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  • About
  • The Global ETD Search service is a free service for researchers to find electronic theses and dissertations. This service is provided by the Networked Digital Library of Theses and Dissertations.
    Our metadata is collected from universities around the world. If you manage a university/consortium/country archive and want to be added, details can be found on the NDLTD website.
301

Synthesis of Taxol™ Analogs as Conformational Probes

Metaferia, Belhu B. 31 July 2002 (has links)
Taxol™, isolated from the bark of Taxus brevifolia in the late 1960s, and the semisynthetic analog Taxotere™ have proven clinical importance for the treatment of ovarian and breast cancer. Taxol™ exerts its biological effect by binding to polymerized tubulin and stabilizing the resulting microtubules. Studies aimed at understanding the biologically active conformation of taxol and its binding environment on β-tubulin are described. This knowledge is important because it could lead to the design of structurally less complicated drugs with better efficacy and better bioavailability. Moreover, the information can be extended to other natural products that possess microtubule-stabilizing properties similar to Taxol™. In this work, the synthesis of a triply labeled taxol analog is described as well as REDOR studies of this compound complexed to tubulin are in progress. Macrocyclic analogs of taxol have been prepared and their biological activities were evaluated. Chemical modeling of these analogs and their activities agrees with the hypothesis that Taxol™ adopts T-shaped conformation. Difficulties were encountered with the key ring-closing metathesis strategy, suggesting that a more flexible and efficient macrocyclization method will be needed to synthesize additional macrocyclic analogs. / Ph. D.
302

Frakcionace a molekulární organizace huminových kyselin / Fractionation and molecular organization of humic acids

Chytilová, Aneta January 2016 (has links)
Humic acids are part of the natural organic matter occurring all around us. The aim of this thesis is to study the molecular organization, conformation of humic acids in aqueous solutions, that always raise a number of questions. For a long time, the scientists all over the world argue, if humic acid are polymers, micelles or supramolecules. Over time, thanks to new technologies, their opinions are moving away from a polymer model and tend rather to supramolecular arrangement of humic acids. Studying humic complex systems is not easy, because they are polydisperse and heterogeneous, which significantly complicates any characterization. Moreover, its molecular organization is affected by many factors such as e.g. pH, ionic strength and etc. For the study of the conformation of humic acids, concentration series of IHSS (International humic substances asociation) Leonardite humic acids stamdards in four different mediums were prepared: 0,1 M NaOH, humic acids in water with pH modified to 12 (basic medium), 0,1 M NaOH + 0,1 M HCl, 0,1 M NaCl (neutral environment). Furthermore it has been performed the fractionation of humic acids for the purpose of simplifying the complicated structure. Prepared concentration series were characterized with several analytical methods such as ultraviolet and visible spectroscopy, dynamic light scattering, electrophoretic light scattering, microrheology, gel permeation chromatography, potentiometric pH determination and direct conductometry. Diploma thesis is built on the previous bachelor thesis in which different sample of humic acids was studied. The measured results indicate that the studied systems show supramolecular behavior and in some cases are subject to aggregation into larger units (micelles).
303

Synthesis and properties of some electrolyte additives for lithium-ion batteries

Bebeda, Avhapfani Wendy 19 February 2015 (has links)
Department of Chemistry / As an alternative energy source, lithium ion batteries have become increasingly important with a wide range of applications in industry, and many international companies are investing in this big project. This study was aimed at the development of safer lithium-ion power sources by using new organic additives to overcome the possible safety problems. In this study, the conformations and energies of several synthesized boronates were investigated through computational study using density functional theory (DFT) with the Becke’s three-parameter hybrid method utilizing the Lee-Young-Parr correlation functional (B3LYP). After initial energy optimization using Møller-Plesset Perturbation theory (MP2), the conformational preferences and energetics in vacuo were investigated using DFT calculations and the 6-31G(d,p) basis set. Subsequently, cyclic voltammetry and electrochemical impedance spectroscopy were used to characterize the compounds in terms of their usefulness as electrolyte additives. At least two of these show excellent promise for use in lithium-ion batteries.
304

