at the molecular adaptationsthat make this possible teaches us a lotabout how proteins work, and some ofthese tough enzymes have highly desirableproperties for practical application.
DR MIKE CASEY
CONWAY SYNTHESIS & CHEMICAL BIOLOGY
The objective of our research group is the
development of new, more selective, and
more efficient ways of preparing organic
compounds, particularly compounds that
exhibit useful biological activity. We are
exploring three ways of achieving this
objective: (i) by developing selective new
catalysts for synthetically important
reactions, (ii) by developing useful new
reactions involving sulfur compounds,
and (iii) by developing novel efficient
synthetic routes to specific highly
biologically active target molecules.
1. NOVEL CATALYSTS
Many important organic molecules,
eg. many pharmaceuticals, are chiral,
ie the molecules are not superimposable
on their mirror images, and therefore they
can exist in two forms. Such molecules are
said to be ‘handed’ because the two forms
have the same relationship to each other
as left and right hands. It is essential that
methods are available for the selective
synthesis of each ‘hand’ of the compound,
because the two forms often have quite
different biological activity and only one
is suitable for administration as a drug.
One very promising method for synthesising
such molecules relies on the use of
catalysts, which not only accelerate the
formation of the compounds but, provided
the catalysts are themselves ‘handed’,
result in selective formation of one ‘hand’
of the product.
We are exploring the use of compounds
called imidazolines, which are proving
useful as chiral catalysts and as
components of more complex chiral
catalysts. We have developed a very
convenient new way of preparing
imidazolines, and have shown that they
are very versatile molecules whose
properties can easily be ‘tuned’ to afford
high reactivity and selectivity. Fig. 1 on
the left shows the structures of a series
of our imidazolines, illustrating how their
shape can be altered in a graduated way
by ‘tuning’ their structures.
2. SULFUR COMPOUNDS
We are studying a family of chiral sulphur
compounds, the sulfoxides, and have shown
that they can be used to carry out unique
chemical reactions, and that they can
control the ‘handedness’ of the products.
For example, we recently achieved a very
short synthesis of the important anticancer
drug precursor podophyllotoxin using
sulfoxides to assemble a complex product
from simple starting materials, in a highly
selective way (see Fig. 2).
3. SYNTHESIS OF BIOLOGICALLY
ACTIVE COMPOUNDS
In addition to our work on
podophyllotoxin, described above, we are
working on the preparation of two other
targets, the pseudopterosins and
himbacine. In both cases, our objective is
to develop synthetic routes that are short,
efficient and flexible. The last point is
important because it will allow us to prepare
series of novel structural analogues
of the target compounds, so that their
bioactivity can be tested. In this way
the structural requirements for high
bioactivity can be determined and useful
new compounds can be discovered.
In summary, the focus of our research is
on the development of improved methods
for the preparation of medicinally useful
compounds, and on the discovery of new
agents that have valuable biological activity.
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OMe
OMe
One
reaction!
MeO
H
S
But
O
OTBDPS
OTBDPS
CO2EtCO2Et
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S
ButO
O
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OMe
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Fig. 1. Imidazolines.
Fig. 2. Synthesis of podophyllotoxin.
DR DECLAN G GILHEANY
CONWAY SYNTHESIS & CHEMICAL BIOLOGY
Our interests lie in the general area of
organic synthesis, for the construction
of both useful and theoretically
interesting molecules. Of particular
interest are enantioselective synthesis;
organophosphorus chemistry; the organic
chemistry of main group elements and the
synthesis of medium and small rings.
ASYMMETRIC OXIDATION
Our most mature work concerns the
chromium-salen catalysed asymmetric
epoxidation of E-alkenes. This methodology
is complementary to the Jacobsen
manganese system in that it allows the
use of the more readily accessible E-alkenes.
We have been working on this system
extensively since 1995 and it has provided
a wealth of interesting information. The
chromium salen system has a stoichiometric
version so that its stereoselectivity can be
studied separately from its catalytic cycle.
Our objective has been to try to understand
the chromium system with a view to gaining
insight into the manganese system. During
this work, we have become very proficient
at implementing the other recently
discovered asymmetric oxidation reactions.
UNUSUAL SUGARS
FOR GLYCOMICS STUDIES
We are using various asymmetric oxidation
methodologies in an exciting and ambitious
programme for the construction of unusual
sugars. The method is extremely flexible
and allows the synthesis of libraries of
substituted versions of all of the hexose
sugars, including both branched and amino
cases. The ready availability of these libraries
is an attractive prospect from the point of
view of the emerging area of glycomics.
Glycomics is analogous to genomics and
proteomics in that it explores the role
of carbohydrates in biological processes.
Unusual sugars are ubiquitous in cells,
especially on cell surfaces. They project
from nearly all the protein and many
of the fat molecules. As a result, these
glycopeptides and glycolipids (of varying
degrees of complexity) are intimately
involved in a wide diversity of biological
processes such as viral entry, bacteria-
host interactions, signal transduction,
inflammation and, especially, the cell-cell
interactions in cancer. A major difficulty
that has afflicted glycomics research
has been the much greater structural
complexity and diversity of the molecules
involved, compared to nucleic acids and
proteins. Repeatedly in the literature,
it is noted that a major stumbling block
to this research is the very limited
availability of modified sugars and amino
sugar systems for use in the biological
studies. We hope to help redress
this situation.
P-CHIRAL PHOSPHORUS COMPOUNDS
This is the other main area of our research
at the present time. We have developed
a general synthesis of this type of
compound wherein the chirality lies
at the phosphorus atom. Historically,
this has been almost impossible to achieve
with reasonable flexibility and yield. The
significance lies in the usefulness of the
compounds as ligands for transition
metal-based catalysis. The breakthrough
has been patented and has formed the
basis for the establishment of a campus
company (Celtic Catalysts). The latter has
received both state and venture capital
funding and shipped its first products
in February 2005.
DR RAPHAEL DARCY
CONWAY SYNTHESIS & CHEMICAL BIOLOGY
SUPRAMOLECULAR CHEMISTRY
This research area is concerned with
molecular design and synthesis directed
at creating molecular assemblies and
causing molecule-molecule or molecule-
cell interactions. We were the first to design
such molecular assemblies (vesicles)
based on cyclodextrins (1). Like biological
cells, these vesicles, since they consist
of cyclodextrin host molecules, can
‘recognise’ and interact with molecules
or cells that come in contact with them.
(Collaboration with University of Twente)
SYNTHESIS OF
TARGETED DRUG VECTORS
The adhesion of liquid-crystalline colloids
(supramolecular assemblies) to proteins,
cell surfaces and DNA is fundamental
to the deliberate targeting of drugs,
for which the colloids are used as vectors,
to their sites of action. Glyconjugates
of these assemblies are being used to
understand and exploit receptor phenomena
at cell surfaces such as the cluster effect.
We have now published details of the first
totally synthetic system for which the
cluster effect has been demonstrated,
specifically between a galactose-targeted
cyclodextrin vesicle and immobilised
lectin (2) (Collaboration with University
of Messina and University of Milan).
DNA AND RNA VECTORS
Gene therapy holds great promise.
However, delivery of genetic material to
biological cells is a major obstacle-course
demanding new synthetic vectors, which
will exploit the ambient biology. The ideal
process, which is being sought, might be
termed ‘symbiotic chemistry’. The new
vectors, which we synthesise for cell
transfection and delivery of oligonucleo-
tides, are based on cyclodextrins (3,4).
Cell-trafficking of the complexes, which
they form with DNA can be studied by
electron and confocal microscopy (Fig. 1).
In the past year, examples of vectors have
been synthesised, which are up to ten
times more efficient than the commercial
vector DOTAP for undifferentiated cells
(that is, over 100,000 times more effective
than unvectorised DNA). New synthetic
methods have been developed, which
have enabled the introduction of bio-
labile groups into the vector molecules
in the hope of accelerating escape from
endosomes after cell entry. Also, initial
experiments directed at delivery of siRNA
have been carried out (Collaboration
with Prof Caitriona O’Driscoll, School
of Pharmacy and Prof Gerry O’Sullivan,
Cork Centre for Cancer Research, UCC).
