Les interactions intermoléculaires entre une protéine et ses différents partenaires représentent des cibles de plus en plus prisées pour l'élaboration de composés thérapeutiques capables d'intervenir dans des processus biologiques. La méthode FBDD (Fragment-Based Drug Design) permet de concevoir des molécules bioactives tels que des inhibiteurs, à partir de la structure tridimensionnelle du complexe formé entre la protéine et une molécule fragment. Dans le cadre de ce projet de thèse nous proposons d'utiliser le déplacement chimique pour l'étude des structures 3D de ces complexes protéine-ligand. Nous nous focaliserons sur la mesure des perturbations de déplacement chimique CSP (Chemical Shift Perturbations) des atomes d'une protéine cible, induites par la liaison d'un fragment. Nous démontrerons la puissance de cet outil RMN à travers la simulation des CSP induits par l'interaction d'un fragment sur une protéine cible et leur comparaison aux CSP expérimentaux. L'analyse sera réalisée sur deux protéines cibles et la comparaison des données expérimentales et simulées permettra dans un premier temps de mettre en évidence un réarrangement structural de la protéine Bcl-xL lors de son interaction avec un fragment. Puis, dans un second temps, nous montrerons que cette analyse quantitative des CSP peut permettre de déterminer l'orientation des fragments dans le site d'interaction de la protéine PRDX5. Nous comparerons alors les performances de la méthode pour différents types de protons proposant ainsi de nouvelles pistes pour la compréhension du comportement des CSP vis-à-vis de leurs contributions électroniques / Intermolecular interactions between protein and its partners represent highly attractive targets for the elaboration of therapeutic compounds abble to interfere in biological processes. A novel approach in drug design called Fragment-Based Drug Design (FBDD) consists of designing bioactive molecules like inhibitors, from the 3D structure of the complex formed between a protein and a fragment molecule (MW < 300g/mol). Here we suggest using the chemical shift, to study these protein-ligand structures. We will particularly focus on the measurement of Chemical Shift Perturbations (CSP) induced by the fragment-binding on protein’s nuclei. We will evidence the potency of this NMR tool through simulation of CSP induced by fragment interaction on protein target and the comparison with experimental CSP. Two protein targets will be used and the comparison between experimental and simulated data will evidence on one hand, the structural rearrangement of the protein Bcl-xL upon fragment-binding. On the other hand, we will demonstrate that this quantitative use of CSP is unable to determinate fragment orientations inside the protein PRDX5 binding site. We will compare the performances of the method for different kinds of protein and proposing answers to better understand the behaviour of CSP toward their different electronic contributions

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第19038号 / 農博第2116号 / 新制||農||1031(附属図書館) / 学位論文||H27||N4920(農学部図書室) / 31989 / 京都大学大学院農学研究科森林科学専攻 / (主査)教授 木村 恒久, 教授 西尾 嘉之, 教授 髙野 俊幸 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

In this thesis a computational complement to experimental observables will be presented. Computational tools such as molecular dynamics and quantum chemical tools will be used to aid in the interpretation of experimentally (NMR) obtained structural data. The techniques are applied to study the dynamical features of biologically important carbohydrates and their interaction with proteins. When evaluating conformations, molecular mechanical methods are commonly used. Paper I, highlights some important considerations and focuses on the force field parameters pertaining to carbohydrate moieties. Testing of the new parameters on a trisaccharide showed promising results. In Paper II, a conformational analysis of a part of the repeating unit of a Shigella flexneri bacterium lipopolysaccharide using the modified force field revealed two major conformational states. The results showed good agreement with experimental data. In Paper III, a trisaccharide using Langevin dynamics was investigated. The approach used in the population analysis included a least-square fit technique to match T1 elaxation parameters. The results showed good agreement with experimental T-ROE build-up curves, and three states were concluded to be involved. In Paper IV, carbohydrate moieties were used in the development of prodrug candidates, to “hide” peptide opioid receptor agonists. Langevin dynamics and quantum chemical methods were employed to elucidate the structural preference of the compound. The results showed a chemical shift difference between hydrogens across the ring for the two isomers as well as a difference in the coupling constant, when taking the dynamics into account. In Paper V, the interaction of the Salmonella enteritidis bacteriophage P22 with its host bacterium, involves an initial hydrolysis of the O-antigenic polysaccharide (O-PS). Docking calculations were used to examine the binding between the Phage P22 tail-spike protein and the O-PS repeating unit. Results indicated a possible active site in conjunction with NMR measurements.