Diffusion and Conformational Dynamics of Semiflexible Macromolecules and Supramolecular Assemblies on Lipid Membranes

Herold, Christoph 07 November 2012 (has links)
Understanding the interaction of polyelectrolytes with oppositely charged lipid membranes is an important issue of soft matter physics, which provides an insight into mechanisms of interactions between biological macromolecules and cell membranes. Despite the fact that many (bio)macromolecules and filamentous supramolecular assemblies show semiflexible behavior, prior to this work very little was known about the conformational dynamics and Brownian motion of semiflexible particles attached to freestanding lipid membranes. In order to address these issues, diffusion and conformational dynamics of semiflexible DNA molecules and filamentous fd-virus particles electrostatically adsorbed to cationic freestanding lipid membranes were studied on the single particle level by means of optical wide-field fluorescence microscopy. Supergiant unilamellar vesicles (SGUVs) with diameters larger than 100 m represent a perfect model of a freestanding membrane. In this work, a method was developed that enabled the reliable and efficient electroformation of cationic SGUVs on ITO-coated coverslips. The utilization of SGUVs as model freestanding lipid bilayers allowed for determination of the previously unknown surface viscosity of DOPC/DOTAP membranes. In particular, the analysis of the translational diffusion coefficients of small (10, 20, 50 nm) membrane-attached anionic polystyrene beads has shown that the surface viscosity of DOPC/DOTAP membranes with CDOTAP = 1–7 mol% is independent of the DOTAP concentration and equals η = (5.9 ± 0.2) × 10−10 Pa s m. The fluorescence video-microscopy investigation of single DNA molecules attached to cationic SGUVs revealed a previously unreported conformational transition of a membrane-bound DNA molecule from a 2D random coil, the original conformation in which DNA attaches to the membrane, to a compact globule. This membrane-mediated DNA condensation is favored at high cationic lipid concentrations in the membrane and long DNA contour lengths. The DNA compaction rate in the coil–globule transition is 124 ± 46 kbp/s, and the resulting DNA globule sizes were found to be 250–350 nm at DOPC membranes containing 1 mol% DOTAP and 130–200 nm for 7 mol% DOTAP, indicating a stronger compaction for higher charge densities in the membrane. Additional experiments with freestanding cationic membranes in the gel state and supported cationic lipid membranes with gel–fluid coexistence suggest that the DNA collapse on a freestanding fluid cationic membrane may be initiated by a local lipid segregation in the membrane and is accompanied by local membrane deformations, which eventually stabilize the compact DNA globule. Furthermore, in this work single molecule studies of random-coil DNA molecules and filamentous fd-virus particles on a freestanding cationic lipid bilayer with a low charge density were carried out. The experiments revealed that these particles can be described as semiflexible chains in 2D. Taken together, DNA molecules and fd-virus particles cover a broad range of the ratio of contour length and persistence length from 0.4 to 82. The results of this work demonstrate that the mobility of such membrane-attached semiflexible particles is strongly affected by hydrodynamics in the lipid membrane and the surrounding bulk fluid, and can in essence be described using a hydrodynamics-based theory for a disk-shaped solid membrane inclusion with a characteristic size approximately equal to the radii of gyration of the particles.
305

Investigating Minor States of the Oncoprotein N-MYC, with Focus on Proline Cis/Trans Isomerisation using NMR Spectroscopy