Fig. 1. Trafficking of CD-DNA complex
in Cos-7 cells as observed over 90 mins
by confocal microscopy: cell nucleus, blue;
DNA, green; cyclodextrin vector, orange;
CD-DNA complex, yellow.
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DR PATRICIA KIERAN
CONWAY SYNTHESIS & CHEMICAL BIOLOGY
Although most research emphasis has
focused on lethal effects of shear stress,
sub-lethal phenomena are of particular
importance for process optimisation.
Our work has involved the identification
and analysis of post-stress responses
exhibited by cell suspensions exposed
to well-defined levels of shear (eg.
in capillary and submerged-jet devices
(Fig. 1) and to less well-defined, but more
practically relevant cultivation conditions
(in a bioreactor), with a long-term view to
ultimately elucidating the mechanism(s)
by which hydrodynamic stress is sensed
and transduced within the cell.
Commercially viable exploitation
of biocatalysts to produce valuable
pharmaceuticals depends crucially on
the ability to speedily and reliably scale
-up a biological process from the laboratory
bench to the production floor. At the heart
of almost every bioprocess, and posing
the most severe scale-up challenges, is the
bioreactor: the vessel in which the organism
is cultivated and/or product formation
occurs. The bases for scale-up are poorly
defined and loss of productivity on scale-
up is common. A key theme, worldwide
and within our group, is the interaction
between suspended cells and the
hydrodynamic environment prevailing
in the bioreactor.
Plant cell culture technology facilitates
the production of valuable chemicals
(including, for example, Taxol, the anti-
cancer agent) under controlled and
reproducible conditions. However, given
the diversity of phytochemicals, the range
of products commercially produced via this
route is extremely limited due to economic
feasibility, which, assuming that a market
for a plant product exists, derives from
a combination of biological and process
-based factors. Plant cells, in common
with mammalian cells, are sensitive to
the hydrodynamic stresses in bioreactors.
Plants have developed an array of defense
mechanisms, which afford them protection
against pathogenic attack. One of the
first measurable responses to infection,
occurring within a few minutes of stress
imposition, is the production and release
of active oxygen species (AOS), known
as the oxidative burst (OB). Our work has
shown that the OB also occurs in response
to non-pathogenic stimuli, including
hydrodynamic stress (Fig. 2) and, further,
that hydrodynamic stress stimulates
transcription-level responses. The OB
is only one in a series of stress responses,
which may culminate in commitment to
a programmed cell death (PCD) pathway
(Fig. 3), similar to that exhibited by
mammalian cells and which seriously
undermines system productivity. The
ultimate objective of this strongly inter-
disciplinary work is the development
of a rational approach to scale-up, based
on a comprehensive understanding
of the interactions between the cell
and its cultivation environment.
RESEARCH PROJECTS CURRENTLY
ONGOING:
Sub-lethal stress responses
in plant cell suspension cultures
(with Dr Rosaleen Devery, DCU
and Dr Paul McCabe, UCD)
Characterisation and optimisation
of liquid-liquid bioreaction systems
(with Dr Kevin O’Connor
and Dr Dermot Malone, UCD)
Development of in-line methodologies
for bioprocess characterisation
- plant and mammalian systems
(with Dr Brian Glennon
and Dr Susan McDonnell, UCD)
Optimisation of secondary metabolite
production by plant cell suspension
cultures (with Mrs Ingrid Hook, TCD)
Fig. 2. DNA and RNA confocal scan images showing
evidence of increased RNA levels (red) in
Arabidopsis thaliana cells (a) after cultivation in a
bioreactor, relative to (b) cells from control cultures.
Images by Paul Jeffers; A. thaliana generously
provided by Dr Paul McCabe.
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DR NOEL FITZPATRICK
CONWAY SYNTHESIS & CHEMICAL BIOLOGY
Current research involves computational
and experimental studies of model
enzymes. The computational studies
use quantum mechanical calculations,
principally the ab initio and density
functional methods. An example of a
typical model is shown below, formed
when the corresponding zinc carboxylate
is reacted with tmen.
A recent theoretical study considered
hydrogen bonds in alkali metal
hydroxamate species. Density functional
geometry optimisation was performed
on the model alkali metal hydroxamates
(MH(RC(O)NHO)2), 1, with M = Li,
K and R = Ph (BA), 4-Me-Ph (MeBA),
4-F-Ph (FBA) and Me (AA) at the
Becke3LYP/3-21G* level of theory in
the gas phase. The optimised structures
were analysed for correlations between
geometric parameters that reflect the
extent of delocalisation in the system
and the strength and symmetry of the
intramolecular ON–H…O’N hydrogen bond.
Also a density functional study of model
complexes of zinc hydrolases and their
inhibition by hydroxamic acids, using the
B3LYP approach and large basis sets, gave
a set of stable pseudooctahedral chelates.
Addition of a water molecule to these
chelates gave hydrates, which in all cases
were energetically more stable than the
corresponding chelates.
Studies on structural variation in dinuclear
model hydrolases and hydroxamate inhibitor
models, using synthetic, spectroscopic
and structural methods, gave interesting
results. Reactions of the model hydrolases
with a number of hydroxamic acids gave a
series of dibridged complexes in which the
bridging hydroxamates exhibited novel
bonding modes.
The complexation and proton transfer
by hydroxamic acids in model inhibited
metallohydrolases showed the formation
of metal hydroxamate trimers. In these
novel species, each hydroxamate bridges
two metal centres.
Ongoing research projects are considering
variations in the bonding and energetics of
hydroxamate species and studies on model
enzymes, especially those with zinc.
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O’c
ON O’N
Fig. 2. Model alkali metal hydroxomates.
pressure
indicator
pressure
vessel
bleed line
cell
suspension
inlet
peristaltic
pump
glass
recieving
vessel
stainless steel
pressure vessel
compressedd
air inlet
Fig. 1. Submerged jet apparatus used to subject
cells to well-defined levels of shear.
Fig. 3. Morinda citrifolia cells (x 100 magnification,
stained with acridine orange), 5 hours post-shear
(submerged jet, 0.85 bar), showing condensed
chromatin, characteristic of PCD. Images by Paul
Jeffers; M. citrifolia generously provided by
Dr Graham Wilson.
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Fig. 1. Zn(O2CCH3)2(tmen).
PROFESSOR T JOSEPH MCKENNA
CONWAY SYNTHESIS & CHEMICAL BIOLOGY
Professor T. Joseph McKenna is Professor
of Investigative Endocrinology, UCD and
Consultant Endocrinologist, St. Vincent’s
Hospital. His research group focuses on
mechanisms of adrenal steroidogenesis
and, in particular, on the defects in adrenal
sex hormone production that promote
virilisation and infertility. Strong
collaborative links are envisaged between
his group and researchers from the
disciplines of animal husbandry and
production that will be subserved by
access to core facilities such nucleic acid
sequencing, GC-MS and the transgenic
holding facility.
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DR BRIAN GLENNON
CONWAY SYNTHESIS & CHEMICAL BIOLOGY
As part of the effort to produce new
therapeutic treatments, it is necessary
to ensure that these innovative products
can be safely and reliably produced on a
large-scale at a reasonable cost, and with
minimum environmental impact.
Throughout the chemical and biochemical
manufacturing industries, one of the
greatest technical challenges is the scale-
up of processes from the laboratory to
production-scale. For many operations,
this is straightforward, with the system
obeying well-defined and well-established
scale-up rules. This is especially true for
large-scale continuous processing (eg.
distillation, extraction, filtration, etc.).
However, for batch processing, scale-up
is generally far more empirical, with heavy
emphasis placed on the use of pilot-plant
studies to provide a technological bridge
between the laboratory and the production
plant. Our research group is interested in
developing better ways to more reliably
facilitate such transfer.
In particular, the scale-up of biological
processes has proved problematic. The
response of a micro-organism to the
processing environment in a production
operation often proves to be significantly
different from that observed in the
laboratory. This variation in response
is understandable when the different
environments are considered in any detail.
In laboratory equipment, typically shake-
flasks, mixing, aeration and substrate
distribution are all quite uniform. Pressure
and temperature gradients are essentially
non-existent, or present over such small
scales as to be negligible. In production-
scale systems, which may range from
100 litres up to 200 m3 in size, the extent
of the variation in local values for all of
these parameters may, by comparison,
be very significant.
