Investigation of the NIR cyanine dye MHI-36 shows binding affinity to charged amino acids. This cyanine dye showed aggregation and dimer formation at higher dye concentration (2.0x10-3 M) induced by lysine. When dye concentration decreased to 1.0x10-4M no strong aggregate formation was viewed. Dye shows strong binding and selectivity properties towards charged amino acids lysine and arginine, compared to neutral leucine. It’s believed the positively charged presence was able to break and disrupt the conjugated π- π bonds at lower dye concentration. Computational work showed intramolecular aggregation of the phenyl groups on the dye. These aggregates are believed to create electron rich environment suitable for lysine interaction.

Kyoto University (京都大学) / 0048 / 新制・課程博士 / 博士(工学) / 甲第15407号 / 工博第3286号 / 新制||工||1495(附属図書館) / 27885 / 京都大学大学院工学研究科合成・生物化学専攻 / (主査)教授 濵地 格, 教授 森 泰生, 教授 白川 昌宏 / 学位規則第4条第1項該当

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第20002号 / 工博第4246号 / 新制||工||1657(附属図書館) / 33098 / 京都大学大学院工学研究科合成・生物化学専攻 / (主査)教授 濵地 格, 教授 森 泰生, 教授 跡見 晴幸 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DFAM

Kyoto University (京都大学) / 0048 / 新制・課程博士 / 博士(工学) / 甲第15039号 / 工博第3188号 / 新制||工||1479(附属図書館) / 27500 / 京都大学大学院工学研究科合成・生物化学専攻 / (主査)教授 濵地 格, 教授 森 泰生, 教授 白川 昌宏 / 学位規則第4条第1項該当

Kyoto University (京都大学) / 0048 / 新制・課程博士 / 博士(工学) / 甲第16886号 / 工博第3607号 / 新制||工||1545(附属図書館) / 29561 / 京都大学大学院工学研究科合成・生物化学専攻 / (主査)教授 濵地 格, 教授 森 泰生, 教授 白川 昌宏 / 学位規則第4条第1項該当

Kyoto University (京都大学) / 0048 / 新制・課程博士 / 博士(工学) / 甲第17599号 / 工博第3758号 / 新制||工||1573(附属図書館) / 30365 / 京都大学大学院工学研究科合成・生物化学専攻 / (主査)教授 濵地 格, 教授 梅田 眞郷, 教授 杉野目 道紀 / 学位規則第4条第1項該当

Labeling proteins with chemical tools is important for examining natural systems, discovering therapeutic agents and developing protein constructs. These methods offer simple but reliable chemistry to the study of peptides and proteins and thus have gained popularity among chemists and biologists. Despite the fact that the number of successful examples has been largely increased over the past decade, there is still an ongoing need for new reagents with better accessibility and reactivity. Diazonium ions are known to selectively react with tyrosine residues for more than a century. But the harsh condition required for diazotization makes it difficult to use this strategy in biological applications. To address this, bench-stable triazabutadienes are made to release diazonium ions upon mild acidification or photoirradiation. Based on our previous study, imidazole N-alkyl substituted triazabutadienes were synthesized and tested for diazonium ion-releasing rates. Surprisingly, the imidazole N-tert-butyl substituted triazabutadiene showed the fastest rate in neutral and basic aqueous solutions. A subsequent NMR study revealed that this rapid release of diazonium ions might be ascribed to the lack of intramolecular π-interactions. In addition, triazabutadienes can be rendered more basic upon photo-isomerization. A water-soluble triazabutadiene was shown to adjust the pH of aqueous solutions. These findings open up new opportunities in protein labeling with unprecedented ease. Moreover, a boronic acid-based photocrosslinker was synthesized to detect protein-protein interactions of glycoproteins. By incorporating benzophenone with a boronic acid and a terminal alkyne, this photocrosslinker is designed to capture the glycoprotein-substrate complex using the combination of photochemistry and bioorthogonal reactions. In conclusion, this dissertation demonstrates progress in developing new probes for protein labeling and protein-protein interactions. These newly developed strategies offer convenient alternatives to those wishing to explore protein activities.

