京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第20388号 / 工博第4325号 / 新制||工||1670(附属図書館) / 京都大学大学院工学研究科材料化学専攻 / (主査)教授 松原 誠二郎, 教授 吉田 潤一, 教授 中尾 佳亮 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DFAM

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Molecular recognition is an important tool for developing tunable controlled release systems and fabricating biosensors with increased selectivity and sensitivity. The development of polymer-based materials that exploit molecular recognition events such as host-guest complexation, enzyme-substrate and enzyme-inhibitor interactions and nucleic acid hybridization was pursued in this thesis. Using polymers as an anchor for molecular recognition can enhance the affinity, selectivity, and the capacity for immobilization of recognition units, enabling the practical use of affinity-based systems in real applications. To introduce the potential for immobilization while preserving or enhancing the affinity of small molecule recognition units, the affinity of derivatized cyclodextrins for the hydrophobic drug, dexamethasone, was investigated. Cyclodextrins (CDs) are molecules that possess a hydrophilic exterior and a hydrophobic cavity capable of accommodating a wide range of small molecule guests. Analysis of the solubilization capacities, thermodynamic parameters and aggregative potentials of carboxymethyl and hydrazide derivatives of CDs established the dextran-conjugated βCD derivative as an ideal carrier of hydrophobic drugs and the hydrazide βCD derivative as an optimal solubilizer of lipophilic pharmaceuticals, both alone and when incorporated in a polymer-based drug delivery vehicle. To enable non-covalent immobilization and stabilization of biomacromolecular recognition units, a printed layer hydrogel was investigated as a selective diffusion barrier for analyte sensing and enzyme inhibitor recognition. A printable hydrogel platform was developed from an established injectable system composed of aldehyde- and hydrazide-functionalized poly(oligoethylene glycol methacrylate) polymers. The printed layer hydrogel effectively immobilized a wide range of enzymes and protected enzyme activity against time-dependent and protease-induced denaturation, while facilitating the diffusion of small molecules. Furthermore, to demonstrate the potential of the printed film hydrogel immobilization layer to enhance the selectivity of the target, the printable hydrogel platform was used to develop a microarray-based assay for the screening of inhibitors of the model enzyme, β-lactamase. The assay was able to accurately quantify dose-response relationships of a series of established inhibitors, while reducing the required reagent volumes in traditional drug screening campaigns by 95%. Most significantly, the assay demonstrated an ability to discriminate true inhibitors of β-lactamase from a class of non-specific inhibitors called promiscuous aggregating inhibitors. Finally, to enable non-covalent immobilization of DNA recognition units, the printable hydrogel-based microarray was tested for its ability to immobilize DNA recognition sites and promote the detection of DNA hybridization events. A long, concatameric DNA molecule was generated through rolling circle amplification and was used as a sensing material for the detection of a small, fluorophore labeled oligonucleotide. The printable hydrogel was able to effectively entrap the rolling circle amplification product. Properties of the printable hydrogel were investigated for their ability to support the detection of DNA hybridization events. / Thesis / Doctor of Philosophy (PhD) / This thesis describes the development of polymer-based materials that exploit molecular recognition events for drug delivery and biosensing applications. First, cyclodextrins (CDs) are molecules that are capable of binding a wide range of small molecules. A comprehensive analysis of the complexation properties of CD derivatives revealed critical insight regarding their application in polymer-based drug delivery vehicles. Second, a printable hydrogel platform was developed to support the immobilization and activity of biomolecules and establish a biosensing interface that facilitates the diffusion of small molecules but not molecular aggregates. A microarray-based assay was developed by employing the printed hydrogel interface for the screening of inhibitors of the model enzyme, β-lactamase, and the detection of DNA hybridization events.

In the last twenty years, chemists have devised numerous synthetic chemical systems in which self-replication operates, demonstrating that molecules can replicate themselves without the aid of enzymes and that self-replication is not a prerogative of nucleic acids only. However, the coupling of replication to other recognition-mediated events and its exploitation in the amplification of large supramolecular assemblies, such as mechanically interlocked molecules, have remained unexplored areas. Among mechanically interlocked molecules, rotaxanes represent particularly attractive targets because of their application as molecular switches. This thesis describes how the recognition-mediated synthesis of a rotaxane can be combined to the amplification of its structure by replication. Kinetic models for the integration of self-replication with the formation of a rotaxane are presented. The logical steps required to convert these models into molecular structures through consideration of the design criteria highlighted by the models are discussed and executed. The macrocyclic component is an essential part of a rotaxane. The synthesis of several novel macrocycles is presented. Their ability to bind guests in their cavities through hydrogen bonds was probed. The best macrocycle/guest pairs were integrated in the formation of rotaxanes. Further investigations on the stoppering reaction and on the various recognition processes involved in the system lead ultimately to the construction of self-replicating rotaxanes.

