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Three Membered Rings As Probes in the Activity Based Protein Profiling

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Three Membered Rings As Probes in the Activity Based Protein Profiling Three membered rings as probes in the activity based protein profiling Dissertation zur Erlangung des Doktorgrades der Fakultät für Chemie der Technischen Universität München von M. Sc. Maximilian Pitscheider geboren am 05.07.1983 in München Technische Universität München Lehrstuhl für organische Chemie II Three membered rings as probes in the activity based protein profiling Maximilian Friedrich Pitscheider Vollständiger Abdruck der von der Fakultät für Chemie der Technischen Universität München zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften genehmigten Dissertation. Vorsitzender: Univ.-Prof. Dr. Johannes Buchner Prüfer der Dissertation: 1: Univ.-Prof. Dr. Stephan A. Sieber 2: Univ.-Prof. Dr. Thomas Brück Die Dissertation wurde am 27.11.2011 bei der Technischen Universität München eingereicht und durch die Fakultät für Chemie am 08.12.2011 angenommen. Meiner Familie Danksagung An erster Stelle danke ich meinem Betreuer Prof. Dr. Stephan A. Sieber für die interessante und vielfältige Themenstellung, die exzellenten Arbeitsbedin- gungen und die große wissenschaftliche Freiheit. Seine große Begeisterungsfä- higkeit für das Thema, die stetige Motivation und seine Unterstützung wäh- rend meiner gesamten Promotionszeit haben entscheidend zum Erfolg dieser Arbeit beigetragen. Vielen Dank auch für die Möglichkeit, durch die Teil- nahme an einer Vielzahl von Konferenzen meinen wissenschaftlichen Horizont zu erweitern. Den Mitgliedern der Prüfungskommission danke ich für ihre Bemühungen und den zeitlichen Aufwand bei der Evaluierung der Arbeit. Prof. Dr. Tho- mas Brück danke ich recht herzlich für die Übernahme des Koreferats. Frau Kerstin Kurz und Frau Mona Wolff danke ich für die hervorragende Hilfsbereitschaft bei allen bürokratischen und organisatorischen Fragen und der unverzichtbaren Hilfe im Laboralltag. Den Mitarbeitern der NMR-Spektro- skopie Dr. David Stephenson und Claudia Dubler an der LMU und dem Ve- rantwortlichen für die small molecule Massenspektrometrie an der TU, Herrn Burghard Cordes danke ich für die schnelle Aufnahme von NMR- und Mas- senspektren. Meiner arbeitskreisinternen Kooperationspartnerin Dr. Nina Mäusbacher danke ich herzlich für ihren unermüdliches Engagement bei der homologen Überexpression und den Knock-out Studien. Sie übernahm dabei die ge- netischen Arbeiten bis hin zur Transformierung und ohne ihren großartigen Einsatz und die zahlreichen fruchtbaren Diskussionen wäre dieses Projekt so nicht möglich gewesen. Frau Dr. Katrin Lorenz-Baath möchte ich in die freundliche und geduldige Einweisung in die Arbeitsmethoden der Zellkultur danken. Ich hoffe ich habe nicht allzuviele Infektionen eingeschleppt. Dem gesamten Arbeitskreis, meinen Freunden und liebgewonnenen Kol- legen aus drei Jahren und zwei Universitäten möchte ich herzlichst für die entspannte und gemeinschaftliche Atmosphäre im Labor und den zahlreichen außeruniversitären Aktivitäten danken. Ohne die stete Hilfsbereitschaft