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研究生:許玉羚
研究生(外文):Yu-Ling Hsu
論文名稱(外文):Design, synthesis and evaluation of chemical probes for biochemical applications
指導教授:羅禮強
口試委員:林敬哲林俊宏洪上程傅淑玲蔡蘊明
口試日期:2015-03-18
學位類別:博士
校院名稱:國立臺灣大學
系所名稱:化學研究所
學門:自然科學學門
學類:化學學類
論文種類:學術論文
論文出版年:2015
畢業學年度:103
語文別:英文
論文頁數:231
中文關鍵詞:分子探針蛋白質體學對苯磺醯氟腺苷穿心蓮內酯α-L-岩藻糖苷酶醌甲基同位素探針
外文關鍵詞:probeprotein profilingandrographolideα-L-fucosidasequinone methideisotope-coded tag
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化學探針能選擇性地標示目標蛋白質,為近代蛋白質體學上其中一種強力不可或缺的工具。本論文合成和設計幾種重要目標蛋白的化學探針,並介紹其發展及在生化方面的應用。第一部分針對蛋白激酶的結構特性設計的二個探針分子庫,皆以平行合成的組合式化學建構:第一個探針分子庫具有5''對苯磺醯氟腺苷和生物素標籤;第二個分子庫以3''疊氮去氧胸苷和腺苷為架構,接上三種親電子基。主架構的疊氮結構使其為一天然標籤基團。二個探針分子庫針對蛋白激酶的標示效能也在本論文進行驗証和比較。
穿心蓮內酯為一多功能的抗發炎和抗癌藥物,但相關的抑制機制卻還未完全明暸,因此建構具螢光團的穿心蓮內酯探針有助於進行生理中抑制和抗癌機制的追蹤和研究。第二部分合成和設計天然物穿心蓮內酯的可穿透細胞螢光探針,第一個可穿透細胞穿心蓮內酯螢光探針的合成經驗也有助於未來此類探針或抑制劑的開發和改良。本論文也合成α-L-岩藻糖苷酶醌甲基生成機制活性探針,以鹼催化置換β變旋異構物成α結構的關鍵中間體,並進而合成帶有螢光團的可穿透細胞

Development of small-molecular tools which selectively react with designated protein families has been found powerful in modern functional proteomics. In this dissertation, we evaluated two kinase probe libraries according to the structure and functions of protein kinases. The first library adopted a 5''-p-fluorosulfonylbenzoyl adenosine (5''-FSBA) skeleton and a biotin reporter. The second library explored a novel molecular framework by attaching three kind of electrophilic warheads on 3''-azido 2'', 3''-dideoxy base (AZT and AZA) recognition unit. The azido group at 3'' position is a native clickable tag without further modification. The labeling performances of these two probe libraries toward kinases were compared.
Despite the therapeutic importance of this multifunctional herbal compound Andrographolide, the inhibition and regulation mechanism are still ambiguious. Herein, we designed a novel andrographolide-based, cell permeable fluorescent probe for in vivo identification of target proteins participating in related cancer or diseases. This first-time synthesized Andrographolide-based, cell permeable fluorescent probe provide valuable information for the synthesis method in the future. In addition, cell-permeable activity-based probes for α-L-fucosidase were evaluated by the key base-promoted epimerization step. These two probes carrying mono or difluoromethylphenyl group would generate reactive quinone methide as a trapping device after hydrolysis. In the last part, quantitative isotope-coded azido tags were synthesized and applied to detect the level of S-nitrosylation proteome with drug treatment.