Haugskott, Frida January 2021 (has links)
MYC is a family of three regulator genes that codes for transcription factors. Expression of Myc proteins from MYC genes is found to be deregulated in 70 % of all cancer forms. The three human homologs C-Myc, N-Myc and L-Myc are mainly associated with cancer in the lymphatic system, nerve tissues and lung cancer, respectively. Even though N-Myc is associated with Neuroblastoma, the cancer variant that is most common among children, the field is focused towards C-Myc. The activation of C-Myc begins with phosphorylation of Serine 62, followed by trans-to-cis isomerisation of Proline 63. Then Threonine 58 becomes phosphorylated leading to that Serine 62 is dephosphorylated and subsequent cis-to-trans isomerisation of Proline 63, and C-Myc is marked for degradation. Cis-trans isomerisation is necessary for regulation of gene expression, and is therefore important to understand. Since N-Myc and C-Myc have identical sequences between residues 47 to residue 69, the hypothesis is that N-Myc is activated in the same manner, but this has not been confirmed. In this project the first 69 amino acids of N-Myc were analysed with NMR spectroscopy. This resulted in a near complete assignment of the major conformation, and of the alternative minor conformations as well. The traditional assignment experiments HNCACB, HN(CO)CACB, HNCO, HN(CA)CO in combination with CCH-TOCSY and HN(CCO)C revealed that the majority of the minor configurations can be explained by cis/trans isomerisation of prolines. In addition, the protein was analysed with direct carbon detected NMR spectroscopy to be able to detect the prolines.
306

Insights Into ER Translocation Channel Gating. Structural Regulation of the Transition Between the Closed and Open Channel Conformations: A Dissertation

Trueman, Steven F. 31 October 2011 (has links)
The transition between the closed and open conformations of the Sec61 complex permits nascent protein insertion into the translocation channel. A critical event in this structural transition is the opening of the lateral translocon gate that is formed by four transmembrane (TM) spans (TM2, TM3, TM7 and TM8 in Sec61p) to expose the signal sequence-binding (SSB) site. To gain mechanistic insight into lateral gate opening, mutations were introduced into a lumenal loop (L7) that connects TM7 and TM8. The sec61 L7 mutants were found to have defects in both the posttranslational and cotranslational translocation pathways due to a kinetic delay in channel gating. The translocation defect caused by L7 mutations could be suppressed by the prl class of sec61 alleles that reduce the fidelity of signal sequence recognition. The prl mutants are proposed to act by destabilizing the closed conformation of the translocation channel. Our results indicate that the equilibrium between the open and closed conformations of the protein translocation channel maintains a balance between translocation activity and signal sequence recognition fidelity. In the opening of the translocation channel, both the lateral and lumenal gate must open in a coordinated fashion for efficient protein translocation to occur. The lumenal gate is composed of a short helix of the loop preceding the second TM span, referred to as the plug helix, and six hydrophobic pore ring residues which form the constriction ring in the center of the channel. We identified three lateral gate polar residues and three hydrophobic residues from the plug domain that affect channel gating. Mutagenesis of the lateral gate polar cluster residues yields either a gain of function (prl phenotype) or a loss of function (translocation defect) phenotype. The combination of polar cluster mutations with each other or with plug domain mutations which cause a prl phenotype resulted in the mutually suppressive or additive phenotypes in double mutant strains. Cooperation between these residues is made possible through a structural link which connects the two translocation channel gates at their interface. The structural link provides a mechanism for the channel to coordinate the movement of multiple domains in the channel gating conformational change. Translocation assays demonstrated that this mechanism of gating regulation is particularly important for efficient protein translocation of substrates using the posttranslational translocation pathway. Our results indicate that residues from the plug and lateral gate domain form a regulatory cluster of residues responsible for efficient translocation channel gating.
307

Clustering approaches for extracting structural determinants of enzyme active sites

Stamatelou, Ismini - Christina January 2020 (has links)
The study of enzyme binding sites is an essential but rather demanding process of increased complexity since the amino acids lining these areas are not rigid. At the same time, the minimization of side effects and the specificity of new ligands is a great challenge in the structure-based drug design approach. Using glycogen phosphorylase - a validated target for the development of new antidiabetic agents - as a case study, this project focuses on the examination of side-chain conformations of amino acids that play a key role in the catalytic site of the enzyme. Specifically, different rotamers of each amino acid were collected to build a dataset of different conformations of the catalytic site. The rotamers were filtered by their probability of occurrence and subsequently, all rotamers that create steric clashes were rejected. Then, these conformations were clustered based on their similarity. Three different clustering algorithms and multiple numbers of clusters were tested using the silhouette scores evaluation for the clustering process. In order to measure the similarity, the Euclidean metric was used which due to the correspondence of the coordinates between the conformations was very similar to the cRMSD metric. Two-level clustering was applied to the dataset for more in-depth observations. According to the clustering results, specific aminoacids with major geometrical variations in their rotamers play the most important role in the separation of the clusters. Additionally, all rotamers of an amino acid can be grouped based on their structure, something that was confirmed using “Chimera” software as a visualization tool. To this end, the ultimate aim of this study is to examine whether the clustering of conformations produces clusters with points geometrically similar to each other, in order to identify near neighbors, i.e. conformations that are quite similar in structure but do not play a determinant role in the function and those that are quite diverse and could be further exploited.
308

