ENDEVAN (european network on the development of artificial nucleases)

European Network on the Development

Of Artificial Nucleases

Coordinator: Professor A. J. Kirby, F.R.S. University of Cambridge

ENDEVAN (European Network on the Development of Artificial Nucleases) was set up in March 2000 by the European Commission under the Research Training Networks activity of the Human Potential Programme of FRAMEWORK V and ran until 29 February 2004.
It brought together seven leading research groups from six European countries in a coordinated interdisciplinary programme, firmly based in Chemistry, aimed at producing new, synthetic catalysts to mimic selected classes of nuclease enzymes.

Objectives
The long-term objective is the development of man-made catalysts for the site-specific cleavage of polynucleotides (specifically the nucleic acids, RNA and DNA). The strategy is to develop efficient catalytic units and attach them to a series of systems, including antisense oligonucleotides, known to bind to target oligo and polynucleotide systems, and to screen them for their ability to catalyse the cleavage of internucleotidic bonds. Artificial nucleases are potentially valuable therapeutic agents, allowing in principle the regulation of the expression of a single gene.

Programme
This is very much interdisciplinary science, needing serious input from chemists of several sorts - structural, synthetic, bioorganic - as well as biochemists and chemical geneticists. All our members work to some extent across these boundaries already, and are involved in informal collaborations with each other and with groups in adjacent areas.
All groups, and all participants are involved in the design of new systems, each contributing their special expertise.

Principal Scientists

Cambridge group Professor A. J. Kirby, F. R. S
GB University of Cambridge

Padova group Professor Paolo Scrimin
IT Universitá di Padova

Frankfurt group Professor Dr. Michael Goebel
DE Johann Wolfgang Goethe-Universität Frankfurt am Main

Linköping group Professor Lars Baltzer
SE Linköping University

Leiden group Professor J. H. van Boom
NL Leiden Institute of Chemistry

Bern group Professor Christian Leumann
CH University of Bern

Karolinska group Professor Roger Strömberg
Dr. Esther Yehielesky
SE Karolinska Institutet, Stockholm

Details and Groups.

Contact: Prof. A. J. Kirby

University Chemical Laboratory, Cambridge CB2 1EW, UK

Tel: +44 1223 336370 FAX: +44 1223 336913

e-mail: ajk1@cam.ac.uk

The Cambridge group is interested in all aspects of organic reaction mechanism in solution, in the general context of mechanism and efficiency in enzyme catalysis. The approach is chemical, and aimed at a firm understanding based on results from systems simple enough to understand in detail (and to synthesise without too much trouble). We want to apply this understanding to design and synthesise systems which can reproduce both the high rates and the stereospecificity of enzyme reactions. We are involved in different ways of developing artificial catalysts which are potentially relevant to anything from academic theory to gene therapy (Prof. Kirby also Coordinates the ENGEMS Network web site www.ch.cam.ac.uk/misc/ENGEMS/). We will know that we really understand enzymes when we can reproduce their properties - especially their efficiency - in artificial catalysts.

Recent publications
1. Enzyme Mechanisms, Models and Mimics. A. J. Kirby, Angew. Chem., Intl. Ed. Engl., 1996, 35, 707-724 (Updated in "Stimulating Concepts in Chemistry" Shibasaki, Stoddart and Vögtle, Wiley-VCH, 2000, (in the press).
2. Mechanisms of Catalysis by Imidazole Buffers of the Hydrolysis and Isomerisation of RNA Models. C. Beckmann, A. J. Kirby, S. Kuusela and D. C. Tickle, J. Chem. Soc., Perkin Trans. 2, 1998, 573-582.
3. Nucleophilic Attack on Phosphate Monoester Dianions by Oxyanions: the Positive Effect of a Cationic General Acid. A. J. Kirby; M. F. Lima; D. da Silva; F. Nome, J. Am. Chem. Soc., 2004, 126, 1350-1351.

Web site: http://www.ch.cam.ac.uk/staff/ajk.html

Padova.

Contact Prof. Paolo Scrimin

Dipartimento di Chimica Organica, Universitá di Padova, Via Marzolo 1, I-35131 Padova, Italy

Tel: +39-049-8275276 fax: +39-049-8275239 e-mail: scrimin@chor.unipd.it

The Padova group is involved in the application of metal ions for the realization of metal ion-based molecular devices such as new and stereoselctive catalysts, artificial metalloenzymes and nanostructures. Current research is focused on the following specific projects: Synthetic models of metallonucleases; Permeability control of synthetic liposomes; Metal ion-mediated self-assemblyof nanostructures; Stereoselective oxidation of organic compounds mediated by chiral peroxocomplexes of transition metal ions; Synthesis and application in stereoselective catalysis of chiral, highly symmetrical polydentate ligands, and Functionalized gold nanoparticles as enzyme models.