In the last decades NMR spectroscopy has become an invaluable tool both in academic research and in the pharmaceutical industry. This thesis describes applications of NMR spectroscopy in biomedicinal research for structure elucidation of biologically active peptides and peptidomimetics as well as in studies of ligand-protein interactions. The first part of this thesis describes the theory and methodology of structure calculations of peptides using experimental restraints derived from NMR spectroscopy. This methodology has been applied to novel mimetics of the peptide hormones desmopressin and Leu-enkephalin. The results of these studies highlight the complicating issue of conformational exchange often encountered in structural determination of peptides and how careful analysis of experimental data as well as optimization of experimental conditions can enable structure determinations in such instances. Although the mimetics of both desmopressin and Leu-enkephalin were found to adopt the wanted conformations, they exhibited no or very poor biological activity. These results demonstrate the difficulties in designing peptidomimetics without detailed structural information of the receptors. A stereoselective synthetic route towards XxxΨ[CH2O]Ala pseudodipeptides is also presented. Such pseudodipeptides can be used as isosteric amide bond replacements in peptides in order to increase their resistance towards proteolytic degradation. The second part of this thesis describes the study of the interaction between compounds that inhibit pilius assembly, pilicides, and periplasmic chaperones from uropathogenic Escherichia coli. Periplasmic chaperones are key components in assembly of pili, i.e. hair-like protein complexes located on the surface of Escherichia coli that cause urinary tract infections. Detailed knowledge about this interaction is important in understanding how pilicides can inhibit pilus assembly by binding to chaperones. Relaxation-edited NMR experiments were used to confirm the affinity of the pilicides for the chaperones and chemical shift mapping was used to study the pilicide-chaperone interaction surface. These studies show that at least two interaction sites are present on the chaperone surface and consequently that two different mechanisms resulting in inhibition of pilus assembly may exist.

This Thesis presents studies of molecular association in aqueous solution and at the liquid/solid interface. The investigated molecular systems range from self-aggregating surfactants to hydration water in contact with micelles or individual molecules. In most studies, combinations of various NMR methods were applied. These vary from simple chemical shift and intensity measurements to more elaborate self-diffusion and intermolecular cross-relaxation experiments. Non-ideal mixed micelles of fluorinated and hydrogenated surfactants were studied by an experimental procedure that allows an analysis in terms of micellar structure, using a minimal number of initial assumptions. Quantitative conclusions about micro-phase separation within mixed micelles were obtained within the framework of the regular solution theory. Additionally, NMR was introduced and developed as a powerful method for studying adsorption of surfactants at solid interfaces. Adsorption isotherms for pure and mixed surfactant systems and non-ideal mixing behavior of fluorinated and hydrogenated surfactants at solid surfaces were quantified. Fluorosurfactant-protein association was investigated using the methods described. Intermolecular cross-relaxation rates between solute and solvent molecules were recorded at several different magnetic fields. The results reveal strong frequency dependence for both small molecules and micelles. This finding demonstrates that intermolecular cross-relaxation is not solely controlled by fast local motions, but also by long-range translational dynamics. Data analysis in terms of recently developed relaxation models provides information about the hydrophobic hydration and micellar structure. / QC 20100914

Chlorine solid-state nuclear magnetic resonance (SSNMR) is an ideal site specific probe of chloride-containing solids as SSNMR tensor properties are sensitive to the local chlorine environment. In this thesis, the development and use of chlorine SSNMR as a method to characterize a wide variety of chemical environments was explored. Ultrahigh field, and multi-field studies were essential to overcome the difficulties associated with the collection of chlorine SSNMR spectra. Benchmark chemical shift (CS) and electric field gradient (EFG) tensor data were collected for organic chloride systems, including several amino acid hydrochlorides. These experiments demonstrated the sensitivity of chlorine SSNMR to slight changes in chemical environment. Quantum chemical calculations were used to complement experimental data, with the gauge-including projector augmented wave DFT (GIPAW-DFT) method shown to yield better agreement than B3LYP or RHF methods. The GIPAW-DFT method was found to slightly, but systematically, overestimate the chlorine quadrupolar coupling constant and the CS tensor span. Other organic chlorides examined by chlorine SSMR included a known ion receptor, meso-octamethylcalix[4]pyrrole. This compound was found to have a very small quadrupole interaction (QI), but significant chemical shift anisotropy (CSA). GIPAW-DFT calculations were also utilized and, in combination with the experimental results, used to identify the solvate structure of the material analyzed by NMR. Chlorine SSNMR was further used to study different solvate structures and polymorphism. The technique was an effective means to distinguish different room temperature polymorphs of benzidine hydrochloride, despite the similarities of the chloride environments. In the case of magnesium chloride, chlorine SSNMR was sensitive to the level of hydration and through the use of GIPAW-DFT calculations, the identity of an unknown hydrate was determined. An analysis of several group thirteen chlorides demonstrated that chlorine SSNMR was also capable of characterizing the chlorine environment in cases where the QI is large, despite the resulting broad line widths. In these systems GIPAW-DFT calculations also yielded excellent agreement with experimental values. Throughout this research, chlorine SSNMR has been shown to be a useful and effective means to study both organic and inorganic chlorides, with computational methods proving to be an important complement to experimental data.