Combining site-directed spin labeling EPR spectroscopy and biomolecular simulations to study conformation and dynamics of membrane proteins

Klose, Daniel 29 January 2015 (has links)
Understanding the conformational and dynamic changes of biomacromolecular complexes in different states, such as the membrane protein photoreceptor-transducer complex NpSRII/NpHtrII, is a key step to gaining insight into the functional mechanism of these important classes of protein complexes, since ~30 % of the human proteome are membrane proteins, yet they are largely underrepresented in terms of structural information with <1 % of all structures in the protein data bank. Hence for the development of methods suitable to study the conformation and dynamics of such complexes there is a strong demand and a vast potential field of applications. Here we combined method development at the interface between biomolecular simulations and model-based analysis of EPR- and fluorescence spectroscopic data with application studies using state-of-the-art spectroscopic techniques in conjunction with site-directed spin- or fluorescence labeling. In an initial benchmark study on the rigid globular protein complex Rpo4/7, we compared experimental inter fluorescence label distances or spin label distance distributions to a variety of predicted inter label distances based on molecular dynamics simulations, Monte Carlo sampling and a discrete rotamer library analysis. We found that while for the molecular dynamics simulations with explicit solvent considerable sampling challenges have to be overcome to reproduce the experimentally observed inter label distance distributions, the Monte Carlo sampling performed well when compared to the experimental data and was computationally less demanding. Significantly more efficient and equally accurate for our examples was the so-called rotamer library analysis available for the spin labels since it relies on a pre-calculated set of rotational isomers. In general, predictions for the mean distances were in agreement within the error margins while distribution shapes were more challenging to reproduce. Overall this study shows a positive evaluation for the assessed tools and the developed simulation protocols as well as their potential applications. Using the combination of EPR and fluorescence spectroscopy for distance determination we studied the structural influence of RNA binding on Rpo4/7, and showed that the protein complex stays conformationally rigid and thereby serves as a guiding rail for the nascent RNA chain that leaves the RNA polymerase along the Rpo4/7 RNA binding interface. To enhance the interpretation of experimentally determined changes of conformation and dynamics in protein complexes and to discuss the observed changes in terms of structural information, we built models of the two transcription factors TFE and the Spt4/5 complex, as well as of Argonaute, a 713 amino acid four-domain protein nuclease from Methanocaldococcus jannaschii. These structural models not only allowed a more accurate planning of fluorescence or EPR labeling experiments, but also the models enabled the discussion of the experimental data in structural terms. Based on such an initial structure further computational analysis techniques may be applied to identify putative structural changes or dynamic modes. This was shown for the histidine transporter HisQMP2, where we combined normal mode analysis to model protein flexibility with the rotamer library analysis to screen for possible conformational changes in comparison to experimental inter spin distance data. The most prominent agreement with one mode led to a working hypothesis of a conformational change and provides the basis for validation in future experiments. Due to the inherent synergy effects, we applied a combined experimental and simulation approach for the EPR-based distance determination in the globular DNA-binding protein LexA to probe conformation and dynamics of the N-terminal DNA-binding domains with respect to the C-terminal domains within the LexA homodimer. While the C-terminal dimerization domains exhibit a well-defined conformation that proved to be independent of DNA-binding, large-scale changes in conformation and dynamics were detected for the N-terminal domains. They were only found in a defined conformation when bound to DNA while in its absence a large rotational freedom of the entire N-terminal domains contributed to the conformational ensemble. Combined with a biochemical characterization of the autocatalytic cleavage of LexA, our data explains how LexA induces the SOS response after DNA damage or under latent antibiotic stress. We further studied the membrane photoreceptor-transducer complex NpSRII/NpHtrII that governs the light-dependent swimming behavior in Natronomonas pharaonis by a two-component signaling system. This system comprises extraordinary features of sensitivity, signal amplification, integration and transducer cooperativity, yet the molecular details of these features are poorly understood, as is signal propagation itself. By combining time-resolved cw EPR spectroscopy of NpSRII/NpHtrII variants spin labeled in the HAMP1 domain with time-resolved optical absorbance spectroscopy to report on the receptor signaling state, we found a tight kinetic coupling of receptor and transducer during the relaxation back to the ground state and hence a prolonged activation period, that with ~500 - ~700 ms is sufficiently long to cause phosphorylation bursts of the cognate kinase CheA. This explains signal amplification already on the level of the NpSRII/NpHtrII dimers. We further determined the transient difference spectra from the time-resolved EPR data that show local differences in dynamics and steric restrictions upon light-activation. Comparing these experimentally observed differences to predictions confirms the assumed two-state structural model and shows this transition between the two states for a single HAMP domain in a light-dependent manner. Additionally, our approach integrates a dynamic view into the model, since the two states are shown to exhibit different local dynamics in a fashion described previously as a competing model for signaling by dynamic differences based on biochemical studies. Here we show unification of the two models into one congruent description encompassing a transition between the two previously suggested states by concerted structural and dynamic changes. In an independent analysis using all-atom and coarse grained molecular dynamics of the NpSRII/NpHtrII complex in the minimal unit that can exert kinase control, the trimer of receptor-transducer dimers, we revealed a distinct dynamical pattern encoded in the primary sequence of the coiled-coil heptad-repeats. Upon receptor activation, these segments alter their dynamics in a concerted fashion with regions such as HAMP1 and the adaptation region becoming more compact, while HAMP2 and the tip become more dynamic, leading to dynamic and to limited structural changes at the CheA-kinase binding sites. Together with an extensive validation against experimental data, these findings suggest the altered dynamics as the mechanism for signal propagation along the extended coiled-coil structure of NpHtrII. This working model, that explains the current body of experimental data, allows for further refinement by all-atom molecular dynamics and provides a basis to devise future experiments for validation. The presented studies outline the versatile methodology of combined experimental and simulation approaches to analyze the conformation and dynamics of biomacromolecules including membrane protein complexes.
309

