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  • 1.
    Adolfsson, Dan E.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Synthesis of Ring-fused Peptidomimetics: Interacting with Amyloid Fibrils2020Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Parkinson's and Alzheimer's disease are the two most common neurological disorders in humans. Both conditions involve progressive death of neurons in the central nervous system, decline in bodily functions and eventually (and invariably), death. So far, no cure exists and the available treatments can only ease symptoms. Despite substantial investments in research, the biomolecular processes are still far from fully understood. However, both diseases are associated with formation of fibrillar protein aggregates called amyloid deposits. Whereas Alzheimer’s disease involves aggregation of the Tau and Amyloid β proteins, α-Synuclein fibrilization plays a key role in Parkinson's disease. Although they are chemically distinct, the deposits consist of protein fibres with similar morphology and fold. Small molecules, such as the thiazoline fused 2-pyridones herein presented, can interfere with the formation of amyloid fibres, or bind to them. Besides having potential for diagnostication and treatment, such small molecules constitute valuable tool compounds in future research, to unravel the mechanisms of amyloid formation and pathology. The first step towards successful treatment, diagnostication and prevention of Alzheimer's and Parkinson's disease is understanding the causes and underlying mechanisms better. This thesis narrates the synthesis and development of novel chemical structures: multi ring fused peptidomimetics with the ability to bind mature amyloid fibrils, consisting of α-Synuclein or Amyloid β. 

    The first project (articles I, III and VI) describes method development for the extension of bicyclic thiazolino 2-pyrdiones by fusion with aromatic nitrogen heterocycles, which enables the desired amyloid binding properties. Derivatisations of the newly generated central scaffold, and variation of the multiple attached substituents, were subsequently performed in efforts to improve binding strength and solubility, and gain selectivity towards certain fibrils. One of the most promising amyloid fibril binders was evaluated in a human cell line and in mice, and found to be protective against accelerator induced neurotoxicity. One pyrimidine fused compound moreover indicated potent inhibition of Amyloid b aggregation. The second project (articles II, IV and V) focuses on development of methods to modify the thiazoline ring. Ring opening induced by electrophiles generates N-alkenyl 2-pyridones but decreases amyloid binding potency. Introduction of a cyclobutane moiety fused with the thiazoline ring is better tolerated, and adds a terminal alkene moiety that can be exploited in future chemical modifications. Expansion of the five membered thiazoline ring to a six membered dihydrothiazine ring, equipped with a nitrophenyl substituent, provides compounds with enhanced fibril binding capacity, which further inhibits Amyloid β fibril formation in vitro. Taken together, the synthetic methodologies allow construction and late stage modification of complex fused heterocycles, with several points of variation. Thus, the developed methods may be of future value in our laboratories and elsewhere.

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  • 2.
    Adolfsson, Dan E.
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Tyagi, Mohit
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Singh, Pardeep
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Deuschmann, Adrian
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Ådén, Jörgen
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Gharibyan, Anna
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Jayaweera, Sanduni Wasana
    Lindgren, Anders E. G.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Olofsson, Anders
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Almqvist, Fredrik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Intramolecular Povarov Reactions for the Synthesis of Chromenopyridine fused 2-Pyridone Polyheterocycles Binding to α-Synuclein and Amyloid-β fibrils2020Ingår i: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 85, nr 21, s. 14174-14189Artikel i tidskrift (Övrigt vetenskapligt)
    Abstract [en]

    A BF3×OEt2 catalyzed intramolecular Povarov reaction was used to synthesize a library of 15 chromenopyridine fused thiazolino-2-pyridone peptidomimetics. The reaction works with a range of O-alkylated salicylaldehydes and amino functionalized thiazolino-2-pyridones, to generate polyheterocycles with diverse substitution. The synthesized compounds were screened for their ability to bind α-synuclein and amyloid β fibrils in vitro. Analogs substituted with a nitro group bind to mature amyloid fibrils, and the activity moreover depends on the positioning of this functional group.