bei kleineren und größeren Problemen sowie die zahlreichen fachlichen Diskussio- nen und den Rückhalt, der mich in so mancher Situation aufgefangen hat, wäre diese Arbeit nicht entstanden. Dies gilt nicht nur für Ronald Orth, Tho- mas Böttcher und Isabell Staub, den Kollegen der ersten Stunde, sondern auch für die Mitglieder des neuen Kreises an der TU, Tanja Wirth, Oliver Battenberg, Jürgen Eirich, Dr. Mathew Nodwell, Georg Rudolf, Franziska Mandl, Mathias Leidl, Dr. Katrin Lorentz-Baath, Maximilian Koch und Ma- ria Damen. Danke für jede Frotzelei, jeden Kalauer und jedes Feierabendbier. Viel Erfolg in eurer weiteren Laufbahn. Macht es einfach! Meinen Bachelorstudenten Lissa Princz und Matthias Westphal sowie mei- nen Forschungspraktikanten Tanja Wirth, Tanja Ossiander, Erwin Wiesen- mayer und Amelie Koch danke ich für ihre hohe Einsatzbereitschaft und Moti- vation beim Bearbeiten der Projekte. Vielen Dank auch an unsere langjährige wissenschaftliche Hilfskraft Mathias Leidl, dessen hilfsbereite und humorvolle Art nicht mehr aus dem Arbeitskreis wegzudenken sind. Ebenso bedanken möchte ich mich für die stete Unterstützung meiner El- tern Petra und Karl Pitscheider während meines gesamten Studiums und der Promotionszeit. Euer Zuspruch hat mir stets Kraft gegeben. Dies gilt auch für meine Geschwister Johannes Hönlinger und Susanne Harper und meiner Schwägerin Doris Witt die bei einem Glas Wein immer ein offenes Ohr für mich hatten. Ihr seid die beste Familie, die man sich wünschen kann! Mein letzter und größter Dank geht an meine Frau Almut Pitscheider, die in jedem Augenblick unserer Beziehung für mich da war und mich aufgebaut hat. Ich danke dir von Herzen für die Geduld, wenn es des Öfteren ein bis zwei Stunden länger als versprochen gedauert hat, oder wenn die Arbeit nicht in der Uni blieb. Du hast mir stets geholfen das Ziel im Auge zu behalten. Eine bessere Unterstützung und eine bessere Partnerin an meiner Seite kann ich mir nicht vorstellen. Introductory remark Parts of this thesis have been published in international journals. Table of Contents 1 Summary . 1 2 Zusammenfassung . 7 3 Introduction . 13 3.1 The return of an old foe . 13 3.2 Proteomics . 17 3.3 Activity-based protein profiling . 18 3.3.1 General . 18 3.3.2 Basic design of an ABPP probe . 19 3.3.3 Tag free-ABPP . 21 3.3.4 Course of a tag free-ABPP experiment . 22 3.3.5 Identification of proteins by mass-spectrometry (MS) . 24 3.4 Natural products in ABPP . 27 3.5 Scope of this work . 28 4 Results . 31 4.1 Synthesis . 31 4.1.1 Cyclopropanes . 31 4.1.1.1 General . 31 4.1.1.2 Synthetic strategy . 33 4.1.2 Oxiranes . 34 4.1.2.1 General . 34 4.1.2.2 Synthetic strategy . 37 4.1.3 Thiiranes . 41 4.1.3.1 General . 41 4.1.3.2 Synthetic strategy . 43 4.1.4 Aziridines . 45 4.1.4.1 General . 45 4.1.4.2 Synthetic strategy . 48 4.2 Summary . 50 I Table of Contents 4.3 Stability . 50 4.4 Proteomics . 54 4.5 Assays . 64 4.5.1 Minimal inhibitory concentration . 64 4.5.2 Toxicity to eucaryotic cells . 66 4.6 Target verification by recombinant overexpression . 68 4.6.1 General . 68 4.6.2 Heterologous overexpression in E. coli . 69 4.7 Mechanism of action . 73 4.7.1 Fatty acid biosynthesis . 73 4.7.2 Genetic Knockout . 