L’Imagerie par Résonance Magnétique (IRM) est une technique prometteuse largement répandue dans les milieux hospitaliers. Elle est non invasive, présente une bonne résolution spatiale et permet de visualiser en profondeur dans un organisme vivant. Elle possède cependant quelques défauts, dont sa faible sensibilité. Pour palier ce problème, il est possible d'utiliser des espèces hyperpolarisables telles que le xénon. Cependant, n’étant spécifique d’aucun récepteur biologique, le xénon nécessite d’être vectorisé. Pour ce faire, des auteurs ont proposé son encapsulation dans une cage moléculaire capable de reconnaître la cible biologique à imager. Les meilleurs candidats à ce jour sont les cryptophanes.Nous nous sommes fixés comme objectif dans cette thèse de concevoir et de synthétiser de nouvelles cages plus adaptées pour les applications en IRM 129Xe ainsi que des biosondes pertinentes pour se rapprocher d’applications in vivo. Dans une première partie de ma thèse, nous nous sommes intéressés au développement de nouvelles cages afin d’étudier et d’affiner les propriétés d’encapsulation du xénon au sein des cryptophanes. Dans les parties suivantes, nous nous sommes concentrés sur la conception de biosondes par fonctionnalisation de cryptophanes déjà décrits pour diverses applications d’intérêt biologique. D’une part, nous avons évalué la possibilité de détecter des métaux de manière plus spécifique et plus sensible grâce à l’IRM xénon hyperpolarisé. D’autre part, nous avons travaillé sur la conception de biosondes bimodales, afin de coupler des techniques complémentaires d’imagerie médicale. / Today, Magnetic Resonance Imaging (MRI) is a powerful clinically used imaging method which provides three-dimensional images with excellent resolution. However, conventional molecular MRI techniques that rely on the observation of water protons still suffer from reduced sensitivity and often lack selectivity. The use of hyperpolarized xenon can improve both the selectivity and sensitivity of the MRI method. As xenon has no specificity for any biological receptor, it needs to be vectorized. For this purpose, authors have proposed to encapsulate xenon inside molecular cages functionalized to recognize specific biological targets. The best candidates so far as biosensors are cryptophanes.The aim of this work is to design and synthesize new cryptophanes that are better suited for 129Xe MRI applications and relevant biosensors for future in vivo applications. In a first part, new cages were developed in order to study the encapsulation properties of xenon inside different cryptophanes. Then, biosensors were synthesized by functionnalization of known water-soluble cryptophanes for different applications of biological interest. We have therefore assessed the possibility of detecting metal ions specifically in a very sensitive way thanks to 129Xe MRI. New bimodal sensors were also designed and tested.

Proteins have evolved over millions of years to serve a plethora of highly specialized functions in biological systems. Given the enormous diversity in structure and function, it is truly surprising that only 20 different amino acids are utilized as the building blocks of proteins. Furthermore, only a small set of metal cations that are biologically available are used as structural or catalytically active cofactors in proteins, whereas rare metal cations such as platinum, ruthenium or rhodium remain absent. In the 20th century myriad catalysts, based on non-biological transition metals, emerged that can facilitate numerous organic transformations. The goal of the thesis was to introduce new functions into proteins by attaching platinum metals and fluorescent metal sensors. Thus, semi-synthetic proteins for catalytic and analytical applications were generated. The replacement of organic solvents by environmentally benign solvents such as water is an imperative step towards achieving "green chemistry". The combination of small molecule catalysts with proteins may introduce new functions and take advantage of the benefits of "both worlds" while avoiding their potential drawbacks. Therefore semi-synthetic catalysts were developed for enantioselective organic reactions in aqueous medium. A suitable reaction, reaction conditions and catalytic system for later utilization in a semi-synthetic protein were designed, developed and characterized. Ruthenium porphyrins catalyzed cyclopropanation reactions with fair yields and high stereoselectivity in aqueous medium. The successful reaction in water was a crucial requirement for a catalytically active semi-synthetic protein. Mechanistic studies did not elucidate the actual catalytic species for the formation of the cyclopropanation product and the side-product diethyl maleate; however, new insights were gained from the analysis of potential reaction pathways. Moreover, studies of the influence of axial ligands, resembling likely residues coordinating to the ruthenium metal center in the active site of a semi-synthetic protein, on the carbene formation of ruthenium porphyrins illustrated that coordination of axial ligands may inhibit the catalytic activity. The generation of ruthenium porphyrin based semi-synthetic proteins and their subsequent catalysis of cyclopropanation reactions was carried out. Myoglobin and myoglobin mutants were successfully reconstituted with a heme-like ruthenium carbonyl porphyrin; however, none of the formed semi-synthetic proteins catalyzed the enantioselective cyclopropanation of styrene. Efforts to determine the reconstitution efficiency of the generated semi-synthetic were hampered by problems to purify the generated semi-synthetic proteins that are probably due to non-specific binding of the ruthenium porphyrin to the protein surface. The exploration of labile metal pools of the biologically relevant transition metals copper, iron and zinc in cells was the goal of developing semi-synthetic proteins for analytical applications. Combining fluorescent proteins with colored or fluorescent metal chelators by forming semi-synthetic proteins allows taking advantage of their beneficial properties while avoiding their downsides. This design offers an attractive platform for in vivo metal sensing. Plasmids encoding fluorescent proteins, targeting sequences and AGT or intein fusion domains (necessary for labeling) for eukaryotic and prokaryotic expression were generated. The targeting of intracellular compartments (mitochondria, nucleus and TGN) was successful (confirmed by light microscopy experiments with transfected mammalian cells). In vitro labeling experiments of expressed and purified fusion proteins with rhodamine derivatives succeeded with AGT based fusion proteins; however, labeling of fusion proteins by trans-splicing with split-inteins failed. A new Zinc(II)-chelator was attached to an AGT based protein and the resulting semi-synthetic protein exhibited strong changes of fluorescence in the presence of zinc(II). This represents an important step towards the goal of in vivo cell imaging of labile zinc(II) pools. Despite extensive efforts, all attempts failed to generate a chelator that forms Cu(I)-complexes with the 1:1 stochiometry (ligand:metal) that is necessary for metal sensing with semi-synthetic proteins.

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