A similar problem faces the production of
bulk pharmaceuticals, whether produced
through chemical or biological synthesis.
In particular, almost all pharmaceuticals
are purified using batch crystallisation in
large stirred tanks (geometrically similar
to bioreactors), which are poorly mixed
due to the limitations of the vessel design.
The crystallisation process is governed by
kinetic transport phenomena, which are
complex functions of the prevailing non-
equilibrium conditions within the vessel.
Thus, heterogeneities in the distribution
of, for example, solute concentration
or temperature will significantly alter
the performance of the process-scale
crystalliser compared to a well-mixed
system, such as may typically prevail in
the laboratory-scale vessel from which
the process has been developed. As with
bioreactor scale-up, the challenge is to
determine the interactions between
identifiable stages of the crystallisation
system, in which different transport
activities prevail.
A variety of technologies are employed
as part of these investigations, ranging
from pilot-scale bioreactors, to in-line
imaging systems.
Images of crystals taken within
a crystallisation vessel.
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PROFESSOR PAT GUIRY
CONWAY SYNTHESIS & CHEMICAL BIOLOGY
Our research group focuses on synthetic
organic chemistry, with interests in both
the development of asymmetric synthetic
methodology through the application
of new chiral ligands in homogeneous
metal-catalysed transformations and
in the total synthesis of compounds
of biological interest.
The preparation of enantiomerically
pure compounds is an important area of
contemporary synthetic organic chemistry
with the market for dosage forms of single
enantiomer drugs predicted to rise to $200
billion by 2008. Asymmetric catalysis, one
approach for their preparation and the
focus of research in both academia and
industry, is a technology that is attractive
both economically and environmentally.
The preparation of new ligands that influence
the stereochemistry of reactions occurring
at the metal template to which they are
complexed is a current focus in our group.
We have developed a range of bidentate
(N,N) , (N,O) and (P,N) ligands exemplified
by structures 1-4, and applied them to
the synthetically important asymmetric
transformations of the Heck reaction (both
intermolecular and intramolecular examples
with enantiomeric excesses (ees) up
to 99%), allylic substitutions (ees up to
98%), transfer hydrogenation of ketones
(up to 96% ee) and rhodium-catalysed
hydroboration of alkenes (up to 99.5% ee).
See Figures 1 and 2.
In addition to the bidentate examples
given, we have also a significant programme
on the development of tridentate ligands,
eg. 5-6 (Fig. 3), and these have proven
to be particularly efficient in two metal-
catalysed processes: (a) allylation and
propargylation of aldehydes employing the
Noazki-Hiyama-Kishi reaction (up to 94%
ee) and (b) the addition of dialkylzincs to
aldehydes (up to 99% ee). We supplement
our synthetic effort with mechanistic studies
on the catalysts we develop. These studies
employ solid-state (X-ray crystallography),
solution state (NMR spectroscopy) and
computational chemistry in an attempt
to understand the origin of the enantio-
differentiation in the key step of the
catalytic cycle and thus further inform
future ligand design.
TOTAL SYNTHESIS PROJECTS
Lipoxins are a group of biologically active
mediators derived from arachidonic acid
through the action of lipoxygenase enzyme
systems. Single-cell types generate lipoxins
at nanogram levels during human neutrophil
-platelet and eosinophil transcellular
biosynthesis of eicosanoids, a class of well
known biologically active products. Lipoxins
are conjugated tetraene-containing
eicosanoids and recent results suggest
that they are associated with human
disease as they modulate cellular events
in several organ systems. Lipoxin A4 (LXA4)
(7) and lipoxin B4 (LXB4) (8) are the two
major lipoxins, Fig. 4. LXA4 (7) has been
identified in bronchoalveolar lavage cells
while a defect in LXA4 (7) production
is observed with cells from patients with
chronic myeloid leukaemia. In light of
the biological activity associated with
this relatively new class of regulators, their
total synthesis is actively investigated by
a range of workers worldwide. Our work
aims to prepare lipoxin analogues with
an active region for biological activity
but which resist, or more slowly undergo
metabolism and therefore have a longer
pharmacological activity. The design
feature will also take into account that the
analogues should be more lipophilic than
the natural lipoxins and therefore are more
readily taken up by biological membranes.
We have a long-standing interest also in
the chemistry and biology of amphetamines
and substituted MDMA analogues
exemplified by 4-MTA
(4-methylthioamphetamine 9).
2 31 4
R
N N
R
R R
OH
Ph Ph
FeFeN
RO
N
FePPh2
N
N
R
PPh2
R
O N ON
NH
R R
65
N
N OH
OH
7
O
LXA4
OH
OH
HO OH
8
LXB4
O
OH
OH
HO OH
9
NH2
MeS
Fig. 2. Representative bidentate ligands prepared within the group.
Fig. 3. Representative tridentate ligands prepared within the group.
Fig. 4. Total synthesis projects.
Fig. 1. Overlay of palladium cations of the 2-
sunstituted quinazolinap ligands (4; R=H (green),
R=I-Pr (red), R=2-(2-pyridyl) (white) and R=2-
(2-pyrazinyl) (yellow).
RESEARCH PROJECTS
CURRENTLY ONGOING:
Electronic effects in quinazoline-
containing ligands for asymmetric
catalysis.
Tridentate quinazoline- and
oxazoline-containing ligands.
Novel ferrocene derived ligands
in diethylzinc additions.
New tridentate and bidentate
oxazoline-containing ligands.
Total synthesis of lipoxin analogues
and a study of their biology (with Prof
Catherine Godson, Conway Institute).
The chemistry and biology of
amphetamines and substituted
phenylethylamines (with Prof Alan
Keenan and Dr Gethin McBean,
Conway Institute).
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2.
3.
4.
5.
6.
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In the hydrogel drug delivery work,
it has been recognised that a sound
interpretation of the mass transport
phenomena over a range of length scales
is critical to the understanding, further
development and design of smart drug
delivery systems. In this project, theoretical
transport phenomena investigations are
undertaken involving poly (N-isopropy-
lacrylamide) (PNIPAM) polymer hydrogels.
The objective of the theoretical studies
is to deliver a fundamental mechanistic
understanding of the transport-phenomena
at both the molecular scale and macro-
scale. The molecular dynamics (MD)
approach will study diffusion in the drug
loaded polymer water matrix. In addition,
the MD study will investigate the underlying
physical basis for the thermoselective
behaviour of the polymer hydrogels.
The macroscopic modelling will investigate
the full spectrum of rate-controlling steps
that determine the behaviour of the drug
delivery device and together with the
experimental studies will improve the
mechanistic understanding of thermo-
selective polymer drug delivery systems.
The capture and sequestration of CO2
is one of the major technological problems
facing society both nationally and
internationally. Currently, anthropogenic
CO2 is primarily produced by combustion
of fossil fuels, and capture of these emissions
at typical combustion temperatures is not
feasible using contemporary methodologies.
In this project, the protocols underlying
the fabrication of new silica and inorganic
metal oxide membranes effective in
separating gas mixtures and hence CO2
capture at high temperatures are being
developed. This project is a continuation
of an earlier project in which theoretical
and experimental work has demonstrated
that such a route to the solution of
this problem is viable. Ultimately,
the sequestration /fixation of CO2
is a major issue and work is currently
underway to evaluate novel approaches
using artificial photosynthesis. The ‘dark’
Calvin cycle reactions will play a central
role in determining the viability of artificial
catalytic routes to a resolution
of this problem.
PROJECTS
Novel membranes for high
temperature separation of CO2
from combustion exhaust gases
Collaboration: M Tacke (Chemistry,
UCD); funded by IRCSET,
Basic Research.
New synthetic and computational
methodologies for microwave
enhanced solid phase organic
synthesis. Collaboration: D O’Shea
(Chemistry, UCD); funded by
Enterprise Ireland, Basic Research.
Atomistic simulation and continuum
models of non-equilibrium phenomena
in hydrogel drug delivery systems.
Collaboration: Damian Mooney,
Eoin Casey; funded by HEA PRTLI
Cycle 3, CSCB.
Amorphous metal oxide
nanomembranes for CO2 recovery
at high temperatures. Collaboration:
Denis Dowling (Mechanical Engineering,
UCD), Damian Mooney); funding
sought from SFI RFP, 2005.