Web site: http://www.chfi.unipd.it/home/p.scrimin

Frankfurt

Contact Prof. Dr. M. Goebel

Institut fuer Organische Chemie der Johann Wolfgang Goethe-Universitaet
Marie Curie Strasse 11, D-60439 Frankfurt am Main, Germany

Tel: +49 69 798 29222 Office: +49 69 798 29221 Fax: +49 69 798 29464

e-mail: M.Goebel@chemie.uni-frankfurt.de

The Frankfurt Group is interested in the application of amidinium and guanidinium ions in the fields of molecular recognition and biomimetic catalysis. These cations by themselves do not exhibit remarkable rate effects, but, putting them together in the correct three-dimensional structure may produce very efficient catalysts. A special focus is on phosphoryl transfer: compared to their non-charged counterparts, bis(guanidinium) alcohols can produce rate increases of more than millionfold (1, 2). Even plasmid DNA can be cleaved by those compounds under physiological conditions.
Guanidinium mediated RNA hydrolysis is a relevant second research focus. (3).

WebSite: http://www.rz.uni-frankfurt.de/fb14/goebel/

Linköping
(This Group has now moved - see details below)

Contact: Prof. Lars Baltzer

Dept of Chemistry, Uppsala University, 58183 LinkÃ¶ping, Sweden.

Tel: +46 13 282595 FAX: +46 13 122587

e-mail: Lars.Baltzer@kemi.uu.se

The Group's research is focused on the design of new proteins for the catalysis of reactions not catalysed by enzymes. Reactive sites built in to 40-50 residue synthetic peptides which fold in solution to form helix-loop-helix motifs and dimerise to form four-helix bundles catalyse familiar reactions with saturation kinetics and accelerations in aqueous solution of more than 1000. Structural characterisation and identification of folded polypeptides, substrates, intermediates and reaction products by NMR and CD spectroscopy as well as by mass spectrometry is strongly emphasised in combination with reaction mechanistic studies of catalysis.

Web site:http://www.ifm.liu.se/Chemistry/People/index.html

Leiden

Contact: Professor J. H. van Boom

Leiden Institute of Chemistry
P.O.Box 9502, 2300 RA Leiden, The Netherlands

Tel: +31 71 527 4274 FAX: +31 71 527 5274

e-mail: J.Boom@chem.leidenuniv.nl

The Leiden Group is a major player in the design and synthesis of molecules of biological importance. Recent work in nucleic acid chemistry has been directed towards the development of antisense probes based on PNA (Polyamide Nucleic Acid). For example, PNA.DNA chimerae, prepared by automated solid phase synthesis, inhibit the translation of the luciferase gene in an RNase H assisted process. The high-affinity hybridization and RNase activity of these and newly designed PNA-DNA chimerae are being explored to inhibit the translation of other specific genes. Preliminary studies led to the development of an artificial nuclease conjugated to PNA.

Web site: http://wwwchem.leidenuniv.nl/biosyn/index.htm

Bern

Contact: Prof. Christian Leumann

Department of Chemistry and Biochemistry
University of Bern, Freiestrasse 3, CH-3012 Bern. Switzerland

Tel: +41-31-631 4355 FAX: +41-31-631 3422

e-mail: leumann@ioc.unibe.ch

The Bern group is primarily interested in the supramolecular chemistry of DNA and RNA. In the last couple of years progress has been made in three main areas:
Design, Synthesis and evaluation of the base-pairing characteristics of oligonucleotide analogs with conformationally restricted phosphodiester-backbones.
Design of a new base to enhance triple-helix stability in the parallel (pyrimidine-purine-pyrimidine) binding motif.
C-H...O hydrogen-bond assisted base-base recognition in triple helical DNA.
For more details go to the group's Web site (see below).

Web site http://dcbwww.unibe.ch/groups/leumann/start.html

Stockholm

Contacts:

Professor Roger Strömberg or Dr. Esther Yeheskiely

Division of Organic and Bioorganic Chemistry,
MBB, Scheele Laboratory, Karolinska Institutet S-17177 Stockholm, Sweden

Tel: +46-8-7287749 FAX: +46-8-311052

e-mail: Roger.Stromberg@mbb.ki.se

The Karolinska group is expert in synthetic nucleic acid chemistry and has developed new methods and strategies for the synthesis of DNA and RNA fragments, as well as of modified oligonucleotides, which are widely used in the academic and commercial worlds. Major recent contributions have been to the synthesis of nucleopeptides and peptide nucleic acids (PNA). The group also has experience in studies of reaction mechanism and catalysis of cleavage of phosphate esters in model systems and of enzyme catalysed reactions.

