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  • 1.
    Bollmark, Martin
    Stockholm University.
    Studies on the synthesis of nucleotide analogues containing P-F and P-Se bonds2001Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In the present work, new synthetic approaches to the synthesis of nucleoside phosphorofluoridate and phosphorofluoridothioate diesters have been developed. These procedures involve either oxidative transformation of the corresponding H-phosphonate or H-phosphonothioate diesters in the presence of fluoride anion or iodine-promoted desulfurization of phosphorothioate or phosphorodithioate diesters in the presence of fluoride anion. Also, efficient protocols for the synthesis of nucleoside phosphorofluoridate, nucleoside phosphorofluoridothioate and nucleoside phosphorofluoridodithioate monoesters were developed.

    Furthermore, the chemistry of a new class of P(III) compounds containing selenium, i. e. H-phosphonoselenoate monoesters was developed and synthetic procedures for the conversion of these compounds into the corresponding diesters were designed. In addition, the usefulness of H-phosphonoselenoate diesters for the preparation of various selenium-containing nucleotide analogues was demonstrated.

    Finally, the possibility of employing triphenylphosphine selenide as a reagent for selenizing P(III) compounds was examined. Under mild conditions, this commercially available reagent was found to convert phosphite triesters and H-phosphonate diesters efficiently into the corresponding phosphoroselenoate derivatives.

  • 2.
    Bowden, Tim
    Stockholm University.
    Studies on glycosylation mechanisms and synthesis of structures related to inositolphosphoglycans2000Doctoral thesis, comprehensive summary (Other academic)
  • 3.
    Buskas, Therese
    Stockholm University.
    Synthesis of lactosamine-containing carbohydrate structures and development for their easy assembly and conjugation1999Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis is based on four publications. The first chapter describes preparation of anomerically pure thioethyl-, thiophenyl-, and n-pentenyl 2-azido-2-deoxy glycosyl building blocks from easily accessible per-acetylated glycosamines.

    In the second part, acetylated, benzylated and non-protected n-pentenyl glycosides are used as substrates for preparing various spacer functionalities, which are obtained by means of radical elongations, oxidations and reductions.

    The syntheses of a trisaccharide,a-D-GlcpNAc-(1-->4)-b-D-Galp-(1-->4)-b-D-GlcpNAc, and fragments thereof, linked to a long lipophilic aglycon, are described in the third part. For the formation of theb-D-Galp-(1-->4)-D-GlcpNAc bond, several differently protected glucosamine acceptors were prepared and their reactivity towards a disaccharide donor evaluated.

    Finally, lactosamine derivatives were prepared by regioselective galactosylation and used as building blocks in the chemical synthesis of various oligosaccharides. The syntheses of polylactosamine di-, tri- and tetramers were achieved by regioselective glycosylation. Also spacer containing sulfated N-acetyllactosamine and Lewis x structures were synthesised.

  • 4.
    Hansson, Jonas
    Stockholm University.
    Synthesis of phosphate-containing oligosaccharides corresponding to capsular antigen structures from Haemophilus influenzae2000Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis describes the synthesis of spacer-equipped di- and trimeric oligosaccharide structures corresponding to fragments of the capsular polysaccharides of Haemophilus influenzae types c and f. Both of these polysaccharides are of the teichoic acid type, built up by disaccharide repeating units linked via interglycosidic phosphodiester bonds. Introduction of the phosphodiester linkages was accomplished employing the glycosyl H-phosphonate method. The syntheses are designed in such a way as to allow the formation of even larger structures, as well as conjugation to a carrier protein. The first section of this thesis presents a general overview of the biological significance and structural features of anomeric phosphodiesters and synthetic approaches towards these structures, including a literature survey of research in this area during the past decade. In the second part, a new approach to the synthesis of anomeric phosphodiester linkages, utilizing non-anomeric glycosyl H-phosphonate acceptors and various galactosyl donors in glycosylation reactions, is described. Finally, synthesis of the capsular polysaccharide fragments of H. influenzae types c and f is discussed.