The influence of microwave fields
on the properties of biomaterials
and inorganic solids. Collaboration:
Damian Mooney, Niall English
(CCG Cambridge).
PROFESSOR DON MACELROY
CONWAY SYNTHESIS & CHEMICAL BIOLOGY
The molecular simulations research group
within the Department of Chemical and
Biochemical Engineering is currently
engaged in a range of studies involving (a)
the influence of electromagnetic fields on
matter, (b) drug delivery using thermo-
responsive hydrogels and (c) carbon
dioxide capture and fixation.
In recent work, it has been demonstrated
that athermal interactions between water
and e/m fields in the range of 100 GHz
lead to significantly enhanced mobility
of the water molecules (up to a factor of
30) due solely to hydrogen bond disruption
within the fluid. Further work has shown
that this disruptive effect can have very
significant effects on the stability of
hydrate crystals as illustrated in Fig. 1.
This work is now being extended to
investigate the influence of e/m fields
on solid phase organic synthesis (SPOS).
Conversion rates in SPOS of low molecular
pharmaceuticals have been found
experimentally to be dramatically enhanced
(up to two orders of magnitude) under
conditions, which are known to be diffusion
limited. The simulation work will provide
insight into the molecular basis for this
enhancement. In another strand of work,
the effects of e/m fields on protein structure
and dynamics is also being examined.
Specifically, this research focuses on
resonant interactions between the
intramolecular hydrogen bonds and the
external fields to determine the extent to
which protein folding and hence bioactivity
is affected by field frequency and intensity.
1.
2.
3.
4.
5.
t = 1 ps t = 18 ps
t = 36 ps t = 48 ps
t = 57 ps t=63ps
t = 72 ps t = 80 ps
Fig. 1. The time sequence for the
break-up of a clathrate hydrate crystal
in an e/m field under isothermal
conditions at 220K. Snapshots of
the cluster configurations for a
clathrate hydrate crystal in a field
of 100 GHz / 0.15 V/Å.
The methane molecules are shown
as grey spheres and the hydrogen
bonds of the water molecules are
shown as lines (note that only the
solid crystalline material is shown,
the liquid mixture of water and
methane surrounding the crystal is
not shown). The electromagnetic field
is directed vertically.
PROFESSOR STEPHEN MAYHEW
CONWAY SYNTHESIS & CHEMICAL BIOLOGY
My research group is interested in the
structures, functions and mechanisms of
action of flavoproteins; a group of yellow
proteins that contain derivatives of the
vitamin riboflavin. They play a major role
in important metabolic reactions of the
cell, and new functions are continually
discovered; for example, it was shown
recently that flavoproteins function in
systems that sense blue light and control
circadian rhythm. Different properties
are conferred on the flavin by different
interactions with host protein but the role
of the protein environment in modifying
the chemical reactivities and redox
properties of the flavin is not yet clear.
Flavodoxins are small FMN-containing
proteins that occur in microorganisms
where they function as electron carriers
in low-potential oxidation-reduction
reactions. We are studying the properties
of flavodoxin from Helicobacter pylori,
a common human pathogen that infects
the stomach, and that is implicated in
ulcers and various cancers. The organism
is becoming resistant to current
therapies, which include treatment with
metronidazole, a compound that depends
for its bacteriostatic action on reduction
by a low-potential donor such as flavodoxin.
The protein may be a suitable target for
new bacteriostats.
Acyl-CoA dehydrogenases catalyse the
first step in the b-oxidation of fatty acids.
Franz Knoop (1904) concluded that
mammals oxidise the side chains of phenyl
alkanoates by b-oxidation, and then
excrete the benzene ring. In contrast,
bacteria completely degrade aromatic
alkanoates using them as the sole source
of carbon and energy. The enzymes that
oxidise the CoA derivatives of such
aromatic compounds have not been
identified.We are studying acyl-CoA
dehydrogenases from Pseudomonas
putida, a bacterium that can grow on
phenyl alkanoates.We are comparing
the properties of these enzymes with
those of acyl-CoA dehydrogenases that
oxidise aliphatic compounds.
Electron-transferring flavoprotein
(ETF) is a partner enzyme for acyl-CoA
dehydrogenases, accepting or donating
electrons in the reaction. The flavin in ETF
is FAD that is bound non-covalently to the
protein. We have shown that it is slowly
modified during storage to give several
derivatives with markedly different optical
spectra. We are identifying these derivatives,
investigating the conditions that determine
their formation and the mechanism
by which they are formed.
Peroxiredoxin reductase couples the
oxidation of NAD(P)H to the reduction
of a variety of small proteins that in turn
reduce H2O2 and organic peroxides, and
that function to protect the cell against
reactive oxygen species. We have cloned
a thermostable enzyme from the bacterium
Thermus aquaticus that has a variety of
potential biotechnological applications.
Although the enzyme is very stable, it loses
activity above about 70oC due to loss of
the non-covalently bound FAD. In an effort
to improve the enzyme’s thermal stability,
we are exploring the structure of the protein
and attempting to covalently couple
it to a chemically-modified flavin.
Protein backbone of H. pylori flavodoxin showing
helices (red) and sheet (cyan). The FMN (yellow)
is bound on one side of the protein with the ribityl
phosphate side chain pointing into the protein.
PROFESSOR JPG MALTHOUSE
CONWAY SYNTHESIS & CHEMICAL BIOLOGY
Humans have a range of proteases, which
are important for a range of processes
including digestion of food, blood clotting,
control of blood pressure, etc. However,
there are specific proteases, which can be
targeted to treat various diseases, eg. the
AIDS virus needs a protease to multiply,
cancers and parasites use proteases to
move through tissues, proteases are used
to produce the amyloid plaque protein
which causes Alzheimer’s disease.
Therefore, to treat such conditions we
need to inactivate the proteases, which
are required for the disease to progress.
This inactivation can be achieved using
protease inhibitors.
There are four main types of proteases:
the thiol proteases, the serine proteases,
the metalloproteases and the aspartyl
proteases. We usually wish to target just
the one protease causing the disease and
not inhibit other proteases, which are
essential for health. We are synthesising
protease inhibitors and using NMR to
determine how they interact with specific
proteases. These studies will help us
optimise their ability to inhibit the specific
proteases involved in a range of diseases.
Our earlier studies utilised substrate
derived chloromethylketone inhibitors,
which alkylated the active site histidine
and formed tetrahedral adducts analogous
to the tetrahedral intermediate formed
during catalysis. From these studies, we
could quantify oxyanion stabilisation in
both chymotrypsin and subtilisiin(1).
We have now extended our studies to
reversible glyoxal inhibitors. In substrate
derived glyoxal inhibitors, the peptide
carboxylate group(-COOH) is converted
into a glyoxal group(-COCHO). We have
synthesized Z-Ala-Pro0Phe-glyoxal and
have found that it is a good inhibitor of
the serine proteases chymotrypsin(2)
and subtilisin(4) with Ki values of 25nM
and 2.3 μM respectively. Using NMR,
we have shown that with both enzymes
the inhibitors form hemiketal complexes,
which mimic the tetrahedral intermediate
formed during catalysis. We have also
synthesized z-Phe-Ala-glyoxal which
we have shown is an extremely effective
inhibitor (Ki =3.3 nM)= of papain (3).
Using NMR, we show that the active site
thiol group of papain reacts with the
glyoxal aldehyde carbon to form a
thiohemiacetal.
We are currently using NMR to determine
how glyoxal inhibitors interact with aspartyl
proteases such as pepsin, beta secretases
and HIV protease. We are also developing
a range of new inhibitors for all these
proteases and we intend to extend
our studies to the metalloproteinases
in the near future.
SELECTED PUBLICATIONS
A 13C-NMR study of how the oxyanion
pKa of subtilisin and chymotrypsin
tetrahedral adducts are affected by
different amino acid residues binding
in the enzymes S1-S4 subsites.
O’Sullivan DB, O’Connell TP,
Mahon MM, Koenig A, Milne JJ,
Fitzpatrick TP, and Malthouse JPG.
Biochemistry (1999) 38, 6187-6194.
A 13C-NMR study of the inhibition
of delta-chymotrypsin by a tripeptide-
glyoxal inhibitor. Djurdjevic-Pahl
A, Hewage C, and Malthouse JPG.