La chimie supramoléculaire est un domaine qui porte sur l’étude des interactions<p>faibles entre molécules. Ces interactions sont très répandues dans les systèmes naturels et de<p>nombreux récepteurs moléculaires synthétiques ont été développés, soit pour un apport<p>théorique à la compréhension de ces processus de reconnaissance, soit pour d’éventuelles<p>applications en biologie ou en chimie analytique par exemple.<p>Les calix[6]arènes sont des composés intéressants pour la reconnaissance moléculaire.<p>Ils possèdent une cavité idéale pour l’inclusion de petites molécules et peuvent être modifiés<p>par l’ajout de divers motifs de reconnaissance. Le premier calix[6]crypturée préalablement<p>étudié au sein du Laboratoire de Chimie Organique est un récepteur dont la cavité aromatique<p>est juxtaposée à un motif de reconnaissance pour anions. Ce dernier est composé d’un<p>chapeau à base de tren (tris(2-aminoéthyl)amine) portant trois groupes urée. Ce récepteur<p>possède notamment une forte sélectivité pour le chlorure et une forte affinité pour les paires<p>d’ions organiques de type chlorure d’ammonium, dans un solvant apolaire (CDCl3).<p>Cependant, ces propriétés de reconnaissance sont beaucoup plus limitées dans un solvant<p>protique (CD3OD), ce qui restreint les éventuelles applications. L’objectif de ces travaux a été<p>de synthétiser de nouveaux dérivés avec une modification autour du site tris-urée pour<p>renforcer les propriétés de reconnaissance, notamment en milieu protique.<p>La première stratégie a consisté à agrandir le chapeau cryptant reliant les trois groupes<p>urée. Trois modes différents de complexation d’ammonium intra-cavitaire ont été mis en<p>évidence dans un solvant apolaire, dont deux sont remarquables. Avec un anion peu<p>coordinant (le picrate), le récepteur protoné inclut l’ammonium selon un processus<p>allostérique pour donner un complexe dicationique. Avec la protonation du récepteur et un<p>anion dichargé (SO4<p>2-), l’inclusion de l’ammonium constitue un complexe cascade, stable en<p>milieu protique.<p>La deuxième stratégie a consisté à supprimer les groupes méthyle du petit col<p>calixarénique via une réaction de déméthylation sélective pour obtenir le calix[6]crypturée<p>1,3,5-trishydroxyle. Dans un solvant apolaire, ce récepteur a montré une plus forte sélectivité<p>pour la complexation de paires d’ions par rapport à la complexation d’anions, permettant par<p>exemple de complexer le chlorhydrate de O,O-diméthyldopamine.<p>La troisième stratégie a été de synthétiser le calix[6]cryptothiourée, un récepteur dont<p>le chapeau comporte trois groupes thiourée. Cette modification structurale a fortement<p>renforcé la complexation d’anions mais n’a pas favorisé la complexation de paires d’ions dans<p>un solvant protique.<p>Enfin, la complexation de zwittérions a été testée sur l’ensemble de ces récepteurs et le<p>calix[6]cryptothiourée s’est avéré être un remarquable complexant de la B-alanine bétaïne.<p>Dans un mélange protique (CD3OD/CDCl3 1:1) la constante d’association est élevée (K ≈ 104<p>M-1) et supérieure d’au moins trois ordres de grandeur par rapport aux autres zwittérions<p>testés. C’est à notre connaissance un des rares récepteurs de bétaïnes et le premier à être<p>sélectif pour la B-alanine bétaïne. Enfin, le biomimétisme du mode de reconnaissance a été<p>montré par comparaison avec une protéine transporteur de bétaïne (Corynebacterium<p>glutamicum). / Doctorat en sciences, Spécialisation chimie / info:eu-repo/semantics/nonPublished