Chlorine solid-state nuclear magnetic resonance (SSNMR) is an ideal site specific probe of chloride-containing solids as SSNMR tensor properties are sensitive to the local chlorine environment. In this thesis, the development and use of chlorine SSNMR as a method to characterize a wide variety of chemical environments was explored. Ultrahigh field, and multi-field studies were essential to overcome the difficulties associated with the collection of chlorine SSNMR spectra. Benchmark chemical shift (CS) and electric field gradient (EFG) tensor data were collected for organic chloride systems, including several amino acid hydrochlorides. These experiments demonstrated the sensitivity of chlorine SSNMR to slight changes in chemical environment. Quantum chemical calculations were used to complement experimental data, with the gauge-including projector augmented wave DFT (GIPAW-DFT) method shown to yield better agreement than B3LYP or RHF methods. The GIPAW-DFT method was found to slightly, but systematically, overestimate the chlorine quadrupolar coupling constant and the CS tensor span. Other organic chlorides examined by chlorine SSMR included a known ion receptor, meso-octamethylcalix[4]pyrrole. This compound was found to have a very small quadrupole interaction (QI), but significant chemical shift anisotropy (CSA). GIPAW-DFT calculations were also utilized and, in combination with the experimental results, used to identify the solvate structure of the material analyzed by NMR. Chlorine SSNMR was further used to study different solvate structures and polymorphism. The technique was an effective means to distinguish different room temperature polymorphs of benzidine hydrochloride, despite the similarities of the chloride environments. In the case of magnesium chloride, chlorine SSNMR was sensitive to the level of hydration and through the use of GIPAW-DFT calculations, the identity of an unknown hydrate was determined. An analysis of several group thirteen chlorides demonstrated that chlorine SSNMR was also capable of characterizing the chlorine environment in cases where the QI is large, despite the resulting broad line widths. In these systems GIPAW-DFT calculations also yielded excellent agreement with experimental values. Throughout this research, chlorine SSNMR has been shown to be a useful and effective means to study both organic and inorganic chlorides, with computational methods proving to be an important complement to experimental data.

Various compounds were studied with solid-state 119Sn and 31P NMR spectroscopy and quantum chemical calculations. Connections were made between the shielding tensors and the geometric and electronic structures of the molecules. First, the 119Sn chemical shielding anisotropy of various para substituted tetraaryl tin compounds was shown to be dependent on the tilt angle of the phenyl rings. Tetrakis(o-tolyl) tin did not have the shielding anisotropy predicted by the tilt angle of the rings. It was suggested that ortho substitution distorts the structures of the phenyl rings causing the discrepancy. Analysis of the solid-state 31P NMR spectra of triphenylphosphorane ylides, Ph3P=CHC(O)R, determined that increasing the electron-donating effects of the R group decreased the δ33 component. Theoretical calculations showed that the component lay along the ylidic bond and was dependent on the difference in phosphorus-carbon bond lengths between the phenyl and ylidic bonds. Another study concerned the solid-state 31P NMR of the series of triphenylphosphine derivatives, PPh3-x(o-tolyl)x where x = 0 to 3. The addition of ortho methyl groups changed the position of the δ11 component which could be the result of the change in energy gap between the lone pair (HOMO) and σ* anti-bonding (LUMO). The solid-state 31P NMR spectra of deuterated piperazinium phosphonate and phosphonic acid were influenced by the shielding, dipolar and spin-spin interactions, as well as, second order quadrupolar effects. The spectrum of deuterated piperazinium phosphonate had a chemical shielding anisotropy of 130 ppm, an effective dipolar coupling of 2500 kHz and a one-bond phosphorus-deuterium J coupling of 90 Hz. The phosphorus-deuterium bond length was predicted to be 1.44(2) Å. A deuterium quadrupolar coupling constant of 104 kHz was obtained from the CP/MAS 2H spectrum. The non-axial symmetry of phosphonic acid complicated the analysis of the 31P spectrum. Phosphorus-deuterium bond lengths of 1.44(5) Å and 1.40(4) Å were obtained for the two inequivalent sites in the unit cell.