Biochem. J. (2002) 362, 339-347.
A 13C-NMR study of the inhibition of
papain by a dipeptide-glyoxal inhibitor.
Lowther J, Djurdjevic-Pahl A, Hewage
C and Malthouse JPG. Biochem. J.
(2002) 366, 983-987.
Ionisations within a subtilisin–glyoxal
inhibitor complex. Djurdjevic-Pahl
A, Hewage C and Malthouse JPG.
Biochimica et Biophysica Acta (BBA)
- Proteins & Proteomics (in press).
Fig. 1. 500MHz NMR in the Conway Institute.
Fig. 2. Structure of a Chymotrypsin after reactioin
with z-Gly-Phe-Cloromethylketone (Acta Crst, 2000,
D56, 280-286).
1.
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3.
4.
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PROFESSOR RORY MORE O’FERRALL
CONWAY SYNTHESIS & CHEMICAL BIOLOGY
The interest of our research group has
been in (a) factors controlling chemical
and enzymatic reactivity and (b)
mechanisms of biologically important
reactions. A recent project supported
by an Investigator Award from Science
Foundation Ireland involves collaboration
with the Department of Industrial
Microbiology and scientists at the Queen’s
University Belfast and Dublin Institute of
Technology. The project is based on access
to oxidative metabolites of aromatic and
heteroaromatic substrates resulting from
the action of mono- and dioxygenase
enzymes. The metabolites comprise arene
oxides, arene hydrates and cis and trans-
arene dihydrodiols, as illustrated below
for derivatives of 3-substituted 1,2-
dihydrobenzenes (Fig.1: 1 – 4).
A major source of the cis-dihydrodiols
is provided by large scale fermentations
using mutant or recombinant strains
of bacteria lacking diol dehydrogenase
enzymes, which in normal metabolism
convert the cis-dihydrodiols (3) to catechols.
Pilot scale production of the cis-dihydrodiols
has been pioneered by the QUESTOR
Centre for biotransformations at Queen’s
University. The unique structure of these
simple molecules (including their
chirality) has made them important
starting materials for the synthesis
of a number of drugs.
A principle objective of the present work
will be to find synthetic or microbiological
pathways from the bioavailable cis-
dihydrodiols (or aromatic substrates
themselves) to the currently inaccessible
trans-isomers, which offer synthetic
access to a new range of potentially
bioactive molecules. The microbiological
studies will be conducted by Dr Kevin
O’Connor. He and Dr Evelyn Doyle will also
oversee the importation of protocols and
microorganisms that will allow relevant
biotransformations to be carried out at
UCD. In collaboration with Dr McDonnell
(DIT) and Dr O’Donoghue (UCD), chemical
studies have focused on anomalies in
structure-reactivity relationships and
stereochemical outcomes in the acid-
catalysed aromatisation of all four families
of metabolites (usually to form phenols).
In the case of arene oxides of ploycyclic
aromatic hydrocarbons (PAHs), the
results are relevant to the mutagenic and
carcinogenic action of these compounds
in alkylating DNA. Further microbiological
work by Dr Doyle will examine the
transformation of phenols to catechols.
Shown in Fig. 2 are some of the personnel
engaged in the project.
Other projects in hand include studies
of thiazolidine ring-opening in models
for penicillin, the mechanism of the
azomethine rearrangement in vitamin
B6-mediated transaminations and
the selective alkylation of mono- and
di-saccharides. I am currently writing
a book on acid-base catalysis.
DR GRACE MORGAN
CONWAY SYNTHESIS & CHEMICAL BIOLOGY
Cellular reduction/oxidation (redox
status) regulates various aspects of
cellular functions such as proliferation,
activation, growth inhibition and cell death.
Biological systems are continuously exposed
to oxidants that can be generated either
exogenously or by endogenous metabolic
reactions, for example from mitochondrial
electron transport during respiration or
during activation of phagocytes. To protect
against exposure to oxidants, cells have
a well-developed antioxidant system that
includes both enzymatic (e.g thioredoxin,
superoxide dismutase, catalase and
glutathione peroxidase) and nonenzymatic
(glutathione) systems. An imbalance
between oxidants and antioxidants, which
favours an excess of oxidants (oxidative
stress) has been directly linked to oxidation
of proteins, DNA and lipids, which may
induce a variety of cellular responses
through the generation of secondary
metabolic reactive oxygen species. Many
metal ions have important biological
roles in redox regulation and ions such
as copper, zinc, iron and manganese are
found at the active site of metalloenzymes,
which facilitate a multitude of chemical
reactions essential for life.
We are interested in the design of redox-
active metal complexes that may halt or
reverse oxidative stress. Metal-complex
function relies heavily on ligand design and
we are developing a library of ligands with
distinct architectures: planar, macrocyclic
and tripodal for the complexation of first
row transition metal ions to investigate
How ligands with extended -systems
may be used to tune ligand field
strength and hence spin-state
and redox-state stabilisation
The potential of donor-poor tripodal
ligands to promote cluster formation
The magnetic interactions between
pairs of metal ions with efficient
bridging ligands such as 1,4-quinone
and pyrazine derivatives.
We are also interested in using redox-
active uncomplexed free ligands as redox
perturbants and are investigating the
inhibitory action of quinone ligands such
as L1 and L2 towards thioredoxin reductase
(TrxR) and glutathione reductase.
N3AN4A
01
N21A
N1
N2
N3N4
01A
N21N2A
N1A
Br1
Br2
C4
C3
N1
C2
D1
C1N2A Br2A
Br1A
N1A
D1A
C7
N2
C5
C6
L1
L2
1.
2.
3.
O
1 2 3 4
OH
OH
OH
OH
OH
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Fig. 1. Rates of inhibition of TrxR.
0 10 20 30 40 50 60
25
20
15
10
5
0
Rate vs {DTNB)
{DTNB) (mcM)
Fig. 2. (L-R) Dr Narain Sharma and Prof Derek Boyd
from the Queen’s University of Belfast; Prof More
O’Ferrall, Dr Nagaraja Rao and Mr Dara Coyne from
University College Dublin.
Fig. 1.
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2004 Research Group
My group is comprised of two Marie Curie
fellows, Dr Trinidad Velasco-Torrijos and
Dr Sebastien Gouin; four SFI postdoctoral
fellows, Dr Sarah Rawe (UK), Dr Christina
Loukou (Greece), Dr Violetta Zaric and Dr
Jérôme Lalot (France); five postgraduate
students, Linda Cronin, Dearbhla Doyle,
Rosaria Leyden, MarieChristine Matos
(France) and Colin O’ Brien. Manuela
Tosin, Ciaran McDonnell and Alan O’ Brien
were conferred with their doctorate
degree in 2004.
ACKNOWLEDGEMENT
I am grateful to Science Foundation
Ireland, The European Commission and
HEA through PRTLI Cycle III for funding.
DR PAUL V MURPHY
CONWAY SYNTHESIS & CHEMICAL BIOLOGY
My research is concerned with the design
and synthesis of novel bioactive molecules
and is focused in a number of areas. These
include synthesis of peptidomimetics
and glycomimetic as medicinal agents,
multivalent ligands for probing mechanisms
of signal transduction at cell surfaces,
natural products and related structural
analoges and synthetic methodology for
glycoconjugate synthesis. In 2004, I was
awarded a Science Foundation Ireland
Programme Investigator grant. In addition,
Dr Maneula Tosin, a graduate from my
research group was awarded the Royal
Irish Academy prize for young chemists.
SYNTHESIS OF ANGIOGENESIS
MODULATORS
This work is carried out in collaboration
with Dr Kathy O’Boyle and more recently
with Dr Evelyn Murphy who are both
principal investigators in the Conway
Institute. Of interest in this project are
(i) oligosaccharides related to heparin and
their potential to modulate bFGF signalling
pathways (ii) small glycoconjugates and
their potential to modulate endothelial
cell growth and migration (iii) synthesis
of migrastatin and other macrolides and
their potential to alter endothelial cell
growth and migration and (iv) synthesis
of castanospermine and related compounds,
which alter endothelial cell surface
glycosylation and consequently inhibit
angiogenesis.