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  • 3.
    Adolfsson, Dan E.
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Tyagi, Mohit
    Singh, Pardeep
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Kaur, Amandeep
    Ådén, Jörgen
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Bharate, Jaideep B.
    Almqvist, Fredrik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Umeå universitet, Medicinska fakulteten, Umeå Centre for Microbial Research (UCMR). Umeå universitet, Medicinska fakulteten, Molekylär Infektionsmedicin, Sverige (MIMS).
    Enhanement of amyloid fibril binding by ring expansion of thiazolino fused 2-pyridone peptidomimeticsManuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    Thiazolino fused 2-pyridones undergo thiazoline ring opening by reaction with 2-nitrobenzyl bromide through thi- oether attack, and base promoted fragmentation of the resulting sulfonium ions. Subsequent deprotonation of the benzylic carbon and intramolecular 1,4-addition leads to ring closure, generating dihydrothiazine fused 2-pyridones by net ring expansion of the thiazoline ring. Application of the ring expansion procedure to the pyridine and pyrimidine fused thiazolino 2-pyridones provided compounds with enhanced fibril binding activity.

  • 4.
    Agnemo, Roland
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten.
    Ligniners reaktioner med alkalisk väteperoxid1981Doktorsavhandling, monografi (Övrigt vetenskapligt)
    Abstract [en]

    Under alkaline conditions hydrogen peroxide can be used either as a 1ignin-degrading or a 1ignin-preserving bleaching agent. If heavy metal ions are present and/or silicate is absent in the reaction medium, hydrogen peroxide decomposes via hydroxyl radicals and superoxide ions to oxygen and water. These decomposition products are able to react for example with phenolic lignin structures and thereby cause a partial degradation of lignin. In such a system peroxide could act as a bleaching and delignifying agent at the same time and these properties can be utilized for the bleaching of chemical pulps.In order to elucidate the factors which influence the degradation of phenolic structures by oxidation with alkaline hydrogen peroxide the lignin model compounds-methylsyringyl alcohol was studied.By determining the first order reaction rate constants for the oxidation, the main results which were obtained indicate that phenolic lignin structures can be efficiently degraded especially if:A. The pH in the bleaching liquor is close to the pK -valueàfor hydrogen peroxide.B. The ionic strength in the bleaching medium is as high as possible.C. A fixed amount of heavy metal ions (manganese) is added to the bleaching liquor.In the presence of silicate and diethylentriaminepenta-acetic acid (DTPA) hydrogen peroxide is stabilized against decomposition. Under these conditions alkaline hydrogen peroxide is able to react only with lignin units containing conjugated carbonyl groups such as quinone, aryl-oe-carbonyl and cinnamaldehyd structures, leading to an elimination of the chromophoric structures without any substantial dissolution of lignin. In this part of work we have elucidated the kinetic behavior and the reaction products from lignin model compounds of the aryl-of- carbonyl and cinnamaldehyde types.1,2-Diarylpropan-1,3,-diol structures constitute an important building unit in native lignins. We have demonstrated that under hydrogen peroxide bleaching conditions the model compound 2,3--bis(4-hydroxy-3-methoxyphenyl)-3-ethoxy-propanol was converted to stilbenes, ûe. structures which when present in pulps may contribute to a rapid yellowing. The results obtained with model compounds under simulated lignin retaining bleaching conditions demonstrate that there are possibilities to improve the bleaching of mechanical pulps with hydrogen peroxide if:A. The remaining heavy metal ions complexed with DTPA are present in their lowest valence states.B. The concentration of hydroperoxy ions can be maintained at a high level at the lowest possible pH-value.

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  • 5. Aguilera, Adriana Freites
    et al.
    Tolvanen, Pasi
    Heredia, Shuyana
    Muñoz, Marta González
    Samson, Tina
    Oger, Adrien
    Verove, Antoine
    Eränen, Kari
    Leveneur, Sebastien
    Mikkola, Jyri-Pekka
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Industrial Chemistry & Reaction Engineering, Department of Chemical Engineering, Johan Gadolin Process Chemistry Centre, Åbo Akademi University, Åbo-Turku, Finland.
    Salmi, Tapio
    Epoxidation of fatty acids and vegetable oils assisted by microwaves catalyzed by a cation exchange resin2018Ingår i: Industrial & Engineering Chemistry Research, ISSN 0888-5885, E-ISSN 1520-5045, Vol. 57, nr 11, s. 3876-3886Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Epoxidation of oleic acid and cottonseed oil was conducted in a semibatch reactor with in-situ-formed percarboxylic acid (peracetic acid or perpropionic acid), using hydrogen peroxide as an oxidizing agent and carboxylic acid (acetic acid or propionic acid) as oxygen carriers. Amberlite IR-120 was implemented as the catalyst. The system was comprised of a loop reactor, where the mixture was pumped through a single-mode cavity in which microwave irradiation was introduced. A heat exchanger was integrated into the system to replace microwave heating, to compare the results obtained via microwave heating versus conventional heating. The catalyst loading effect was studied, as well as the influence of microwave irradiation and the implementation of the SpinChem rotating bed reactor (RBR), in hopes of decreasing the influence of the internal mass transfer. The application of microwave irradiation results in an improvement of the reaction yield in the absence of a catalyst.

