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Classification of Metabolic Reactions Based on Physicochemical Properties and Search for Enzyme Inhibitors

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Classification of Metabolic Reactions Based on Physicochemical Properties and Search for Enzyme Inhibitors Classification of Metabolic Reactions based on Physicochemical Properties and Search for Enzyme Inhibitors Den Naturwissenschaftlichen Fakultäten der Friedrich-Alexander-Universität Erlangen-Nürnberg zur Erlangung des Doktorgrades vorgelegt von Martin Johann Reitz aus Forchheim Als Dissertation genehmigt von den Naturwissenschaftlichen Fakultäten der Universität Erlangen-Nürnberg Tag der mündlichen Prüfung: 11. Mai 2007 Vorsitzender der Prüfungskomission: Prof. Dr. E. Bänsch Erstberichterstatter: Prof. Dr. J. Gasteiger Zweitberichterstatter: Prof. Dr. H. Sticht Danksagung Meinem Doktorvater Prof. Dr. Johann Gasteiger danke ich für die Überlassung des interessanten Themas sowie die vielfältige Unterstützung und die wertvollen Anregungen wodurch das Gelingen der Arbeit erst ermöglicht wurde. Zu besonderem Dank bin ich verpflichtet: Herrn Alexander von Homeyer für die Zusammenarbeit im Rahmen der gemeinschaftlichen Publikation und des Buchkapitels sowie seine Unterstützung bei den Strukturüberlagerungen. Dr. Oliver Sacher für die Zusammenarbeit im Rahmen des BFAM Projektes sowie die stete Hilfsbereitschaft rund um BioPath, Cactvs und Cora. Weiterhin danken möchte ich Dr. Thomas Kleinöder, Dr. Lothar Terfloth und Dr. Yongquan Han für die anregenden wissenschaftlichen Diskussionen sowie zusammen mit Dr. Achim Herwig, Herrn Thomas Tröger und Dr. Markus Sitzmann für die tatkräftige Unterstützung im Rahmen der Linux-Administration. Danke auch an die Herren Jan Griebsch, Arno Buchner und Hanjo Täubig vom Lehrstuhl für Effiziente Algorithmen der TU München für die Zusammenarbeit im Rahmen des BFAM Projektes. Darüber hinaus danke ich allen derzeitigen und ehemaligen Mitarbeitern des Arbeitskreises, welche hier nicht namentlich erwähnt sind, sowie den Sekretärinnen für die stete Hilfsbereitschaft und Bereitstellung einer funktionierenden Infrastruktur sowie für die stets angenehme Arbeitsatmosphäre. Ganz besonders herzlichen Dank meiner Freundin Silvia sowie meiner ganzen Familie, insbesondere meinen Eltern, für die Geduld und Unterstützung in jeglicher Hinsicht beim Verfassen dieser Arbeit. Dem Bundesministerium für Bildung und Forschung (BMBF) danke ich für die Finanzierung der Arbeit durch das BFAM-Projekt. Contents 1 Introduction......................................................................................................................1 1.1 Scientific Background.................................................................................................. 4 1.1.1 Connection Table.................................................................................................. 4 1.1.2 Atom-Atom Mapping............................................................................................ 5 1.1.3 Reaction Center Marking ..................................................................................... 6 1.2 Exploiting the Data...................................................................................................... 7 References .............................................................................................................................. 9 2 Enabling the Exploration of Biochemical Pathways .....................................................11 2.1 General Introduction................................................................................................. 11 References ............................................................................................................................ 11 Abstract ................................................................................................................................ 12 2.2 Introduction ............................................................................................................... 12 2.3 The BioPath Database................................................................................................ 15 2.3.1 The Data Model................................................................................................... 15 2.3.2 Chemical Structures............................................................................................ 15 2.3.3 Chemical Reactions............................................................................................. 16 2.3.4 Enzymes............................................................................................................... 18 2.3.5 Augmenting the Contents .................................................................................. 18 2.3.6 Data Input............................................................................................................ 18 2.3.7 Data Processing and Storing ............................................................................... 19 2.4 The C@ROL Retrieval System .................................................................................. 21 2.5 Searching in the BioPath Database ........................................................................... 24 2.5.1 Searching in the Molecule Database .................................................................. 24 2.5.2 Name and Name Fragment Searching................................................................ 24 2.5.3 Gross-formula Searches.......................................................................................27 i 2.5.4 Full Structure and Substructure Searches.......................................................... 28 2.5.5 Property Retrieval............................................................................................... 32 2.5.6 3D-Substructure Searches................................................................................... 32 2.5.7 Searching in the Reaction Database................................................................... 34 2.5.8 Searching with Chemical Structures.................................................................. 34 2.5.9 Searches on the Reaction Centre........................................................................ 35 2.5.10 Searching on Enzymes ........................................................................................ 38 2.5.11 Combined Searches............................................................................................. 40 2.6 Conclusions ................................................................................................................ 41 Acknowledgements ............................................................................................................. 41 Table of Acronyms............................................................................................................... 42 References ............................................................................................................................ 43 2.7 Improvements on the BioPath Database .................................................................. 45 2.7.1 Data Cleanup & Improvement ........................................................................... 45 2.7.2 C@ROL Interface................................................................................................ 45 References ............................................................................................................................ 49 3 Query Generation to Search for Inhibitors of Enzymatic Reactions ............................50 3.1 General Introduction................................................................................................. 50 References ............................................................................................................................ 51 Abstract ................................................................................................................................ 52 3.2 Introduction ............................................................................................................... 53 3.3 Materials and Methods .............................................................................................. 55 3.4 Results and Discussion............................................................................................... 60 3.5 Conclusions ................................................................................................................ 75 Acknowledgement............................................................................................................... 75 ii References ............................................................................................................................ 76 3.6 Further Conclusions.................................................................................................. 79 References ............................................................................................................................ 79 4 Database Screening for Enzyme Inhibitors....................................................................80 4.1 Introduction ............................................................................................................... 80 4.2 Preparation of data..................................................................................................... 81 4.3 Computation............................................................................................................... 83 4.4 The Fitness Function................................................................................................. 84 4.5 Results......................................................................................................................... 87 4.6 Conclusions ...............................................................................................................
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