SYNTHESIS OF PEPTIDOMIMETICS
Peptidomimetics are defined as non-
peptides that bind to peptide receptors,
with potentially better bioavailability,
biostability, and selectivity than
endogenous or synthetic peptide ligands.
These structures are often based on
scaffolds that have been structurally
modified to display side chains of amino
acids and other pharmacophoric groups.
Our research is concerned with efforts to
develop (i) mimics of b-strands (ii) a-helical
mimetics (iii) b-turn mimetics.
Mechanisms of activation of signal
transduction pathways at cell surfaces
using constrained and structurally
defined multivalent carbohydrates
Recently, the synthesis of bivalent
mannosides by the grafting of a-D-
mannopyranoside onto monosaccharide
acceptors and conjugation to terephthalic
acid or phenylenediamine has been
described within our group. This constitutes
a collection of structurally diverse bivalent
mannosides on saccharide scaffolding.
Mannose-mannose orientations and
distances are determined by location on
the scaffold and preferred glycosidic and
terephthalamide torsions. Each compound
has a distinct 3D structural profile. Their
biological properties are currently being
evaluated by Dr Sabine Andre and
Professor Hans Joachim Gabius in Munich
who are specialists in lectin biochemistry.
Migrastatin
OMe
OH
O
O
O
O
O
OH
OH
O
N
H
O
O
Charged and
H-bond donor
Castanospermine
Peptidomimetic analogue
based on deoxymannojirimycin
has been synthesized
O
P3
P1
P1
N
HO
HO
HO
OH
Fig. 1. Molecular structure.
Fig. 3. Work is underway for development of iminosugar based peptidomimetics targeting G-protein
coupled receptors.
OH
HN H
N
OH
OH
OH
HO HO OHH
N
H
O
O
O
O
O
O
O
O O
O
O
ON
CO2H
CO2H
N3
N3
OH
OH
HO
HO
HO OHH
N
H
O
O O
O
OH
OH
ON
OH
OH
HO OHH
N
H
O
O
HO
HO
O
OH
OH
ON
O
HO
HO
HO
Fig. 2. Overlay of peptidomimetic and peptide based
HIV protease inhibitor.
Fig. 4. Multivalent carbohydrates.
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IN VITRO RACEMISATION
OF THALIDOMIDE AND
AMINO ACID DERIVATIVES
Surprisingly, despite the infamy of the
thalidomide story, there is only one existing
publication to our knowledge of a rate of
in vitro racemisation of thalidomide (Roth
et al, Chirality 1995, 7, 44). This paper
records a single point measurement for
chiral inversion at 37oC and mentions
a competing “degradation” reaction. By
contrast, in our preliminary studies we
have found that deuterium exchange at
the only chiral carbon of thalidomide does
not compete with hydrolysis of thalidomide
at 25oC at pD values of 8 and above. We
are further investigating the racemisation
of thalidomide in vitro.
CARBON ACID PKA VALUES
OF N-HETEROCYCLIC CARBENES
There has been a resurgence of interest
in the structures and reactivities of carbenes
in the last decade since the report of the
synthesis and isolation of stable heterocyclic
diaminocarbenes by Arduengo. Heterocyclic
diaminocarbenes have emerged as
successful alternatives to phosphine
and phosphite ligands in organometallic
catalysts. A common term of reference
long used for predicting the sigma-donor
ability of phospine ligands are the pKa
values of the conjugate acids of the
phosphines. Despite the increasing
applications of N-heterocyclic carbenes
in organometallic catalysis and elsewhere,
there is a surprising absence of literature
data on their solution pKa values.
PROBING THE MECHANISMS
OF ASYMMETRIC BRØNSTED
ORGANOCATALYSIS
Asymmetric Brønsted acid catalysis
has recently emerged as a useful tool
in synthetic methodology. However, the
mechanisms of chirality transfer in the
transition states of these reactions are
not clear and we are studying these
mechanistic questions. An improved
mechanistic understanding of
organocatalytic reactions is needed for
the design of better asymmetric Brønsted
catalysts. We propose to investigate this
using a structure-reactivity approach
and hence probe the origin of the enantio
-selectivities. This will provide a measure
of the extent of proton transfer necessary
to achieve good enantioselectivities for a
particular system. With this knowledge in
hand, we will be able to design and optimise
effective Brønsted acid catalysts.
PROTON TRANSFER IN IONIC LIQUIDS
The development of ionic liquids as novel
solvent systems, including those based on
imidazolium cations, has been very rapid
in recent years. A large variety of ionic
liquids are now commercially available
and have been used widely as solvents
for organic synthesis. However, recently,
attention was drawn to the potential
of imidazolyl carbene-mediated side
reactions as a concern for the general
use of ionic liquids as solvents for organic
reactions. Imidazolyl carbenes are
generated by deprotonation of imidazolium
ions at the C2 position. We are applying
our hydrogen/deuterium exchange
methods to estimate rate constants for
deprotonation of imidazolium cations at
the C2 position in ionic liquids, and hence
predict the likelihood of carbene-mediated
side reactions.
DR ANNMARIE O’DONOGHUE
CONWAY SYNTHESIS & CHEMICAL BIOLOGY
Our group is interested in the analysis
of biological and organic reaction
mechanisms and in novel biocatalyst
design. A deeper knowledge of the
strategies natural enzymes employ
to achieve efficient catalysis is crucial
to the design of successful enzyme mimics.
There is a strong driving force for enzymes
to follow the same mechanism observed
for the corresponding non-enzymatic
reaction in solution. Thus, an understanding
of non-enzymatic solution chemistry
is a prerequisite to the study of enzyme
mechanisms, and is also a key principle
of our research. We employ an
interdisciplinary array of techniques
from chemistry and biology in our research
including site-directed mutagenesis and
direction evolution methodologies. Kinetic
methods include UV-Vis spectrophotometry
and high resolution NMR spectroscopy
as well as fast reaction techniques such
as stopped flow spectrophotometry.
CURRENT RESEARCH INTERESTS:
FLUOROCARBON BIOREMEDIATION
THROUGH MECHANISTIC ENZYMOLOGY
AND EVOLUTION
At present, the biocatalytic scope of
haloalkane dehalogenases is limited
to bromo and chloroalkanes and many
key compounds including fluoroalkanes
are poor substrates. However, under
conditions of high concentration and
extended reaction times haloalkane
dehalogenases may show small amounts
of promiscuous activity towards fluorinated
molecules. We are applying directed
evolution to increase any small amounts
of promiscuous catalytic activity of existing
haloalkane dehalogenases towards
fluoroalkanes with the ultimate aim
of using these new protein catalysts for
bioremediation. Enzymes that catalyse the
dissociation of the C—F bond in fluorinated
substrates (but not fluoroalkanes) do exist
and thus it is not unreasonable to expect
HDHs to yield fluoroalkane dehalogenases
on directed evolution.
APPLICATIONS OF BIOTECHNOLOGY
TO OXIDATIVE BIOTRANSFORMATIONS
OF AROMATIC SUBSTRATES
We are investigating the production,
downstream processing and cytotoxicity
of oxidative metabolites of aromatic
substrates. This project is based upon
collaboration between Departments
of Chemistry and Industrial Microbiology
in University College Dublin and the
Department of Chemistry in Queen’s
University of Belfast.
MECHANISM-GUIDED DIRECTED
EVOLUTION OF TRIOSEPHOSPHATE
ISOMERASE AND METHYLGLYOXAL
SYNTHASE: TOWARDS ALTERED
PRODUCT SPECIFICITIES
To date, there have been few attempts to
tailor the product selectivities of enzymes
by directed evolution. Often biocatalytic
processes on non-natural substrates lead
to a range of products. This project is
a proof of concept experiment that aims
to show that directed evolution techniques
may be used to afford complete suppression
of unwanted side reactions in a proton
transfer system that does not involve
cofactors. Our model systems are the
enzymes, methylglyoxal synthase (MGS)
and triosephosphate isomerase (TIM),
which catalyse the elimination and
isomerisation reactions of the same
substrate dihydroxyacetone phosphate
(DHAP). We are using directed evolution
strategies to convert TIM into MGS. We
envisage the generation of a spectrum
of new enzyme catalysts between TIM
and MGS that span a range of product
outcomes from 100% isomerisation
to 100% elimination.