  • 6. Aguilera, Adriana Freites
    et al.
    Tolvanen, Pasi
    Oger, Adrien
    Eränen, Kari
    Leveneur, Sébastien
    Mikkola, Jyri-Pekka
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Laboratory of Industrial Chemistry and Reaction Engineering, Department of Chemical Engineering, Johan Gadolin Process Chemistry Centre, Åbo Akademi University, Turku-Åbo, Finland.
    Salmi, Tapio
    Screening of ion exchange resin catalysts for epoxidation of oleic acid under the influence of conventional and microwave heating2019Ingår i: Journal of chemical technology and biotechnology (1986), ISSN 0268-2575, E-ISSN 1097-4660, Vol. 94, nr 9, s. 3020-3031Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background: For many chemical systems, it is of great importance to find a durable, active and efficient catalyst that improves the process performance. Epoxidation of oleic acid with peracetic acid (Prilezhaev oxidation) was carried out in an isothermal loop reactor in the presence of heterogeneous catalysts. The kinetic experiments conducted under microwave heating (MW) were compared with identical experiments carried out under conventional (conductive/convective) heating. Extensive screening of heterogeneous catalysts was conducted and the influence of microwave irradiation on the reaction kinetics was studied. Several ion exchange resins were screened to explore their applicability and activity in the epoxidation of oleic acid. The perhydrolysis reaction (peracetic acid formed in situ from acetic acid and H2O2) was promoted with the use of various solid acid catalysts: Amberlite IR-120, Amberlyst 15, Smopex®, Dowex 50x8-100, Dowex 50x8-50, Dowex 50x2-100 and Nafion™.

    Results: From the selected group of catalysts, Dowex 50-x8100 and Dowex 50x8-50 produced the highest yield of epoxidized oil. Only minor differences in the reactant conversion and the product yield were found in the experiments carried out under microwave exposure compared to the conventionally heated experiments in the presence of several ion exchange resins.

    Conclusions: The catalytic effect was much more prominent than the microwave effect, because the solid acid catalysts enhanced the slow step of the process, the perhydrolysis of acetic acid. The catalytic effect was very dominant and a considerable improvement of the oleic acid conversion and the epoxide yield was observed in the presence of the top-performing catalysts.

  • 7.
    Albers, Michael F
    et al.
    Department of Chemical Biology, Max Planck Institute for Molecular Physiology.
    Hedberg, Christian
    Amino acid building blocks for Fmoc solid-phase synthesis of peptides phosphocholinated at serine, threonine, and tyrosine2013Ingår i: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 78, nr 6, s. 2715-2719Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Phosphocholination of eukaryotic host cell proteins has recently been identified as a novel post-translational modification important for bacterial pathogenesis. Here, we describe the first straightforward synthetic strategy for peptides containing phosphocholinated serine, threonine, or tyrosine residues using preformed functional amino acid building blocks, fully compatible with standard Fmoc solid-phase peptide synthesis.

  • 8.
    Albers, Michael F
    et al.
    Department of Chemical Biology, Max-Planck Institute of Molecular Physiology.
    van Vliet, Bart
    Hedberg, Christian
    Amino acid building blocks for efficient Fmoc solid-phase synthesis of peptides adenylylated at serine or threonine2011Ingår i: Organic Letters, ISSN 1523-7060, E-ISSN 1523-7052, Vol. 13, nr 22, s. 6014-6017Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The first straightforward building block based (non-interassembly) synthesis of peptides containing adenylylated serine and threonine residues is described. Key features include final global acidolytic protective group removal as well as full compatibility with standard Fmoc solid-phase peptide synthesis (SPPS). The described Thr-AMP SPPS-building block has been employed in the synthesis of the Thr-adenylylated sequence of human GTPase CDC42 (Ac-SEYVP-T(AMP)-VFDNYGC-NH(2)). Further, we demonstrate proof-of-concept for the synthesis of an Ser-adenylylated peptide (Ac-GSGA-S(AMP)-AGSGC-NH(2)) from the corresponding adenylylated serine building block.