  • 5.
    Höög, Christer
    Stockholm University.
    Three-dimensional structure of oligosaccharides from molecular dynamics simulations2000Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis focuses on the conformation and flexibility of oligosaccharides around the glycosidic linkage. The methods employed for the elucidation of the three-dimensional structures of biomolecules are briefly described. The main techniques used here are computer simulations and molecular dynamics simulations in aqueous solution in particular. The experimental data derived from these simulations have been compared with nuclear magnetic resonance measurements. The results obtained demonstrate the occurrence of more than one conformation, even though at the same time the high value of the generalised order parameter indicates rigidity. Of special interest are the folded conformers discovered at the same linkage in a vicinally substituted trisaccharide dissolved in water. Such, folded conformers have been detected in carbohydrates earlier, but never at the same linkage.

    The free energy simulation methods thermodynamic perturbation and thermodynamic integration are described briefly and have been used to calculate the anomeric ratio of the monosaccharides D-xylose in water and methyl D-xyloside in methanol. Solvent effect of the a/b ratios were found to be small. The solvent structures surrounding these four monosaccharides were investigated utilising radial and spatial distribution functions.

  • 6.
    Johansson, Karl-Jonas
    Stockholm University.
    Studies of the anomeric center: mechanism and synthesis2000Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis is based on three publications and one appendix and is divided into two parts. The first part is a mechanistic study of the anomerization reaction of both aldo and keto glycosides and the second part is a synthetic study of a unusual type of glycosidic linker found in the lipopolysaccharide core Proteus Mirabilis 0270.

    The first chapter contains a general introduction to the thesis.The second chapter treats the anomerization reaction of alkyl furanosides both by trapping experiments and kinetics. The conclusion from these studies is that the reaction proceeds via a concerted endo-cyclic C-O bond cleavage.The third chapter concerns the anomerization of alkyl pyranosides by the same techniques as those used in chapter 2. The results from these studies confirm that the reaction proceeds via exo-cyclic C-O bond cleavage.In the fourth chapter the anomerization of methyl fructosides has been investigated by trapping experiments. The outcome of this study is that the anomerization of fructosides occur via exo-cyclic C-O bond cleavage and that the anomerization reaction proceeds faster than ring-interconverison.In the final chapter an analogue of the unusual type of glycosidic linker fond in Proteus Mirabilis 0270 has been synthesised i.e. methyl ((1S)-arabinosyl o-(1Æ4,6))-a-D-galactopyranoside.

  • 7.
    Karlström, A. Sofia E.
    Stockholm University.
    Copper- and nickel-catalyzed cross-coupling reactions: synthesis of 2-substituted 1,3-dienes and mechanistic and synthetic studies of the copper-mediated allylic substitution reaction2000Doctoral thesis, comprehensive summary (Other academic)
  • 8.
    Kers, Annika
    Stockholm University.
    Towards synthesis of biologically important phosphate analogues: exploring H-phosphonate and C-phosphonate chemistry1999Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis is based on studies directed towards the development of methods for the preparation of phosphorus containing natural products, with the focus on C-phosphonate nucleic acid analogues.

    Mechanistic studies concerning formation of the phosphorus-carbon bond resulted in development of two efficient protocols for the synthesis of C-phosphonates from the corresponding H-phosphonate derivatives. These were applied, inter alia, to the synthesis of a novel type of nucleotide analogue containing the 4-pyridylphosphonate internucleotide bond. Also, synthesis of new nucleoside 5'-methylenephosphonate building blocks, suitable for incorporation into oligonucleotides or their conjugates, and a new method for the preparation of alkyl H-phosphonates, are discussed. Finally, mechanistic investigations related to C-phosphonates formation via N->C phosphorus migration in certain complexes of DBU with chlorophosphates, are presented.

  • 9.
    Kers, Inger
    Stockholm University.
    Nucleoside phosphoramidates and related compounds: development of synthetic methods based on H-phosphonate chemistry1999Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In this thesis, studies directed towards development of new synthetic methods for the preparation of nucleotide analogues of potential medical value as antisense, antigene or antiviral agents, are described.