Caractérisation des nanomédecines pour la clinique : développement de méthodes évaluant les interactions nanoparticules-protéines plasmatiques pour une application en contrôle qualité / Nanomedicine characterization for the clinics : development of methods evaluating the interactions nanoparticles-plasmatic proteins for a quality control purpose

Coty, Jean-Baptiste 12 December 2017 (has links)
Les nanomédecines injectées par voie intraveineuse interagissent avec les éléments biologiques qui les entourent dans le compartiment sanguin. Parmi ces interactions, celles avec les protéines sanguines se révèlent être très importantes dans le devenir de ces nanovecteurs, leur conférant une identité biologique influençant leur chemin jusqu’au tissu et aux cellules cibles. La compréhension et le contrôle de ces phénomènes reste un enjeu crucial dans le développement des nanomédecines. Des méthodes permettant une étude facilitée de ces interactions sont nécessaires à cet égard. Les travaux de cette thèse ont eu pour but de développer des méthodes, utilisables en routine, permettant une caractérisation fine des nanomédecines et de leurs interactions avec les protéines plasmatiques, applicables dans un contexte clinique. Ils s’inscrivent dans un projet intitulé « Nano Innovation for CancEr » (NICE, BPI France) regroupant un consortium de partenaires industriels en développement clinique de nanomédecines.Dans un premier temps, un travail bibliographique sur les méthodes actuellement mises en œuvre pour une telle caractérisation ont pu mettre en avant deux limitations majeures. (i) D’une part, la complexité des méthodes actuelles disponibles pour lesquelles la spécificité des équipements et l’expertise requise limitent une utilisation à large échelle. (ii) D’autre part, les propriétés aujourd’hui caractérisées en routine (taille, morphologie globale, charge) ne sont que grossières comparées à la finesse des processus biologiques qui interagissent et « analysent » les nanovecteurs une fois introduits dans le milieu biologique. Ces deux aspects limitent aujourd’hui un développement plus sûr des nanomédecines pour une bonne reproductibilité en clinique et garantir des essais de contrôle qualité fiables.Au cours de nos travaux, nous avons développé des méthodes permettant de répondre en partie à la problématique posée par la caractérisation des nanomédecines. Une méthode d’analyse à haut débit de l’activation du système du complément par immunoélectrophorèse en deux dimensions a été développée et validée. Elle permet l’analyse reproductible de l’activation de la protéine C3. Elle est applicable à l’étude de l’effet de la présence de nanoparticules dans le sérum humain et leur degré d’action sur la cascade du complément. Cette méthode a été utilisée pour mener une étude plus fondamentale du mécanisme de l’activation du système du complément en regard de l’architecture de la surface de nanoparticules.Une deuxième méthode d’étude de l’activation du complément produit par des nanomédecine a été proposée sur la base de la résonnance plasmonique de surface (SPR). Une puce permettant un screening automatisé de l’activation du complément a été développée. L’application de cette méthode comparée à d’autres méthodes d’études de l’activation du système du complément (Immunoélectrophorèse 2D, ELISA) a permis d’identifier des biais lors de leur application à l’évaluation des nanomédecines.Enfin, une approche originale de caractérisation de la surface de nanoparticules a été proposée utilisant des protéines pour sonder la capacité de la surface des nanoparticules à adsorber ou repousser ces dernières. Dans cette méthode, l’électrophorèse capillaire