Structural and thermodynamic characterization of inhibitor binding to aldose reductase [Elektronische Ressource] : insights into binding modes, driving forces and selectivity determinants / vorgelegt von Holger Steuber

Structural and Thermodynamic Characterization of
Inhibitor Binding to Aldose Reductase:
Insights into
Binding Modes, Driving Forces,
and Selectivity Determinants



Dissertation
zur
Erlangung des Doktorgrades
der Naturwissenschaften
(Dr. rer. nat.)




dem
Fachbereich Pharmazie
der Philipps-Universität Marburg
vorgelegt von



Holger Steuber
aus Hagen/Westfalen



Marburg an der Lahn, 2007


























































































Vom Fachbereich Pharmazie der Philipps-Universität Marburg als Dissertation
angenommen am: 05.06.2007


Erstgutachter: Prof. Dr. G. Klebe

Zweitgutachter: Prof. Dr. C. A. Sotriffer

Tag der mündlichen Prüfung: 05.06.2007


Die Untersuchungen zur vorliegenden Arbeit wurden auf Anregung und in der
Arbeitsgruppe von Prof. Dr. G. Klebe am Institut für Pharmazeutische Chemie des
Fachbereichs Pharmazie der Philipps-Universität Marburg in der Zeit von März 2003
bis Oktober 2006 durchgeführt.







































Der Fortgang der wissenschaftlichen Entwicklung
ist im Endeffekt
eine ständige Flucht vor dem Staunen.

(Albert Einstein)
















The following scientific contributions (ordered by type and date of publication)
emanated from this thesis:

1. Journal Articles
• Petrova T., Steuber H., Hazemann I., Cousido-Siah A., Mitschler A., Chung R.,
Oka M., Klebe G., El-Kabbani O., Joachimiak A., Podjarny A.,
Factorizing selectivity determinants of inhibitor binding toward aldose and
aldehyde reductases: structural and thermodynamic properties of the aldose
reductase mutant Leu300Pro-fidarestat complex
J. Med. Chem. 2005, 48, 18, 5659-5665
• Steuber H., Zentgraf M., Podjarny A., Heine A., Klebe G.,
High resolution crystal structure of Aldose Reductase complexed with the novel
sulfonyl-pyridazinone inhibitor exhibiting an alternative active site anchoring
group
J. Mol. Biol., 2006, 356, 45-56
• Steuber H., Zentgraf M., Gerlach C., Sotriffer C. A., Heine A., Klebe G.,
Expect the unexpected or caveat for drug designers: multiple structure
determinations using Aldose Reductase crystals treated under varying
conditions reveal surprising challenges for structure-based ligand design
J. Mol. Biol., 2006, 363, 174-187
• Steuber H., Heine A., Klebe G.,
Structural and thermodynamic Study on Aldose Reductase: nitro-substituted
inhibitors with strong enthalpic binding contributions
J. Mol. Biol., 2007, 368, 618-638
• Steuber H., Zentgraf M., La Motta C., Sartini S., Heine A., Klebe G.,
Evidence for a novel binding site conformer of aldose reductase in ligand-bound
state
J. Mol. Biol., in press
• Zentgraf M., Steuber H., Koch C., La Motta C., Sartini S., Sotriffer C. A.,
Klebe, G.,
How reliable are current docking approaches for structure-based drug design?
Lessons from aldose reductase
Angewandte Chemie Int. Ed. Engl., in press
• Gerlach C., Smolinski M., Steuber H., Sotriffer C. A., Heine A., Hangauer D.,
Klebe G.,
Thermodynamic inhibition profile of a cyclopentyl- and a cyclohexyl derivative
towards thrombin: The same, but for different reasons
Submitted
• Steuber H., Czodrowski P., Sotriffer C. A., Klebe G.,
Tracing changes in protonation: A prerequisite to factorize thermodynamic
data of inhibitor binding to aldose reductase
Submitted
• Steuber H., Heine A., Podjarny A., Klebe G.,
Merging the binding sites of aldose and aldehyde reductase for detection of
inhibitor selectivity-determining features
To be submitted
• Zentgraf M., Steuber H., Klebe G. & Sotriffer C. A.,
Evaluating MM-PBSA in case of a flexible binding pocket: the Aldose Reductase
test case. To be submitted.
• Zentgraf M., Steuber H., Klebe G. & Sotriffer C. A.,
Extending charted space: comparative MD simulations of Aldose Reductase.
To be submitted.
• Eisenmann M., Steuber H., Zentgraf M., Klebe G., Schlitzer M.,
Design, synthesis, biological and structural evaluation of novel aldose
reductase inhibitors
Manuscript in preparation
• Silber K., Steuber H., Jaeger R., Sohn C., Heine A., Klebe G.,
Successful lead identification for metalloproteinases: a fragment-based
approach using virtual screening
Manuscript in preparation






2. Oral presentations
• Steuber H., Sotriffer C. A., Klebe G.,
Aldose Reductase and Aldehyde Reductase - a model system for selectivity
determinants involved in protein-ligand interactions
Meeting on experimental and computational approaches to understand protein-
ligand interactions, BASF AG, Ludwigshafen, Germany, 2004
• Steuber H., Heine A., Sotriffer C., Klebe G.,
Aldose Reductase Inhibition from a structural and thermodynamic point of view
DFG-Evaluation of the Research Training Group “Protein function at the atomic
level”, Marburg, Germany, 2004
• Steuber H., Heine A., Klebe G.,
Aldose reductase inhibition from the thermodynamic point of view
Bilateral Joint Aldose Reductase Meeting, IGBMC, Illkirch, France, 2005


3. Posters
• Steuber H., Sotriffer C., Heine A., Klebe G.,
How to design selective drugs? Aldose Reductase and Aldehyde Reductase as a
model system
High Resolution Drug Design, Bischenberg-Strasbourg, France, 2004
• Eisenmann M., Steuber H., Zentgraf M., Klebe G., Schlitzer M.,
Structure-based drug design of Aldose Reductase inhibitors
Joint Meeting of the German Pharmaceutical Society (DPhG), Regensburg,
Germany, 2004
• Silber K., Steuber H., Reinscheid U., Klebe, G.:
A Fragment-based Screening Approach for Metalloproteinase Inhibitors,
Gordon Research Conference on Computer Aided Drug Design, Tilton, NH,
USA, 2005
• Zentgraf M., Sotriffer C., Steuber H., Klebe G.,
Thermodynamic characterization of Aldose Reductase inhibitors by
comparative MD simulations
Gordon Research Conference on Computer Aided Drug Design, Tilton, NH,
USA, 2005 • Gerlach C., Steuber H., Velec H.F.G, Smolinski M., Hangauer D., Heine A.,
Klebe G.,
Docking and direct design in the binding pocket - libraries for serine protease
inhibitors
Young Modellers` Forum, London, UK, 2005
• Eisenmann M., Steuber H., Zentgraf M., Klebe G., Schlitzer M.,
Design of new Aldose Reductase inhibitors – a structure-based approach
Joint Meeting on Medicinal Chemistry, Vienna, Austria, 2005


























Abbreviations
AKR aldo-keto reductase
ALR1 Aldehyde Reductase
ALR2 Aldose
BSASA Buried solvent accessible surface area
HTS High Throughput Screening
IDD Institute for Diabetes Discovery
ITC Isothermal titration calorimetry
k binding constant b
MD molecular dynamics simulation
n.d. not determined
NMR Nuclear Magnetic Resonance
PB Poisson-Boltzman
PEOE Partial Equalization of Orbital Electronegativities
PDB Protein Data Bank
RMSD Root mean square deviation
VS Virtual Screening
WT wild type