Chlorine solid-state nuclear magnetic resonance (SSNMR) is an ideal site specific probe of chloride-containing solids as SSNMR tensor properties are sensitive to the local chlorine environment. In this thesis, the development and use of chlorine SSNMR as a method to characterize a wide variety of chemical environments was explored. Ultrahigh field, and multi-field studies were essential to overcome the difficulties associated with the collection of chlorine SSNMR spectra. Benchmark chemical shift (CS) and electric field gradient (EFG) tensor data were collected for organic chloride systems, including several amino acid hydrochlorides. These experiments demonstrated the sensitivity of chlorine SSNMR to slight changes in chemical environment. Quantum chemical calculations were used to complement experimental data, with the gauge-including projector augmented wave DFT (GIPAW-DFT) method shown to yield better agreement than B3LYP or RHF methods. The GIPAW-DFT method was found to slightly, but systematically, overestimate the chlorine quadrupolar coupling constant and the CS tensor span. Other organic chlorides examined by chlorine SSMR included a known ion receptor, meso-octamethylcalix[4]pyrrole. This compound was found to have a very small quadrupole interaction (QI), but significant chemical shift anisotropy (CSA). GIPAW-DFT calculations were also utilized and, in combination with the experimental results, used to identify the solvate structure of the material analyzed by NMR. Chlorine SSNMR was further used to study different solvate structures and polymorphism. The technique was an effective means to distinguish different room temperature polymorphs of benzidine hydrochloride, despite the similarities of the chloride environments. In the case of magnesium chloride, chlorine SSNMR was sensitive to the level of hydration and through the use of GIPAW-DFT calculations, the identity of an unknown hydrate was determined. An analysis of several group thirteen chlorides demonstrated that chlorine SSNMR was also capable of characterizing the chlorine environment in cases where the QI is large, despite the resulting broad line widths. In these systems GIPAW-DFT calculations also yielded excellent agreement with experimental values. Throughout this research, chlorine SSNMR has been shown to be a useful and effective means to study both organic and inorganic chlorides, with computational methods proving to be an important complement to experimental data.

Conselho Nacional de Desenvolvimento Científico e Tecnológico / This dissertation first describes the collection of literature data among the years 2005 to 2011 for the subsequent data analysis of 1H NMR chemical shifts and coupling constants and 2JHH 3JHH with emphasis on the synthesis of 3,5-diaryl-4,5-dihydro-1H-pyrazoles. Initially, was analyzed the data from X-ray diffraction of compounds 4,5-dihydro-1H-pyrazoles with a focus on the molecular structure description. Posteriorly, the X-rays data was correlated with the 1H NMR chemical shifts observing the influence of different substituents on the pyrazole ring. The coupling constants 2JHH 3JHH were correlated with bond angles and dihedral angles observed respectively for the molecules of 3,5-diaryl-4,5-dihydro-1H-pyrazoles. / A presente dissertação descreve inicialmente a coleta de dados da literatura entre os anos de 2005 e 2011 para a posterior análise de dados de deslocamento químico de RMN 1H, e constantes de acoplamento 2JHH e 3JHH com ênfase à síntese de 3,5-diaril-4,5-diidro-pirazóis. Primeiramente, foram analisados os dados de difração de raios-X de compostos 4,5-diidro-1H-pirazóis com foco na estrutura molecular descrita. A seguir, correlacionou-se os dados de raios-X com os deslocamentos químicos de RMN 1H observando a influência dos diferentes substituintes sobre o anel pirazolínico. Foram correlacionadas as constantes de acoplamento 2JHH e 3JHH com os ângulos de ligação e ângulos diedros observados, respectivamente, para as moléculas de 3,5-diaril-4,5-diidro-1H-pirazóis.