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Macromolecular Mechanisms

PD Dr. Roman Fedorov

 

Institute for Biophysical Chemistry
Hannover Medical School (MHH)

 

Phone: +49 511 532 3705
Fax:      +49 511 532 5966
E-mail: fedorov.romanmh-hannover.de

 

 

 

Research Focus


Our research is focused on fundamental studies of the molecular mechanisms underlying the function of nucleotidyltransferases and the development of new medical applications involving these enzymes. The nucleotidyltransferases form a large superfamily of proteins involved in many key cellular processes, including RNA polyadenylation and editing, DNA repair, chromatin remodelling, regulation of protein activity, intracellular signal transduction and antibiotic resistance. They catalyze the nucleoside monophosphate transfer from NTP to an acceptor group belonging to a protein, nucleic acid or small molecule. Allosteric regulation plays an important functional role on all levels of structural organisation of these proteins. The nucleotidyltransferase function can be affected by single amino-acid residues located far away from the active site, by functional loops and other elements of secondary structure, by substrate induced changes in tertiary structure and by the different oligomerization states. Elucidating these complex mechanisms and structure-function relationships in nucleotidyltransferases is essential for understanding fundamental biological processes regulated by these enzymes, and for drug-design and biotechnological applications.

Projects


Allosteric regulation of UDP-glucose and UDP-sugar pyrophosphorylases: a way to design new anti-leishmanial drugs

Parasites of the Trypanosomatidae family include Trypanosoma brucei, Trypanosoma cruzi and several Leishmania species that cause major diseases in humans. The diseases caused by these pathogens cause about 60 million deaths annually. To date there are no vaccines or effective drugs to fight these parasites. Several reports highlight the importance of the central nucleotide sugar UDP-glucose (UDP-Glc) in the growth of trypanosomatid parasites. It was demonstrated that suppressing the biosynthesis of UDP-galactose (UDP-Gal) leads to cessation of the parasites’ growth. The enzymes involved in UDP-Gal/UDP-Glc biosynthesis are thus potential drug targets in these organisms.
This project is focused on the development of highly-specific allosteric inhibitors of L. major UGP and USP that will be used as drug candidates. The project combines two lines of research. One line involves mechanistic studies to provide a description of the complete L. major UGP and USP enzymatic cycles. In another line of the project we utilize the mechanistic information to construct and optimize specific allosteric inhibitors.


The project is conducted by Johannes Cramer, Petra Baruch and Dr. Roman Fedorov in close cooperation with Prof. Dr. Rita Gerardy-Schahn, Dr. Jana Führing and Prof. Dr. Françoise Routier from the Institute for Cellular Chemistry, Hannover Medical School.  

Designing allosteric OAS activators as potential anti-viral agents

An early response to acute viral infection is the production of interferon by the infected cell. Interferons induce an antiviral state resulting from enhanced transcription of many genes, including 2’-5’-oligoadenylate synthases (OASes). The OASes are nonprocessive nucleotidyltransferases which in vitro utilize a broad range of substrates. OASes are activated by binding to dsRNA, a PAMP produced during viral replication. OASes then convert ATPs to 2’-5’-linked oligoadenylates (2-5A). 2-5A binds to a latent RNase L and triggers the formation of the active dimeric enzyme, which degrades viral and some cellular RNAs, blocking viral spread. Many viruses possess mechanisms to evade this pathway: for example, herpesviruses and the influenza A viruses camouflage the dsRNA with a protein coat. The OASes therefore remain latent. Activation of OAS with exogenous compounds would overcome this mechanism of viral evasion and lead to degradation of viral RNA.

This project is focused on the study of molecular mechanisms of OAS activation, substrate binding, catalysis and product release and development of small-molecule allosteric activators of OAS.

The project is conducted by Jan Lohöfener, Petra Baruch and Dr. Roman Fedorov in close cooperation with Dr. Penelope Kay-Fedorov (Institute for Virology) and Prof. Dr. Dietmar J. Manstein (Institute for Biophysical Chemistry) from Hannover Medical School, and with Dr. Alexey Nikulin, Dr. Svetlana Tishchenko, Prof. Dr. Maria Garber and Prof. Dr. Stanislav Nikonov from the Institute of Protein Research, Russian Academy of Science.  

People

Petra Baruch
Phone: +49 511 532 4420
Fax:     +49 511 532 5966
E-mail: Baruch.Petra@mh-hannover.de

                          

Methods

In our work we use a highly interdisciplinary approach combining wide range of methods from the fields of biochemistry, biophysics, structural and molecular biology, physical and quantum chemistry, molecular modelling and drug-design. Particularly in X-ray crystallography applications we use various implementations of MR, MIR, MAD, SAD and their combinations; methods of Kinetic Crystallography and Cryo-Crystallography. For structural studies and other experiments involving biophysical methods we use the facilities of the Institute for Biophysical Chemistry / Structure Analysis (Prof. Dr. Dietmar J. Manstein) as well as synchrotron radiation sources: ESRF (Grenoble, France), DESY (Hamburg, Germany), BESSY (Berlin, Germany) and MAX II (Lund, Sweden). For protein production, enzymatic kinetics experiments and functional tests of the inhibitors and effectors we use the facilities of the Institute for Cellular Chemistry (Prof. Dr. Rita Gerardy-Schahn) and the Institute for Virology (Prof. Dr. Thomas Schulz). The small molecule inhibitors and effectors are synthesized in cooperation with Prof. Dr. Chris Meier (University of Hamburg).

Our Cooperation Partners


Our ongoing projects are conducted together with:

Institute for Biophysical Chemistry, Hannover Medical School
Prof. Dr. Dietmar J. Manstein, Dr. Ute Curth, Dr. Igor Chizhov, Dr. Elena Korenbaum

Institute for Cellular Chemistry, Hannover Medical School
Prof. Dr. Rita Gerardy-Schahn, Dr. Jana Führing and Prof. Dr. Francoise Routier

Institute for Virology, Hannover Medical School
Dr. Penelope Kay-Fedorov

Institute of Protein Research, Russian Academy of Science
Dr. Alexey Nikulin, Dr. Svetlana Tishchenko, Prof. Dr. Maria Garber and Prof. Dr. Stanislav Nikonov

Department of Chemistry, Organic Chemistry, University of Hamburg
Prof. Dr. Chris Meier

Our Sponsors


Intramural grant ("HiLF") of Hannover Medical School

Hannover Biomedical Research School (HBRS) and the PhD program Molecular Medicine
www.mh-hannover.de/hbrs.html

About the Group

Our group was founded in 2012 with the support from Prof. Dr. Dietmar J. Manstein (Institute for Biophysical Chemistry) and Prof. Dr. Rita Gerardy-Schahn (Institute for Cellular Chemistry), Hannover Medical School.

Patents

Dietmar J. Manstein, Roman Fedorov, Georgios Tsiavaliaris, Hans-Joachim Knölker, René Martin, Juliane Kirst, Herwig O. Gutzeit, Markus Böhl, Marcus Furch. „Means for treating myosin-related diseases“ (WO/2009/065600), International Application No.: PCT/EP2008/009891; Publication Date: 28.05.2008; International Filing Date: 21.11. 2008.