誌謝 i
中文摘要 ii
ABSTRACT iii
CONTENTS iv
LIST OF FIGURES ix
LIST OF SCHEMES xii
LIST OF TABLES xiv
ABBREVIATION xv
Chapter 1 Introduction of chemical strategies for proteomic researches 1
1.1 Proteomic researches 1
1.2 Chemical probes for protein profiling 1
1.2.1 Overview of Activity-based protein profiling 2
1.2.2 Affinity-based probes (AfBPs) 3
1.2.3 Compound-centric chemical proteomics 3
1.2.4 The structure of chemical probes 4
1.2.4.1 Recognition head 4
1.2.4.2 Reporters 7
1.2.4.3 Linker 9
1.2.5 Applications of ABPP 10
1.2.5.1 In vivo cell image 10
1.2.5.2 Inhibitor/drug screening 11
1.2.5.3 Diagnosis and biological mechanism discovery 11
1.3 Conclusion 12
1.4 References 13
Chapter 2 Construction of two protein kinase probe libraries 17
2.1 Introduction of kinases 17
2.1.1 Importance of kinases 17
2.1.2 The structure and catalytic mechanism of kinases 17
2.2 Design and synthesis of FSBA skeleton probe library 22
2.2.1 Development of kinase inhibitors and probes 22
2.2.2 Synthesis and evaluation of probe library for protein kinases 23
2.2.2.1 Precursor 7 and 9 for amide or ester probes 24
2.2.2.2 Parallel synthesis of probe library 26
2.2.2.3 Attachment of fluorosulfonyl benzoyl group 27
2.2.3 The labeling performance of probes 2-5 28
2.2.3.1 *Comparative labeling study of probes 2-5 to kinase 28
2.2.3.2 The labeling properties of probe 3 30
2.2.4 Experimental section 33
2.2.4.1 Materials 33
2.2.4.2 Synthesis of compounds 34
2.3 3''-azido-2'',3''-dideoxy base skeleton kinase probe library 42
2.3.1 Challenges for design of selective kinase probes: 42
2.3.2 The concept of novel kinase probes with various electrophiles 45
2.3.3 The 3''-azido-2'', 3''-dideoxy base skeleton probe library 46
2.3.3.1 Probes with benzylsulfonyl fluoride 47
2.3.3.2 Probes with glycyl electrophile 47
2.3.4 Result and discussion 48
2.3.4.1 Synthesis of the probes 22-26 48
2.3.4.2 The labeling property of probes 22-26 55
2.3.4.3 Validation of probe 24, 25 docking results 60
2.3.5 Experimental section 65
2.3.5.1 Synthesis of the probes 22-26 65
2.3.5.2 RP-HPLC time course study 78
2.3.5.3 Protocol for biological assays 78
2.3.5.4 Computational methods 80
2.4 Conclusion 81
2.5 References 83
Chapter 3 Design and synthesis of novel andrographolide-based probes 87
3.1 Introduction 87
3.1.1. Importance of andrographolide 87
3.1.2. The structure activity relationship (SAR) analysis of Andro 88
3.1.3. The mechanism of Andro 93
3.1.4. Development of Andro-based probes 94
3.1.4.1. Existing probes 94
3.1.4.2. Evaluation of our Andro-based fluorescent probes 96
3.1.4.3. Probes for Andro target proteins research 97
3.2 Results and discussion 98
3.2.1 Synthesis of the probe 62 98
3.2.2 Synthesis of the probe 63 103
3.2.3 *The biological results of probe 62 105
3.3 Conclusion 110
3.4 Experimental section 111
3.4.1 Synthesis of Andro-based probes 111
3.5 References 118
Chapter 4 Activity-based probes for α-L-fucosidase detection in cell 123
4.1 Introduction 123
4.1.1 The importance of α-L-fucosidase 123
4.1.2 Catalytic mechanism of α-L-fucosidase 123
4.1.3 Quinone methide based-activity probes for α-L-fucosidase labeling 125
4.2 Results and discussion 128
4.2.1 Synthesis of the molecular probe 70a and 70b 128
4.2.2 *Biological performances of probe 70a and 70b 132
4.3 Conclusion 136
4.4 Experimental section 137
4.5 References 154
Chapter 5 Isotope-coded affinity tag for quantitative analysis of protein expression level in proteome 157
5.1 Introduction 157
5.1.1 Quantitative proteomic research 157
5.1.2 Chemical labels 158
5.1.2.1 Isotope-coded affinity tag (ICAT) 158
5.1.2.2 Cleavable 13C-isotope-coded affinity tag (cICAT) 159
5.1.2.3 Other tags used for quantitative proteomic research 160
5.1.3 Isotope incorporated in probe or inhibitor for proteomic researches 162
5.1.4 The principle of our isotope-coded azido tag 164
5.2 Result and discussion 168
5.2.1 Synthesis of probe 83a and 83b 168
5.2.2 Quantification and amplification property of probe 83a and 83b 171
5.3 Conclusion 174
5.4 Experimental section 175
5.5 References 180
Chapter 6 Conclusion 182
Appendix 185

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