4742 Resaerch Profs 17 - UCD Research Profiles 2004.pdf · CONTINUOUS CHEMOSTAT CULTURE AT...

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


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


DR EOIN CASEY


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


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


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

O

S

ButO

O

O

OMe

OMeMeO

O

O

Fig. 1. Imidazolines.

Fig. 2. Synthesis of podophyllotoxin.

DR DECLAN G GILHEANY


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


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


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


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.

HN H’N

R

M

H

RO’c

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


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.

013 <> 014

DR BRIAN GLENNON


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


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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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


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


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


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.

2.

3.

4.

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PROFESSOR RORY MORE O’FERRALL


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


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


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


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


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


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


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


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


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


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


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.

1.

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4742 Resaerch Profs 17 - UCD Research Profiles 2004.pdf · CONTINUOUS CHEMOSTAT CULTURE AT...

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Transcript of 4742 Resaerch Profs 17 - UCD Research Profiles 2004.pdf · CONTINUOUS CHEMOSTAT CULTURE AT...