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The chemical synthesis of compounds
can sometimes be difficult, expensive
and environmentally unfriendly. Chemical
catalysts can be less specific than biological
catalysts (enzymes) thus generating
byproducts that have no use and are
potentially toxic and/or detrimental
to the environment eg. indigo, a compound
commonly used to dye cotton, is
manufactured chemically. The manufacture
of indigo is a multi step process with
byproducts that cause pollution. We have
a bacterial strain that synthesises indigo
with no byproducts formed (Fig. 2).
We are attempting to improve the synthesis
of indigo using heterologous gene expression
and molecular techniques. Microbial
enzymes exhibit a high degree of specificity
in the reactions they catalyse. Consequently,
we are engaged in a number of projects
for the conversion of arenes (aromatic
compounds) to specific products such
as phenols, catechols and epoxides. These
compounds have uses as building blocks
in the synthesis of pharmaceutical drugs.
RESEARCH PROJECTS
CURRENTLY ONGOING:
Biochemical characterisation of
the styrene degrading and PHA
accumulating bacterium P. putida CA-3.
Improving PHA synthesis from styrene.
Accumulation of novel
polyhdroxyalkanoates.
Purification and biochemical
characterisation of enzymes involved
in phenylalkanoic acid metabolism.
Purification and biochemical
characterisation of bacterial tyrosinase.
Directed evolution of bacterial
tyrosinase.
Directed evolution of styrene
monooxygenase.
Generation of a biocatalyst for
the biotransformation of arenes.
DR KEVIN O’CONNOR
CONWAY SYNTHESIS & CHEMICAL BIOLOGY
Our research group is interested in
biocatalysis and metabolic engineering.
We focus on two major areas 1) biopolymer
synthesis by bacteria and 2) bacterial
oxidoreductases in the transformation
of aromatic and aliphatic substrates.
The pressures on society to control waste
generation has seen a rise in the amount
of recycling and a levy on products that
are considered environmentally unfriendly
ie. Irish government plastic bag levy. We
have also seen a growing interest in the
manufacturing of materials that are
biodegradable. Our research group is
investigating the ability of bacteria to
synthesise biodegradable polymers with
biotechnological potential, namely polyhy
-droxyalkanoates (PHAs). PHAs have
previously been used to manufacture
the Greenpeace biodegradable credit card.
Our research focuses on the conversion
of waste materials and toxic compounds
to this type of biodegradable plastic using
bacteria. In doing so, we are attempting
to prevent pollution, through toxic waste
removal and biodegradable plastic synthesis.
The understanding of the biochemical
pathways utilised by bacteria for polymer
synthesis as well as the diversity of polymers
accumulated are key points of interest in
our research. Styrene, a starting compound
and waste material from the petrochemical
based plastics industry, is a major
environmental pollutant. We have
successfully converted styrene to polyhy-
droxyalkanoate (PHA) (Fig. 1), which is
flexible, heat stable and water resistant,
using a bacterium Pseudomonas putida
CA-3. We are currently engaged in
improving biopolymer synthesis from
styrene through fermentation technology
and metabolic engineering.
1.
2.
3.
4.
5.
6.
7.
8.
Fig. 1. A) Transmission electron micrograph of the
biodegradable plastic (PHA) accumulating within
the bacterium P. putida CA-3. The isolated thin film
of plastic from the bacteria.
Fig. 2. The bacterium Pseudomenas putida CA-3
incubated with indole on an agar plate. The black
/blue dye formed after 24 hours of growth is indigo.
Fig. 1. B)
A
B
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DR DONAL O’SHEA
CONWAY SYNTHESIS & CHEMICAL BIOLOGY
Research interests include the following
(a) heterocyclic combinatorial solution and
solid phase synthesis, (b) the development
of multi-component reactions for library
synthesis of bioactive heterocycles, (c)
new routes to specifically substituted
imidazoles and imidazolothiazoles are
currently being established, (d) development
of new experimental techniques for the
rapid generation of parallel combinatorial
libraries utilising microwave parallel
synthesis, (e) the development of new
synthetic methodology exploiting
organolithium additions to unactivated
alkenes, (f) demonstration of a new multi-
component route to diversely functionalised
indoles, (g) the development of new non-
porphyrinic therapeutic window
photosensitisers; the BF2 chelates of
tetra-aryl-azadipyrromethenes, with
applications as photodynamic therapeutic
agents for cancerous tumour treatment
and as in vivo molecular biosensors.
DR JENS ERIK NIELSEN
CONWAY SYNTHESIS & CHEMICAL BIOLOGY
The research in my group is aimed at
providing experimental and theoretical
tools for understanding and engineering
enzymes. Specifically, we are interested
in being able to understand the changes
in the catalytic activity of enzymes that
result from point mutations.
Our main objective is to be able to predict
the change in catalytic activity that results
from a single point mutation. The inner
workings of the energetic properties of
proteins, and thereby enzymes, are much
too complicated for the human brain to
comprehend, and we therefore rely on
computational analysis of enzymes to
achieve our goals.
A major activity in the group is to develop
new computer algorithms that help us to
understand and engineer enzymes. We
always try to design these algorithms so
that they will be useful to experimental and
theoretical researchers alike. Specifically,
we make sure that our algorithms predict
quantities that can be measured in real-
world experiments.
In addition to a significant effort in
engineering new software for experimental
and theoretical researchers, we perform
experiments ourselves. We consider it
essential to validate our theoretical
predictions with wet experiments before
we release our algorithms to the scientific
community, and once released we
encourage and value feedback on our
predictions. With these efforts, we hope
to improve the communication between
theoretical and experimental researchers
working on enzymes and thus make
significant headway in tackling some of
the most pressing problems in industial
and medical enzymology.
RESEARCH PROJECTS
CURRENTLY ONGOING:
Improving methods for FDPB-based
protein pKa calculations.
The activation process of protein
kinase A.
Development of computational tools
for experimental researchers.
Prediction of structural changes
resulting from point mutations.
Studies of the correlation between
structural changes and changes in
catalytic activity.
1.
2.
3.
4.
5.
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DR PETER RUTLEDGE
CONWAY SYNTHESIS & CHEMICAL BIOLOGY
Chemists have long taken inspiration from
nature in their endeavour to understand,
control and harness biological processes.
The origins of aspirin in willow bark,
contraceptive steroids derived from
a Mexican yam, and penicillin cropped
from mouldy bread offer three important
examples. However, the abuse of chemistry
has also wrought a highly negative effect
on the natural world in some contexts:
industrial pollution from polymer synthesis,
wood treatment, oil refining and mining
for example have wrought highly
deleterious effects in many places.
Nonetheless, Nature shows remarkable
adaptability, and various organisms have
evolved mechanisms for living with and
utilising previously toxic chemicals. These
organisms are the basis for the emerging
science of bioremediation.
Bioremediation harnesses biological
systems to clean up and reclaim
contaminated environments, and our
research interests lie in the chemical
biology of bioremediation, applying the
principles and tools of chemistry to probe
these biological problems. Specifically,
we use aspects of synthetic chemistry and
structural biology in the study of enzyme
mechanism and the development of
improved catalysts for bioremediation
and synthesis. Current research falls
under three broad themes: development
of new systems for the oxidation
of polycyclic aromatics and other
hydrocarbons, based on enzymes from
the non-heme iron(II) oxidase family;
the generation of new catalysts for
nitrile hydrolysis, building from the
enzyme nitrile hydratase; and the
design and synthesis of peptide-based
systems for heavy metal binding
and sensing applications.
Specific projects include:
Preparation of model complexes to
mimic nitrile hydratase catalysis for
the bioremediative breakdown of
organic nitriles.
Synthesis of ferrocene-linked metal-
binding peptides, based on bacterial
metal-binding proteins, for application
to mercury and cadmium sensing.
Development of non-heme iron
oxygenase mimics for hydrocarbon
oxidation.
Elucidation of new routes to Ni-hydroxy
amino acid derivatives for use in metal
binding systems.
1 2
H2O
Cys109
Cys112
Cys114
OH2
Ar
O
O
His
His
NH
HN
Asp
X
N
N
Fe
N N
O
O
N
NH
HN
S
SS
Fe
O
O
O
O
1.
2.
3.
4.