est utilisée comme outil analytique permettant une analyse directe de l’échantillon sans séparation préalable des nanomédecines.Les méthodes développées au cours de ces travaux peuvent être appliquées à la caractérisation de nanomédecines et proposées comme des méthodes de contrôle en routine de façon plus générale. Un développement de la caractérisation dans ce sens constitue l’un des leviers pour une translation plus fructueuse des nanomédecines entrant en phase clinique. / Nanomedicines injected intravenously interact with surrounding biological elements in the bloodstream. Among these interactions, those with blood proteins turn out to be very important regarding the becoming of the nanovectors. They acquire a biological identity upon interaction with proteins which influence their path to target tissue and cells. The understanding and mastering of these phenomena remains a crucial issue in nanomedicine development. Methods allowing an easier study of these interactions are needed. The aim of these PhD thesis was to develop such methods, usable on a routine basis in a clinical context, allowing a fine characterization of nanomedicines and their interactions with plasmatic proteins. This PhD is part of the project “Nano Innovation for CancEr” (NICE, BPI France), gathering a consortium of industrials partners developing clinical nanomedicines.In a first time, a bibliographic study about current methods used for such a characterization could identify two major limitations. (i) On one hand, the complexity of current available methods for which the equipment specificity and required expertise prevent their use at a large scale. (ii) On the other hand, properties today characterized on a daily basis (size, morphology, charge) are too rough compared to the sharpness of biological processes who interact and “analyze” the nanovectors introduced in biological media. These two aspects are limiting a safer development of nanomedicines as well as a good reproducibility of their action in clinics.During this thesis, we developed methods allowing a beginning of answer to the wide problematic of nanomedicine characterization. A method for a high throughput analysis of complement activation by nanomedicines via 2D immunoelectrophoresis was developed and validated. It allows the reproducible analysis of protein C3 fragmentation. This method is applicable to the study of the impact of nanoparticles in human serum and their degree of action on the complement cascade. This method has been used for a more fundamental study on complement activation pathways activated according to the architecture of nanoparticles surface.A second method for the study of complement activation produced by nanoparticles has been proposed using surface plasmon resonance (SPR). A chip allowing an automated screening of complement activation has been developed. This method was compared to other methods for complement activation study (2D immunoelectrophoresis, ELISA) and allowed the identification of bias during nanomedicine evaluation.Finally, an original approach for the characterization of nanomedicine’s surface architecture using proteins as molecular probes has been proposed. In this method, capillary electrophoresis has been used as analytical tool to allow a direct analysis of sample without preliminary nanoparticle removal step.Methods developed during this work can be applied to the characterization of nanomedicines and proposed as routine methods for quality control. A development of nanomedicines characterization in this direction constitute one of the lever for a more fruitful translation of nanomedicines entering in clinical phase.
310