Web site: http://www.mbb.ki.se/resea.html

ENDEVAN Young Researchers, Vadstena (SE), May 2002

Laurent Azéma is French. He did his first degree, then a PhD ('Synthesis, action mode and vectorisation of class I aldolase inhibitor') in the Organic Biological Chemistry Group of Prof. Jacques Périé, in Toulouse. He worked in Cambridge for 2 years from September 2000.

Jessica Becaud is French, and a graduate student working towards her PhD in Bern. She has a Master's degree in Biochemistry from the University of Grenoble, and a Postgraduate Diploma (DEA) in Molecular Chemistry (supervisor Prof. Pascal Dumy) involving the synthesis of peptides of rigid conformation.)

Eva Bencze was born in Romania, and has her first (Chemical Engineering) diploma-from Babes-Bolyai-University, Cluj Napoca. She moved to Hungary in 1993, to study for her PhD at the University of Veszprem. From 1997 she worked as research associate at Institute of Isotope and Surface Chemistry of the Hungarian Academy of Sciences in Budapest; finally obtaining her PhD ("Spectroscopic and theoretical study of organometallic compounds") in 2000. She then worked for a year in Germany as an 'Alexander von Humboldt' postdoctoral research fellow at the Technical University of Munich. Eva is married to Fabio.

Florence Bodar-Houillon is French. She has her first degree and PhD (1996, on synthesis and fluorescence measurements of new europium cryptates and podands, supervisor Prof. A. Marsura) from the University of Nancy. She has also worked as a Marie-Curie Fellow for 2 years in an industrial biochemistry lab in Germany, preparing new fluorescent sensors. Florence is married to Denis Bodar, and they have two children.

Petri Heinonen is Finnish, and has his first degree and PhD from the University of Turku. His PhD (Solution and Solid Phase Synthesis of ₂-Adrenergically Active Compounds) involved close collaborations with industry. From 1.2.2000-1.3.200 he was coordinator of the Graduate School of Bioorganic Chemistry in Finland.

Jesus Razkin is Spanish. He studied general chemistry at the Basque Country University, before moving to the University of Zaragoza, where he acquired his degree in Organic Chemistry in 1989. He then worked for two years as a chemist in industry before moving as Associate Professor to the Public University of Navarra; where he won his Ph. D. degree with a Thesis on the stereoselective synthesis of pheromones. An EU-JSPS postdoctoral fellowship then took him to Japan for two years to work with Prof. Kenji Mori on the asymmetric synthesis of insect pheromones, at the Science University of Tokyo. He is married to Marisol.

Jim Rickard is English, and did his first degree and PhD (under the supervision of Prof. Mike Blackburn on "Chemical Selection of Catalytic Antibodies") at the University of Sheffield. During his PhD he spent 3 months in Japan with Prof. Kenji Uneyama learning specialist techniques of synthetic organofluorine Chemistry. He was in Leiden from October 2000 - May 2002, when he moved to an industrial post in England.

Christo Roussev is Bulgarian, and has BS and MS degrees from Sofia University 'Sv. Kl. Ohridski'. He did his PhD on model ribozyme reactions:in the Institute of Organic Chemistry of the Bulgarian Academy of Sciences (also in Sofia), under the supervision of Prof Dimeter Petkov His first postdoctoral post was also with ENDEVAN, with Tony Kirby in Cambridge.

Theo Ryan is Irish, and has a BA in Natural Science from Trinity College Dublin: where he also did his Ph.D. ('Towards Carbohydrate Recognition in Aqueous Media') under the supervision of Prof.Tony Davis.

Lene Petersen is Danish. She studied Chemistry at Odense University (now the University of Southern Denmark), and worked there for her Ph.D. (1998-2002) with Professor Erik Bjerregaard Pedersen, on inhibitors of HIV-1 reverse transcriptase. She spent 9 months of this time at the University of Southampton, working with Professor Jeremy Kilburn on the synthesis of phosphonates as transition state analogues.

Claudio Gnaccarini is Italian, and received his degree in Chemistry and Pharmaceutical Technology, specialising in Biotechnology, from the University of Padua in 2002, studying under the supervision of Professor Paolo Scrimin. He is working for his PhD in Frankfurt under the supervision of Professor Michael Gobel.