Fig. 1. The active site metal binding environments of the nitrile-degrading enzyme nitrile hydratase (1),
and the non-heme iron (II) dependent dioxygenase enzyme family (2), which includes naphthalene and
toluene dioxygenases.
DR WILHELM RISSE
CONWAY SYNTHESIS & CHEMICAL BIOLOGY
POLYMER CHEMISTRY
Transition metal catalysed polymerisation
reactions of linear and cyclic olefins
including ring-opening olefin metathesis
polymerisations (ROMP) and insertion
polymerisations; polymer optical fibres,
fluorinated polymers; rigid-rod polymers
and polymers with good thermal stability.
We are investigating transition metal
catalysed polymerisation reactions,
in particular of strained cyclic olefins
These reactions can occur according
to two different routes; (a) vinyl addition
polymerisation or (b) ring-opening olefin
metathesis polymerisation.
Thereby, it is possible to obtain two
different polymer structures from the
same monomer. The vinyl-addition
polymerisation leads to saturated polymers,
the products from ring-opening olefin
metathesis contain carbon-carbon double
bonds. Structure-property relationships
of new materials will be studied. NMR
analyses can provide insight in the
microstructure of polymers. The
stereochemistry is influenced by
the substitution pattern of monomers
and by the nature of the catalysts.
Mechanistic studies aim at the elucidation
of the reaction mechanisms involved in the
polymerisation. We recently found that the
Pd(2+)-catalysed addition polymerisation
of norbornene is a polymerisation reaction
with rare chain transfer and chain
termination indicating a polymerisation
with ‘living’ character. Further studies are
directed at developing an understanding
of the initiation mechanism.
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RESEARCH PROJECTS
CURRENTLY ONGOING:
Synthesis of novel titanocenes
(Clara Pampillon, Nigel Sweeney,
Katja Strohfeldt, Matthias Tacke).
Modelling of titanocene DNA
interactions to discover the mode of
action (Oscar Mendoza, Matthias Tacke).
Application of titanocenes against
ovarian, cervix and prostate cancer
(Dr William Gallagher, Dr Margaret
McGee, Dr William Watson, all from
the Conway Institute).
Systematic cell testing and renal
cell mouse model (Prof Heinz-Herbert
Fiebig, Dr Iduna Fichtner, both from
the CESAR (Central European Society
of Anti-Cancer Research) network).
Ex-vivo testing against freshly
explanted human carcinoma cells
(Prof Axel Hanauske, Dr Olaf
Oberschmidt, St. Georg’s Oncology
Hospital, Hamburg, Germany).
Ehrlich`s ascitic tumor (EAT)
mouse model (Prof Mary Queiroz,
Dr Marize Bozinis, Universidade de
Campinas, Brazil).
033 <> 034
DR MATTHIAS TACKE
CONWAY SYNTHESIS & CHEMICAL BIOLOGY
My research group is interested in
synthesising novel titanocene anti-cancer
drugs and to evaluate them biologically
in cell tests and mouse models.
Additionally, we want to get an insight
into the mechanism of apoptosis from
a biological and chemical point of view.
The targets for our titanocenes are
mamma-carcinoma, renal cell, cervix,
ovarian and prostate cancer.
Our experimental approach starts by
reacting cyclopentadiene with aromatic
aldehydes to synthesise substituted
6-phenyl-fulvenes. Currently, we
concentrate on synthesising 6-anisylfulvene
(1), 6-(p-N,N dimethylamino) fulvene
(2), 6-(2`,4`,6`-trimethoxy)fulvene (3)
and 6-(3`,5`-bis-N,N dimethylamino)
fulvene (4) as starting materials
as illustrated in scheme 1.
SCHEME 1: SYNTHESIS (A) OF
TARGETED 6-PHENYLFULVENES (B)
These fulvenes can be reductively
dimerised with titanium dichloride
to yield ansa-titanocenes; the titanium
dichloride is synthesised from the
tetrachloride on addition of two moles
of n-butyl lithium in dry THF at low
temperature. In the second synthesis,
aryl lithium or aryl magnesium bromide
are added to the fulvenes and are
transformed into highly substituted
cyclopentadienides, which then can be
reacted with titanium tetrachloride to
form the wanted titanocene. In a further
reaction sequence, sodium hydride or
other hydride sources and titanium
tetrachloride give access to unbridged
titanocenes. These three reactions, which
are summarised in Scheme 2, transform
a single fulvene into three different
metallocenes, which shows a very
economic approach.
B (1) (2) (3) (4)
A
pyrrolidine pyrrolidine
H
MeO Me2N
He2O
N
H
NMe2
Me2NMeO
MeO
MeO
H
HHH
O
H
H H
Ar
Ar
H
H
Ti
Cl
Cl
1. 2LiR
TiC12.2 THF
2. TiCl4
2. TiCl4
1. 2NaH
Ar
Ar
H
H
H
H
Ti
Cl
Cl
Ar
Ar
H
H
Ar
ArTi
Cl
Cl
2
1.
2.
3.
SCHEME 3: LLC-PK CELL ASSAY
COMPARING TITANOCENE DICHLORIDE,
CIS-PLATINUM AND TITANOCENES
X AND Y
From these assays, we can conclude that
our titanocenes X and Y are significantly
better than titanocene dichloride itself
and that we are approaching the
cytotoxicity of cis-platinum. For the near
future, we want to use mouse models
to evaluate our best titanocenes further.
1E - 1 0 1E - 9 1E - 8 1E - 7 1E - 6 1E - 5 1E - 4 1E - 3
0.0
0.2
0.4
0.6
0.8
1.0
1.2
No
rma
lise
d c
ell
via
bil
ity
log10 drug concentrations
cis-Platin, IC50: (3.3+/-0.5)E-6
Cp2 TiCl2, IC50: (2.0+/-1.0)E-3
Titanocene X, IC50: (2.7+/-0.1)E-4
Titanocene Y, IC50: (2.1+/-0.1)E-5
SCHEME 2: TITANOCENES SYNTHESISED
FROM FULVENES USING CARBANIONS,
HYDRIDE OR TITANIUM DICHLORIDE
To reach our goals, we rely on using the
x-ray and spectroscopic resources (NMR,
UV-VIS, Raman, and IR) as well as the
computational resources of the Centre for
Synthesis and Chemical Biology (CSCB)
and the Chemistry Department.
In typical cell assays using pig kidney
carcinoma cells LLC-PK, we try to establish
a structure-activity relationship of our
compounds and rank the compounds with
respect to their cytotoxicity. In scheme 3,
two of our best titanocenes (X, Y) can be
compared against titanocene dichloride,
which reached Phase II studies against
mamma carcinoma and renal cell cancer
in the past, and cis-platinum, which is one
of the most regularly used metal-based
anti-cancer drugs.
4.
5.
6.
Scheme 1. Synthesis (a) of targeted
6-phenylfulvenes (b).
Scheme 2. Titanocenes synthesised from fulvenes
using carbanions, hydride or titanium dichloride.
Scheme 3. LLC-PK cell assay comparing titanocene
dichloride, cis-platinum and titanocenes X and Y.
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DR EDWARD TIMOSHENKO
CONWAY SYNTHESIS & CHEMICAL BIOLOGY
My research focuses on the development
and application of statistical mechanical
and computational techniques for studying
the conformational structure and dynamics
of biological and synthetic polymers.
THEORY AND COMPUTATION GROUP
CURRENT PROJECTS INCLUDE:
Monte Carlo, Brownian and Molecular
Dynamics simulations of conformational
transitions of polymers in dilute and
semidilute solutions.
Finding mechanisms for controlled
self-assembly of water soluble
polymers and oligopeptides in solution.
Studies of conformations of dendrimers,
star copolymers and polymers with
ionomers in dilute solution.
Modelling conformations and dynamics
of nucleic acids and polypeptides and
kinetics of protein folding.
Development of novel computational
methods for determination of polymer
conformations based on the BBGKY,
RISM and s-GSC techniques among
some others.
Long term interests are in the
direction of computations and direct
simulations for polymeric systems
approaching the complexity of realistic
biological macromolecules of relatively
short length such as globular and
fibrous proteins, oligonucleotides,
nucleic acids, polysacharides, lipids,
and studying their mutual interactions.
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