Characterization of binding pocket flexibility of aldose reductase [Elektronische Ressource] / vorgelegt von Matthias Zentgraf

Matthias Zentgraf

Sujets

• Gesundheit

Informations

• Publié par: philipps-universitat_marburg
• Publié le: 01 janvier 2006
• Nombre de lectures: 12
• Langue: English
• Poids de l'ouvrage: 6 Mo

Extrait

C haracterization of Bin ding P ocket Flexibility of Aldose
Reductase
D ISSE RTATIO N
ZUR
E RLANG UNG DE S D O K TO RG RADE S
DE R NATURWISSE NSCHAFTE N
(D R. RE R. NAT.)
dem
Fachbereich Pharm azie de r
PHILIPPS-UNIVE RSITÄT MARBURG
vorgelegt von
Matthias Z entgraf
aus Fulda
Marburg a n der Lahn, 2006Vom Fachbereich Pharm azie de r PHILIPPS-UNIVE RSITÄT MARBURG als Dissertation
angenomm en am : 15.11.2006
E rstgutachter: Prof. D r. G. Klebe
Z weitgutachter: Dr. C. S otriffe r
Tag de r mündlichen Prüfung: 16.11.2006I
Table of Contents
Aldose Reductase and the sorbitol pathway.................................................................1
Introduction..............................................................................................................1
Structure of AR and related enzymes.......................................................................1
Mechanism and kinetics of the AR catalyzed reaction............................................2
The sorbitol pathway and its influences on metabolism..........................................4
Aldose Reductase inhibitors.....................................................................................5
Why consider protein flexibility in structure-based drug design?................................9
Addressing protein flexibility and ligand selectivity by "in-situ cross-docking".......21
Introduction............................................................................................................21
Results and Discussion...........................................................................................22
Summary and Conclusion......................................................................................28
Supporting Information A: Computational Methods.............................................28
Protein setup and grid calculations. ..................................................................28
Ligand setup......................................................................................................29
Docking ............................................................................................................30
Supporting Information B: Docking to trypsin and thrombin................................31
Sting Information C: Docking to multiple conformers by grid-based
averaging................................................................................................................32
Extending charted space: comparative MD simulations of Aldose Reductase...........35
Introduction............................................................................................................35
Materials and Methods...........................................................................................38
Crystal structure analysis...................................................................................38
MD simulations.................................................................................................41
Generation of 2D rms plots...............................................................................42
Docking with AutoDock....................................................................................42
Results and Discussion...........................................................................................43
Comparative crystal structure analysis..............................................................43
Comparative MD simulations analysis..............................................................63
Simulations of AR complexes......................................................................64
MD of AR in complex with sorbinil.............................................................64
MD of AR in complex with tolrestat............................................................67
MD of AR in complex with idd 594.............................................................70
MD of AR in complex with the Pfizer compound........................................73
MD of AR in complex with the zopolrestat compound................................76
MD of AR in complex with the 47d compound...........................................78
MD of AR in complex with the JFD com...........................................81
Simulations of the holo enzyme...................................................................83
Summarizing the results....................................................................................89
Implications for the binding pocket.................................................................104
Addressing the new binding pocket conformations........................................108
Summary and Conclusions...................................................................................120II
Evaluating MM-PBSA in case of a flexible binding pocket: the AR test case.........122
Introduction..........................................................................................................122
Methodology....................................................................................................123
Setup and workflow.........................................................................................124
Literature overview.........................................................................................129
The test system: Aldose Reductase.................................................................135
Materials and Methods.........................................................................................138
Data set............................................................................................................138
ITC measurements...........................................................................................138
Molecular Dynamics Simulations ..................................................................140
MM-PBSA calculations...................................................................................141
Calculation of Predictive Indices (PI).............................................................143
Results and Discussion.........................................................................................144
MD trajectories................................................................................................144
Sampling the reference state............................................................................146
MM-PBSA results...........................................................................................151
Summary and Conclusions...................................................................................159
Expect the Unexpected while working with AR.......................................................163
Introduction..........................................................................................................163
Results and Discussion.........................................................................................165
Conclusions..........................................................................................................176
Summary and Outlook..............................................................................................178
Zusammenfassung.....................................................................................................185
Appendix A...............................................................................................................193
The Molecular Dynamics Database (MDDB)......................................................193
Introduction.....................................................................................................193
Database and program architecture.................................................................194
Data content.....................................................................................................194
Using MDDB...................................................................................................195
Appendix B...............................................................................................................197
Additional crystal structures for MD simulations................................................197
Structure Determination..................................................................................197
The sorbinil complex structure........................................................................198
The tolrestat complex structure.......................................................................199
Usage of crystal structures from collaboration partners...........................................202
References.................................................................................................................203
Publications arising from this work..........................................................................223
Articles.................................................................................................................223
Oral Communications..........................................................................................224
Posters..................................................................................................................224
Acknowledgments.....................................................................................................226
Curriculum vitae....................................................................