Doctor of Philosophy / Department of Chemistry / Christer B. Aakeroy / The ability to predict and control molecular arrangements without compromising the individual molecules themselves still remains an important goal in supramolecular chemistry. This can be accomplished by establishing a hierarchy of intermolecular interactions such as hydrogen and halogen bond, which may facilitate supramolecular assembly processes. Several acetaminopyridine/acetaminomethylpyridine supramolecular reactants (SR’s) were prepared with aliphatic carboxylic acids in order to determine patterns of molecular recognition preferences of the N-H moiety. The results obtained revealed the formation of molecular cocrystals through heteromeric O-H…N/N-H…O hydrogen bonds with the acetaminopyridine/acetaminomethylpyridine binding site. Furthermore, the SR’s also reacted with metal ions resulting in robust 1D and 2D metal-containing architectures. A series of pyridyl/pyrazine mono-N-oxide compounds were synthesized and reacted with a variety of halogenated benzoic acids, in order to assess the ability of these molecules to establish binding selectivity when both a hydrogen and halogen bond donor is present. The results obtained revealed that the pyridyl/carboxylic acid synthon formed 7/7 times and halogen bonds (N-O…I or N-O…Br) extended the SR/acid dimers into 1D and 2D networks. These results were rationalized via charge calculations as well as through the hierarchical view of intermolecular interactions consisting of hydrogen and halogen bonds. Furthermore, a series of thienyl compounds were synthesized and allowed to react with halogen bond donors to determine whether the halogen bond is purely electrostatic or based on the hard and soft acids and bases principles. The results obtained showed that of the 34 reactions between a halogen bond donor and thienyl compounds, the halogen bond is predominantly electrostatic in nature. Finally, as a result of our improved understanding on molecular recognition, we were able to carry out systematic structure-property studies on a series of cocrystals of anti-cancer drug molecules with aliphatic carboxylic acids. This study revealed that systematic changes to the molecular nature of the co-crystallizing agent combined with control over the way individual building blocks are organized within the crystalline lattice makes it possible to establish predictable links between molecular structure and macroscopic physical properties, such as melting behavior, solubility, dissolution rate, etc.

Doctor of Philosophy / Department of Chemistry / Christer B. Aakeroy / Supramolecular synthesis relies upon the creative and rational use of the common intermolecular forces and a proper understanding of these forces is critical for design and assembly of molecular building blocks into extended networks. The strength of seven substituted pyridines as hydrogen-bond acceptors was probed using a series of fifteen mono/dicarboxylic acids to demonstrate the interrelationship between the charge on the substrate and its ability to form co-crystals/salts. The higher charge in the acceptor led to proton transfer (100% yield) from the hydrogen bond donor to give a salt, whereas the lower charge led to co-crystals. This specificity observed for small molecules was extended to an investigation of selectivity in ditopic molecules. A series of nineteen hydrogen-bond donors, including fifteen carboxylic acids and four cyanoximes, were tested for binding preferences against ten ditopic ligands with variable charges. The overall supramolecular yield of 82% (9/11) proved a high degree of reliability in terms of best acceptor/donor approach, hence establishing the efficiency of the calculated charges as a guideline for molecular recognition processes. Solubility and thermal properties of pharmaceutical drug mimics were altered via formation of co-crystals/salts. The ligands and their co-crystals/salts with five even-chain dicarboxylic acids were synthesized and their comparative solubility in pure water and in pH 6.8 buffer solution measured. Solubility enhancement to a degree of 9x is observed for pharmaceutical drug haloperidol, whereas decrease in solubility down to 81% is achieved for 2-amino-5-(3-pyridyl)pyrimidine (which has agrochemical significance). Also the thermal and solubility behavior of these co-crystals were shown to reflect the properties of their parent co-crystallizing agents, allowing for a modulation of physical properties. Finally, the specificity and selectivity of the intermolecular interactions observed for small molecules were applied in the synthesis of hydrogen and halogen-bonded capsules. Several resorcinarene-based cavitands were synthesized and their upper rim decorated with acetamidopyridyl, aminopyrazinyl, 3-pyridyl, and 4-pyridyl moieties with hydrogen and halogen-bonding potentials. A homomeric hydrogen-bonded capsule was formed with self-assembly of acetamidoethynylcavitand via N-H···O=C interactions, whereas a heteromeric halogen-bonded capsule, the very first of its kind, was formed with N···I halogen-bonded interaction between 3-pyridylcavitand and tetrafluoroiodo-substituted calixarene.