Cambridge group	Professor A. J. Kirby, F. R. S	GB	University of Cambridge
Padova group	Professor Paolo Scrimin	IT	Universitá di Padova
Frankfurt group	Professor Dr. Michael Goebel	DE	Johann Wolfgang Goethe-Universität Frankfurt am Main
Linköping group	Professor Lars Baltzer	SE	Linköping University
Leiden group	Professor J. H. van Boom	NL	Leiden Institute of Chemistry
Bern group	Professor Christian Leumann	CH	University of Bern
Karolinska group	Professor Roger Strömberg Dr. Esther Yehielesky	SE	Karolinska Institutet, Stockholm
Karolinska group	Professor Roger Strömberg Dr. Esther Yehielesky	SE	Karolinska Institutet, Stockholm

	Laurent Azéma is French. He did his first degree, then a PhD ('Synthesis, action mode and vectorisation of class I aldolase inhibitor') in the Organic Biological Chemistry Group of Prof. Jacques Périé, in Toulouse. He worked in Cambridge for 2 years from September 2000.
	Jessica Becaud is French, and a graduate student working towards her PhD in Bern. She has a Master's degree in Biochemistry from the University of Grenoble, and a Postgraduate Diploma (DEA) in Molecular Chemistry (supervisor Prof. Pascal Dumy) involving the synthesis of peptides of rigid conformation.)
	Eva Bencze was born in Romania, and has her first (Chemical Engineering) diploma-from Babes-Bolyai-University, Cluj Napoca. She moved to Hungary in 1993, to study for her PhD at the University of Veszprem. From 1997 she worked as research associate at Institute of Isotope and Surface Chemistry of the Hungarian Academy of Sciences in Budapest; finally obtaining her PhD ("Spectroscopic and theoretical study of organometallic compounds") in 2000. She then worked for a year in Germany as an 'Alexander von Humboldt' postdoctoral research fellow at the Technical University of Munich. Eva is married to Fabio.
	Florence Bodar-Houillon is French. She has her first degree and PhD (1996, on synthesis and fluorescence measurements of new europium cryptates and podands, supervisor Prof. A. Marsura) from the University of Nancy. She has also worked as a Marie-Curie Fellow for 2 years in an industrial biochemistry lab in Germany, preparing new fluorescent sensors. Florence is married to Denis Bodar, and they have two children.
	Petri Heinonen is Finnish, and has his first degree and PhD from the University of Turku. His PhD (Solution and Solid Phase Synthesis of ₂-Adrenergically Active Compounds) involved close collaborations with industry. From 1.2.2000-1.3.200 he was coordinator of the Graduate School of Bioorganic Chemistry in Finland.
	Jesus Razkin is Spanish. He studied general chemistry at the Basque Country University, before moving to the University of Zaragoza, where he acquired his degree in Organic Chemistry in 1989. He then worked for two years as a chemist in industry before moving as Associate Professor to the Public University of Navarra; where he won his Ph. D. degree with a Thesis on the stereoselective synthesis of pheromones. An EU-JSPS postdoctoral fellowship then took him to Japan for two years to work with Prof. Kenji Mori on the asymmetric synthesis of insect pheromones, at the Science University of Tokyo. He is married to Marisol.
	Jim Rickard is English, and did his first degree and PhD (under the supervision of Prof. Mike Blackburn on "Chemical Selection of Catalytic Antibodies") at the University of Sheffield. During his PhD he spent 3 months in Japan with Prof. Kenji Uneyama learning specialist techniques of synthetic organofluorine Chemistry. He was in Leiden from October 2000 - May 2002, when he moved to an industrial post in England.
	Christo Roussev is Bulgarian, and has BS and MS degrees from Sofia University 'Sv. Kl. Ohridski'. He did his PhD on model ribozyme reactions:in the Institute of Organic Chemistry of the Bulgarian Academy of Sciences (also in Sofia), under the supervision of Prof Dimeter Petkov His first postdoctoral post was also with ENDEVAN, with Tony Kirby in Cambridge.
	Theo Ryan is Irish, and has a BA in Natural Science from Trinity College Dublin: where he also did his Ph.D. ('Towards Carbohydrate Recognition in Aqueous Media') under the supervision of Prof.Tony Davis.
	Lene Petersen is Danish. She studied Chemistry at Odense University (now the University of Southern Denmark), and worked there for her Ph.D. (1998-2002) with Professor Erik Bjerregaard Pedersen, on inhibitors of HIV-1 reverse transcriptase. She spent 9 months of this time at the University of Southampton, working with Professor Jeremy Kilburn on the synthesis of phosphonates as transition state analogues.
	Claudio Gnaccarini is Italian, and received his degree in Chemistry and Pharmaceutical Technology, specialising in Biotechnology, from the University of Padua in 2002, studying under the supervision of Professor Paolo Scrimin. He is working for his PhD in Frankfurt under the supervision of Professor Michael Gobel.