    Two methods for synthesis of N3'->P5' and P3'->N5' phosphoramidate analogues with the nitrogen atom in bridging position of the internucleotide linkage was developed. Both of them make use of the readily available H-phosphonate monoesters as starting materials and permit the introduction of multiple modifications at the phosphorus center. In conjunction with these, a simple and efficient method for the preparation of nucleoside H-phosphonothioates, as a starting material for various phosphate analogues was also developed. As part of theses studies, base-induced disproportionation of aryl H-phosphonates was investigated.

    A new type of prodrugs for AZT, symmetrical phosphoramidates, have been synthesised as potential anti-retroviral agent.

  • 10.
    Krog-Jensen, Christian
    Stockholm University.
    Development of methods for stereospecific synthesis of α- and β-D-fructofuranosides and β-D-glucuronic acid pyranosides and application of these methods in the assembly of bacterial polysaccharide structures1997Doctoral thesis, comprehensive summary (Other academic)
  • 11.
    Linnerborg, Malin
    Stockholm University.
    Structural elucidation of the O-antigen polysaccharides of five Escherichia coli strains1999Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The cell walls of bacteria are composed to a large extent of different polysaccharides. In order to understand and thereby, be able to utilise the physical, biological and immunological properties of polysaccharides, it is important to determine their structures. In the present thesis, structural investigations of the O-antigen polysaccharides from five strains of Escherichia coli, serogroups O138, O164, O167, O173 and O159, are described.

    Nuclear Magnetic Resonance (NMR) spectroscopy was the primary technique employed. Fast Atom Bombardment Mass Spectrometry (FAB-MS) and Electrospray Mass Spectrometry (ESI-MS) together with chemical degradations of the polysaccharides were also utilised.

    The possibilities, advantages and disadvantages of certain available methods for such studies are discussed.

  • 12.
    Löfstedt, Joakim
    Stockholm University.
    Selective palladium-catalyzed 1,4-functionalization: allenes and dienes in palladium chemistry and total syntheses of (+)-pseudoconhydrine and (+)-monomorine I2002Doctoral thesis, comprehensive summary (Other academic)
  • 13.
    Mühlman, Anna
    Stockholm University.
    Synthesis of inhibitors against the human immunodeficiency virus: diol-based inhibitors of the HIV-1 protase and 4-substituted carbocyclic nucleoside analogues2000Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The pandemic spread of HIV infection and AIDS has resulted in intensive research designed to develop effective therapeutic agents. Development of inexpensive inhibitors is necessary to allow treatment of HIV infections in the Third World.

    In the present thesis, the design and synthesis of several inhibitors of the HIV-1 virus are described. The first section presents a general overview of the life-cycle of HIV, i.e., the replication cycle and the functions of the HIV reverse transcriptase and HIV protease, as well as the strategies underlying anti-HIV chemotherapy. The design of C2-symmetric inhibitors of the HIV-1 protease, incorporating C-terminal duplication is also outlined. On the basis of molecular modelling, L-mannaric acid was selected as a general scaffold, i.e., the chiral template from which carbohydrate-based inhibitors were developed. By varying the pattern of substitution on this L-mannaric acid template, structural analogues that retained high anti-HIV activity were designed.

    The second section of the thesis describes four different syntheses of the C2-symmetric inhibitors of the HIV-1 protease, two of which provide access to potent inhibitors in a relatively few steps. These procedures open the possibility of developing cost-effective drugs.

    Finally, construction and synthesis of two 4-substituted carbocyclic nucleoside analogues, targeted against the HIV reverse transcriptase, are described.