<p>Virtually all biologically relevant functions and processes are mediated by non-covalent, molecular recognition events, demonstrating astonishingly diverse affinities and specificities. Despite extensive research, the origin of affinity and specificity in aqueous solution - specifically the relationship between ligand binding thermodynamics and structure - remains remarkably obscure and is further complicated in the context of multivalent interactions. Multivalency describes the combinatorial interaction of multiple discrete epitopes across multiple binding surfaces where the association is considered as the sum of contributions from each epitope and the consequences of multivalent ligand assembly. Gaining the insight necessary to predictably influence biological processes with novel therapeutics begins with an understanding of the molecular basis of solution-phase interactions, and the thermodynamic parameters that follow from those interactions. Here we continue our efforts to understand the basis of aqueous affinity and the nature of multivalent additivity.</p><p>Multivalent additivity is the foundation of fragment-based drug discovery, where small, low affinity ligands are covalently assembled into a single high affinity inhibitor. Such systems are ideally suited for investigating the thermodynamic consequences of multivalent ligand assembly. In the first part of this work, we report the design and synthesis of a fragment-based ligand series for the Grb2-SH2 protein and thermodynamic evaluation of the low affinity ligand fragments compared to the intact, high affinity inhibitor by single and double displacement isothermal titration calorimetry (ITC). Interestingly, our investigations reveal positively cooperative multivalent additivity - a binding free energy of the full ligand greater than the sum of its constituent fragments - that is largely enthalpic in origin. These results contradict the most common theory of multivalent affinity enhancement arising from a "savings" in translational and rotational entropy. The Grb2-SH2 system reported here is the third distinct molecular system in which we have observed enthalpically driven multivalent enhancement of affinity.</p><p>Previous research by our group into similar multivalent affinity enhancements in protein-carbohydrate systems - the so-called "cluster glycoside effect" - revealed that evaluation of multivalent interactions in the solution-phase is not straightforward due to the accessibility of two disparate binding motifs: intramolecular, chelate-type binding and intermolecular, aggregative binding. Although a number of powerful techniques for evaluation of solution-phase multivalent interactions have been reported, these bulk techniques are often unable to differentiate between binding modes, obscuring thermodynamic interpretation. In the second part of this work, we report a competitive equilibrium approach to Molecular Recognition Force Microscopy (MRFM) for evaluation of ligand binding at the single-molecule level with potential to preclude aggregative associations. We have optimized surface functionalization strategies and MRFM experimental protocols to evaluate the binding constant of surface- and tip-immobilized single stranded DNA epitopes. Surprisingly, the monovalent affinity of an immobilized species is in remarkable agreement with the solution-phase affinity, suggesting the competitive equilibrium MRFM approach presents a unique opportunity to investigate the nature of multivalent additivity at the single molecule level.</p> / Dissertation

Until very recently, synthetic chemistry has focussed on the creation of chemical entities with desirable properties through the programmed application of isolated chemical reactions, either individually or in a cascade that afford a target compound selectively. By contrast, biological systems operate using a plethora of complex interconnected signaling and metabolic networks with multiple checkpoint controls and feedback loops allowing biological systems to adapt and respond rapidly to external stimuli. Systems chemistry attempts to capture the complexity and emergent phenomena prevalent in the life sciences within a wholly synthetic chemical framework. In this approach, complex phenomena are expressed by a group of synthetic chemical entities designed to interact and react with many partners within the ensemble in programmed ways. In this manner, it should be possible to create synthetic chemical systems whose properties are not simply the linear sum of the attributes of the individual components. Chapter 1 discusses the role of complex networks in various aspects of chemistry- related research from the origin of life to nanotechnology. Further, it introduces the concept of Systems chemistry, giving various examples of dynamic covalent networks, self-replicating systems and molecular logic gates, showing the applications of complex system research. Chapter 2 discusses the components of replicator design. Further, it introduces a network based on recognition mediated reactions that is implemented by length- segregation of the substrates and displays properties of self-sorting. Chapter 3 presents a fully addressable chemical system based on auto- and cross- catalytic properties of product templates. The system is described by Boolean logic operations with different template inputs giving different template outputs. Chapter 4 introduces a dynamic network which fate is determined by a single recognition event. The replicator is capable of exploiting and dominating the exchanging pool of reagents in order to amplify its own formation at the expense of other species through the non-linear kinetics inherent in minimal replication. Chapter 5 focuses on the development of complex dynamic systems from structurally simple molecules. The new approach allows creating multicomponent networks with many reaction pathways operating simultaneously from readily available substrates.