74 4.7.3 Homologous overexpression . 76 4.7.4 Point mutation . 80 4.8 Summary . 83 5 Experimental section . 85 5.1 Organic chemistry . 85 5.1.1 Materials . 85 5.1.1.1 General . 85 5.1.1.2 TLC Stains . 86 5.1.2 Synthesis . 87 5.1.2.1 Ethyl (2R,3R) oxirane-2,3-dicarboxylate, (1) . 87 5.1.2.2 Ethyl (2R,3R) 3-(N -propargylaminocarbonyl) oxirane- 2-carboxylate (2, OxyEt) . 87 5.1.2.3 (2R,3R) 3-(N -propargylaminocarbonyl) oxirane- 2- carboxylic acid (3) . 88 5.1.2.4 Butyl (2R,3R) 3-(N -propargylaminocarbonyl) oxirane- 2-carboxylate (4, OxyBut) . 89 5.1.2.5 Hexyl (2R,3R) 3-(N -propargylaminocarbonyl) oxirane- 2-carboxylate (5, OxyHex) . 90 5.1.2.6 Octyl (2R,3R) 3-(N -propargylaminocarbonyl) oxirane- 2-carboxylate (6, OxyOc) . 91 5.1.2.7 Dodecyl (2R,3R) 3-(N -propargylaminocarbonyl) oxirane- 2-carboxylate (7, OxyDode) . 92 5.1.2.8 Benzyl (2R,3R) 3-(N -propargylaminocarbonyl) oxirane- 2-carboxylate (8, OxyBenz) . 93 II Table of Contents 5.1.2.9 Allyl (2R,3R) 3-(N -propargylaminocarbonyl) oxirane- 2-carboxylate (9, OxyAll) . 94 5.1.2.10 Ethyl (2S,3S) 3-(N -propargylaminocarbonyl) thiirane- 2-carboxylate (10, ThiEt) . 95 5.1.2.11 Butyl (2S,3S) 3-(N -propargylaminocarbonyl) thiirane- 2-carboxylate (11, ThiBut) . 96 5.1.2.12 Hexyl (2S,3S) 3-(N -propargylaminocarbonyl) thiirane- 2-carboxylate (12, ThiHex) . 97 5.1.2.13 Octyl (2S,3S) 3-(N -propargylaminocarbonyl) thiirane- 2-carboxylate (13, ThiOc) . 98 5.1.2.14 Dodecyl (2S,3S) 3-(N -propargylaminocarbonyl) thiirane- 2-carboxylate (14, ThiDode) . 99 5.1.2.15 Benzyl (2S,3S)-3-(N -propargylaminocarbonyl) thiirane- 2-carboxylate (15, ThiBenz) . 100 5.1.2.16 Allyl (2S,3S)-3-(N -propargylaminocarbonyl) thiirane- 2-carboxylate (16, ThiAll) . 101 5.1.2.17 General procedure for the preparation of the aziri- dine probes: . 102 5.1.2.18 (E)-ethyl 4-oxo-4-(prop-2-yn-1-ylamino)but-2-enoate (17, MichEt) . 102 5.1.2.19 Ethyl (2R*,3R* )-3-(N -propargylaminocarbonyl) aziridine- 2-carboxylate (18, AziEt) . 103 5.1.2.20 (E)-4-oxo-4-(prop-2-yn-1-ylamino)but-2-enoic acid (19) . 104 5.1.2.21 (E)-octyl 4-oxo-4-(prop-2-yn-1-ylamino)but-2-enoate (20, MichOc) . 105 5.1.2.22 (E)-benzyl 4-oxo-4-(prop-2-yn-1-ylamino)but-2-enoate (21, MichBenz) . 106 5.1.2.23 Octyl (2R*,3R* ) 3-(N -propargylaminocarbonyl) aziridine- 2-carboxylate (22, AziOc) . 107 5.1.2.24 Benzyl (2R*,3R* )3-(N -propargylaminocarbonyl) azi- ridine -2-carboxylate (23, AziBenz) . 108 5.1.2.25 Diethyl cyclopropane-1,2-dicarboxylate (24) . 108 5.1.2.26 2-(ethoxycarbonyl)cyclopropane-carboxylic acid (25)109 III Table of Contents 5.1.2.27 1-ethyl 2-hex-5-yn-1-yl cyclopropane-1,2-dicarboxylate (26, CycloEt) . 109 5.2 Biochemistry . 111 5.2.1 Microbiology . 111 5.2.1.1 Materials . 111 5.2.1.1.1 Bacteria . 111 5.2.1.1.2 Antibiotic stocks . 111 5.2.1.1.3 Media . 112 5.2.1.1.4 Agar plates . 113 5.2.1.2 Methods . 113 5.2.1.2.1 Cryostocks . 113 5.2.1.2.2 Competent cells . 114 5.2.2 Cell culture . 117 5.2.2.1 Materials . 117 5.2.2.1.1 Buffers . 117 5.2.2.2 Methods . 117 5.2.2.2.1 Cultivation and splitting . 117 5.2.2.2.2 Counting . 118 5.2.2.2.3 MTT Assay . 119 5.2.3 Genomics . 121 5.2.3.1 Materials . 121 5.2.3.1.1 Buffers . 121 5.2.3.1.2 Enzymes .
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