  • 14.
    Oscarsson, Karin
    Stockholm University.
    Rational design and synthesis of protease inhibitors: targeting HIV-1, Malaria Plm I and II and Hepatitis C virus NS3 proteases2002Doctoral thesis, comprehensive summary (Other academic)
  • 15.
    Pettersson, Ethel
    Stockholm University.
    Mechanism Studies of Catalytic RNA, and RNA and DNA Model Compounds1999Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis describes mechanism studies of transesterifications of phosphate esters. The aim of the studies concerns two fields. First, the catalytic mechanism that group I introns use in self-splicing. The focus was on metal ion coordinating groups at the catalytic site. Studies were performed on a (almost) full-length group I intron. A 2'-amino modification was introduced in the co-substrate and metal ion switch experiments were carried out. In the presence of magnesium ions the reaction rate decreased but introducing nitrogen preferring metal ions as for example manganese, this negative trend could be reversed. Further studies of the catalytic mechanism were performed on the same group I intron but converted to a ribozyme by deleting the substrate site. We introduced a 2'-amino group in the leaving group nucleoside, in a chemical synthesized substrate and metal ion switch experiments were carried out. At most we could study the cleavage reaction with two 2'-amino modifications at the catalytic site, in the co-substrate and in the substrate. In the presence of two 2'-amino modifications we obtained more than additive effects on the rate, in the presence of manganese ions. These experiments showed how one catalytic metal ion coordinated to the 2'-position in the co-substrate and a second one to the 2'-position in the leaving sugar nucleoside. An alternative model of the earlier proposed two metal ion mechanism used by group I introns, is presented.

    Five RNA model compounds, methyl furanosides with a 5-diphenyl phosphate group were synthesized. The metal ion promoted intramolecular cyclisation reaction, where the 3-hydroxyl attacks the 5-diphenyl phosphate was studied in the presence of different divalent metal ions. Two derivatives contained a 2-amino group and higher reaction rates were obtained in experiments with nitrogen preferring metal ions. These studies showed the effect of an adjacent position, on the hydroxy nucleophile, via coordination of a metal ion and also give data supporting the mechanism model for the catalytic RNA. The other field in this thesis concerns investigations on why ethylene oxide causes more DNA damages, than propylene oxide. To exclude that the intramolecular phosphate transesterification reaction was responsible for the observed differences, two dithymidine alkyl phosphates were synthesized and studied. Further, to see that the respective epoxide did not have different alkylation rates toward a phosphate center, the alkylation rate for the respective epoxide was studied. Neither of these events could be ascribed to be responsible for the earlier observations concerning ethylene oxide and propylene oxide.

  • 16.
    Rundlöf, Torgny
    Stockholm University.
    NMR studies of Carbohydrate Structure and Dynamics in Solution1998Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Methods for studies of the structures of carbohydrates in solution and their dynamics are presented. Approaches employing nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry (MS), force-field computer simulations and chemical methods are described.

    First, methods for determinations of the structures of natural carbohydrates are described, exemplified by the galactofuranoside and glycerol residues and the phosphodiester moiety found in the O-antigenic polysaccharide from Escherichia coli O28. These structures are determined by the use of NMR spectroscopy, MS and chemical degradations/derivatizations.

    Subsequently, approaches for determination of the three-dimensional structures and dynamics of oligosaccharides in solution are presented. Carbon-13 NMR spin relaxation times and nuclear Overhauser effects (NOEs) were measured for the pentasaccharide lacto-N-fucopentaose-1 and for a vicinally disubstituted trisaccharide. Carbon relaxation data were used to describe the dynamics in terms of overall and internal correlation times and generalized order parameters according to the model-free approach. In addition, three-bond proton-carbon coupling constants, proton NOEs and transverse rotating-frame Overhauser effects (TROEs) across the glycosidic linkages were measured for the trisaccharide. The proton NOEs and TROEs were used to calculate proton-proton distances within and between the different sugar residues.

    Langevin dynamics and Metropolis Monte Carlo simulations were performed for the trisaccharide. Averaged proton-proton distances obtained from the simulations were compared to distances obtained from the NOE and TROE measurements. Three-bond proton-carbon coupling constants were calculated from the simulations and compared to the couplings determined by NMR. The comparisons of interglycosidic distances and coupling constants in many cases reveal poor agreement.