Investigation of the Structure and Dynamics of Regioisomeric Eu³⁺ and Gd³⁺ Chelates of NB-DOTMA: Implications for MRI Contrast Agent Design

Webber, Benjamin Charles 18 November 2013 (has links)
The detection of disease and abnormal pathology by magnetic resonance imaging (MRI) has been aided significantly by the use of gadolinium (Gd3+)-based contrast agents (CAs) over the past three decades. MRI and MRI CAs play a critical role in diagnosing tumors and diseases of the central nervous system. The agents used clinically have been shown to safely increase MRI contrast despite the toxicity of Gd3+, owing to the high kinetic and thermodynamic stability of these chelates. However, current CAs enhance contrast at a small fraction of what is theoretically possible. This leads to the necessity of introducing high CA doses in practice in order to afford sufficient contrast. Lanthanide (Ln3+) chelates based on 1,4,7,10–tetraazacyclododecane–1,4,7,10–tetraacetate (DOTA) have been shown to be particularly stable and effective. Chelates of DOTA exist in two interconverting coordination geometries which have varying water exchange rates. Researchers have envisioned a way to increase the per-dose efficacy both by control of the Gd3+–inner–sphere water exchange rate and via binding specificity (i.e. to tumors). The efficacy gains using these approaches have thus far been modest. A thorough structural characterization of europium (Eu3+) chelates of a DOTA-derivative which cannot undergo conformational exchange was carried out. These studies show that a single enantiomer of the ligand (S)–2–(4-nitrobenzyl)–1,4,7,10–tetraazacyclododecane–1,4,7,10–tetra(α–methyl)acetate (NB–DOTMA) can yield chelates which are both diastereoisomeric (previously reported) and regioisomeric (not previously speculated). Molecular mechanics simulations generated from the characterization data indicate that the nitrobenzyl (NB) substituent is oriented in different directions for the two possible regioisomers. The NB group can be chemically converted to confer macromolecular binding capability, and the orientation of the NB substituent may have a significant impact on the binding and/or relaxation behavior of a prototypical CA. The nuclear magnetic resonance (NMR) spectra of Eu–NB–DOTMA at various temperatures were compared. Unexpectedly, the chelates showed time-averaged structures which differ with a change in water exchange rate — the faster the rate, the greater the deviation from the expected structure. Consideration of the structures of Ln3+ chelates without accounting for their dynamic behavior does not yield an accurate value for the time-averaged hydration state. These observations suggest the "optimal" water exchange rate calculated using Solomon-Bloembergen-Morgan (SBM) theory may not lead to the highest-efficacy CAs. Binding and relaxometric studies of macromolecule-targeting derivatives of Gd–NB–DOTMA both by the author and in another lab showed that the coordination isomer with the slower water exchange rate should lead to more effective contrast, in direct opposition to the prevailing view of water exchange in the MRI community. Preliminary data do not indicate that regioisomeric chelates have significantly different relaxivity or macromolecular binding behavior. The ratios between regioisomeric Ln–NB–DOTMA chelates formed were shown to be dependent on the concentration and pH of the chelation reaction, but conditions were not found which led to the production of a single regioisomer. Attempts to carry out an efficient synthesis of a Ln3+ chelate with no potential for regioisomerism were unsuccessful.

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