    A recent method for studies of biomolecular three-dimensional structure in solution was employed to the tetrasaccharide lacto-N-neotetraose (LNnT). It was dissolved in an aqueous dilute liquid crystalline medium and residual dipolar couplings were measured. The orientations of the interatomic vectors in the molecule were obtained from a structure generated by molecular modeling. The measured couplings showed good agreement with couplings calculated from the orientations of the vectors in the three-dimensional structure of LNnT.

  • 17.
    Salakdeh, Esmail Yousefi
    Stockholm University.
    Synthesis of nucleotide, peptide and lipid containing molecular tools for life science studies2000Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis is based on five parts. The first and second chapters describes two synthetic routes, employing different protecting group strategies for synthesis of uridine 3'-(ethyl, 2-ethoxyethyl, 2-chloroethyl, 2,2-dichloroethyl and 2,2,2-trichloroethyl) phosphate. In the first synthetic route, uridine was protected with acid labile protecting groups, 4-methoxytetrahydropyran-4-yl for the 2'-OH group and 4-methoxytriphenylmethyl for the 5'-OH group. In the second synthesis route the tert-butyldimethylsilyl (TBDMS) was used for protection of the 2'- and 5'- hydroxyls. Silyl deprotection was performed using triethylamine trihydrofluoride.

    In the third chapter a method for O- and S-palmitoylation of non-protected peptides is described. The procedure consists of treatment of the peptides with excess of palmitoyl chloride in neat trifluoroacetic acid for 10 minutes at room temperature. The tripeptides Gly-Cys-Phe and Gly-Ser-Phe were S- and O-palmitoylated and the hydrophobic Pulmonary Surfactant Protein-C model peptides were converted to the respective S,S- and O,O-dipalmitoylated peptides.

    The production of S-citronellyl-L-cysteine and S-dolicyl-L-cysteines for use as mass spectrometry standards is described in chapter four. For formation of the thioether linkage, a mesylated citronellol and/or mesylated dolichols and L-cysteine ethyl ester were employed.

    Finally, in the last chapter a route for synthesis of 8-aminoadenosine 5'-(aminoalkyl phosphates), analogues of aminoacyl adenylates is described. The 5'-H-phosphonate of 2', 3'-O, O-benzylidene-8-bromoadenosine, with unprotected base was condensed with benzyloxycarbonyl (Z) protected amino alcohols (L-isoleucinol, L-histidinol and L-methioninol), in the presence of bis(2-oxo-oxazoline-3-yl)phosphonic chloride. After oxidation the 8-bromo was transformed into the 8-azido moiety by sodium azide in dimethyl sulfoxide. Deprotection of the benzylidene and benzyloxycarbonyl (Z) groups as well as reduction of the azido to the desired amino function was accomplished in a single step by catalytic transfer hydrogenation (palladium-carbon or palladium black in 80% acetic acid).

  • 18.
    Sehgelmeble, Fernando W.
    Stockholm University.
    Stereospecific synthesis of β-D-fructofuranosides: synthesis of sucrose and structures related to plant and bacterial polysaccharides2002Doctoral thesis, comprehensive summary (Other academic)
  • 19.
    Sigurdsson, Susannah
    Stockholm University.
    Studies aimed at improving the H-phosphonate approach for solid phase oligonucleotide synthesis2002Doctoral thesis, comprehensive summary (Other academic)
  • 20.
    Söderman, Peter
    Stockholm University.
    Synthesis of oligosaccharides for structural, conformational and molecular recognition investigations1999Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Carbohydrates are involved cell-cell interaction. Synthesis of small and medium sized oligosaccharides is important to gain more understanding about the their physical properties that are crucial for their action in molecular recognition events. The first paper describes the synthesis, structural and conformational analysis of four different trisaccharides. The second paper describes a stereospecific synthesis of methyl a-(4-2H)-cellobioside, applying a regioselective oxidation stereospecific reduction sequence. In the third paper investigation of 1,3-dibromo-5,5-dimethylhydantoin in regioselective oxidation of stannylene acetals of different monosaccharide diols is described. The fourth study describes the synthesis of three different trisaccharides related to Escherichia coli O35 and Salmonella arizona O62, where the selective oxidation of a hydroxymethyl group using TEMPO is the key step. The last work summarize the synthesis of a model hexasaccharide from the core region of a Haemonchus contortus glycoprotein. The key steps in this synthesis are regioselective glucosidation to form a trisaccharide core followed by trifucosylation and conversion of a b-glucoside to the corresponding b-mannoside.

  • 21.
    Turek, Dominika
    Stockholm University.
    Synthesis of complex carbohydrates corresponding to the Lewis b blood group antigen and Vibrio cholerae polysaccharide structures2000Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis is divided into two parts. The first part describes the syntheses of the Lewis b blood group antigen hexasaccharide and parts thereof. The Leb blood group antigen is one of the binding epitopes for the Helicobacter pylori bacteria in the human stomach. The oligosaccharides containing N-acetyl glucosamine, galactose and fucose, were synthesised as their 8-methoxycarbonyloctyl or 2-azidoethyl spacer glycosides and were conjugated to proteins using activated esters or the diethyl squarate methodology for binding studies with H. pylori. In the second part, structures from the lipopolysaccharide and capsular polysaccharide of Vibrio cholerae O139 synonym Bengal and Vibrio cholerae O22 were synthesised as 2-(4-benzyloxyamidophenyl)ethyl spacer glycosides for the study of their immunological properties. Unusual features of these oligosaccharides are the presence of a 6-membered cyclic phosphate diester and the 2,6-dideoxysugar colitose.

    The glycosylation reactions included halide-assisted couplings of the bromosugars of fucose and colitose, AgOTf promotion of galactosyl bromides, and DMTST or NIS promotion of thioethyl glycosides.

  • 22.
    Wachtmeister, Johanna
    Stockholm University.
    Synthesis of Potential Inhibitors Against HIV1999Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis describes the syntheses of various potential inhibitors of HIV, e.g. some 3´-hydroxymethyl-substituted carbocyclic nucleoside analogues as reverse transcriptase inhibitors and some symmetry-based peptidomimetics as protease inhibitors.

    Enantiomerically pure (3S,4S)-bis-(hydroxymethyl)cyclopentanone ethylene glycol ketal was used in the syntheses of eight functionalized cyclopentanol intermediates. These were either condensed with 6-chloropurine bases using the Mitsunobu reaction or converted into the corresponding cyclopentylamines, on which the purine bases were built up.

    The influence of the central hydroxyl groups on the anti-viral activity of L-mannaric acid based HIV-1 protease inhibitors was investigated. L-Iditol was used as the chiral precursor in the synthesis of the inhibitors with inverted configuration at C-3 and C-4.

    All target compounds described in this thesis were evaluated for anti-viral activity against the human immunodeficiency virus.

  • 23.
    Öhberg, Liselotte
    Stockholm University.
    Synthesis of a key derivative of glycosylphosphatidylinositol substances and synthesis of spacer glycosides for use in the formation of glycoconjugates and of self-assembled monolayer surfaces1998Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The first chapter of this thesis describes glycosylation strategies for obtaining derivatives of 2-amino-2-deoxy-a-D-glucopyranosyl-(1-->6)-D-myo-inositol, a key building block for synthesis of glycosylphosphatidylinositol anchor substances and also proposed to be part of a second messenger for insulin.

    The second chapter describes the synthesis of bifunctional oligoethylene glycol spacers and glycosylation of these for use in formation of glycoconjugates. Synthesis of glycosyl succinimides and their conversion into glycoconjugates are also described.

    In the third chapter, synthesis of various terminated alkane thiols are described for use in formation of self-assembled monolayer surfaces. Globotriose linked alkane thiols with or without oligoethylene glycol spacers in between were mixed with hydroxyl or oligoethylene glycol terminated alkane thiols for formation of model surfaces.

1 - 23 of 23
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