  • 9.
    Albers, Michael Franz
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Synthesis and investigation of bacterial effector molecules2016Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    During infections, bacterial microorganisms initiate profound interactions with mammalian host cells. Usually defense mechanisms of the host destroy intruding bacteria in rapid manner. However, many bacterial pathogens have evolved in a way to avoid these mechanisms. By use of effector molecules, which can be small organic molecules or proteins with enzymatic activity, the host is manipulated on a molecular level. Effectors mediating post-translational modifications (PTMs) are employed by many pathogens to influence the biological activity of host proteins. In the presented thesis, two related PTMs are investigated in detail: Adenylylation, the covalent transfer of an adenosine monophosphate group from adenosine triphosphate onto proteins, and phosphocholination, the covalent transfer of a phosphocholine moiety onto proteins. Over the past years, enzymes mediating these modifications have been discovered in several pathogens, especially as a mechanism to influence the signaling of eukaryotic cells by adenylylating or phosphocholinating small GTPases. However, the development of reliable methods for the isolation and identification of adenylylated and phosphocholinated proteins remains a vehement challenge in this field of research. This thesis presents general procedures for the synthesis of peptides carrying adenylylated or phosphocholinated tyrosine, threonine and serine residues. From the resulting peptides, mono-selective polyclonal antibodies against adenylylated tyrosine and threonine have been raised. The antibodies were used as tools for proteomic research to isolate unknown substrates of adenylyl transferases from eukaryotic cells. Mass spectrometric fragmentation techniques have been investigated to ease the identification of adenylylated proteins. Furthermore, this work presents a new strategy to identify adenylylated proteins. Additionally, small effector molecules are involved in the regulation of infection mechanisms. In this work, the small molecule LAI-1 (Legionella autoinducer 1) from the pathogen Legionella pneumophila, the causative agent of the Legionnaire’s disease, was synthesised together with its amino-derivatives. LAI-1 showed are a clear pharmacological effect on the regulation of the life cycle of L. pneumophila, initiating transmissive traits like motility and virulence. Furthermore, LAI-1 was shown to have an effect on eukaryotic cells as well. Directed motility of the eukaryotic cells was significantly reduced and the cytoskeletal architecture was reorganised, probably by interfering with the small GTPase Cdc42.

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  • 10. Almroth, Bethanie M. Carney
    et al.
    Gunnarsson, Lina M.
    Cuklev, Filip
    Fick, Jerker
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Kristiansson, Erik
    Larsson, D. G. Joakim
    Waterborne beclomethasone dipropionate affects the physiology of fish while its metabolite beclomethasone is not taken up2015Ingår i: Science of the Total Environment, ISSN 0048-9697, E-ISSN 1879-1026, Vol. 511, s. 37-46Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Asthma is commonly treated with inhalable glucocorticosteroids, including beclomethasone dipropionate (BDP). This is a synthetic prodrug which is metabolized to the more active monopropionate (BMP) and free beclomethasone in humans. To evaluate potential effects of residual drugs on fish, we conducted a 14 day flow-through exposure experiment with BDP and beclomethasone using rainbow trout, and analyzed effects on plasma glucose, hepatic glutathione and catalase activity together with water and body concentrations of the BDP, BMP and beclomethasone. We also analyzed hepatic gene expression in BDP-exposed fish by micro-array and quantitative PCR Beclomethasone (up to 0.65 mu g/L) was not taken up in the fish while BDP (0.65 and 0.07 mu g/L) resulted in accumulation of both beclomethasone, BMP and BDP in plasma, reaching levels up to those found in humans during therapy. Accordingly, exposure to 0.65 mu g/L of BDP significantly increased blood glucose as well as oxidized glutathione levels and catalase activity in the liver. Exposure to beclomethasone or the low concentration of BDP had no effect on these endpoints. Both exposure concentrations of BDP resulted in significantly higher transcript abundance of phosphoenolpyruvate carboxykinase involved in gluconeogenesis, and of genes involved in immune responses. As only the rapidly metabolized prodrug was potent in fish, the environmental risks associated with the use of BDP are probably small. However, the observed physiological effects in fish of BDP at plasma concentrations known to affect human physiology provides valuable input to the development of read-across approaches in the identification of pharmaceuticals of environmental concern.

  • 11.
    Andersson, Barbro
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten.
    Analysis of plant growth regulating substances1982Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Natural plant growth regulators (phytohormones) are a group of organic compounds which, in very small amounts, act as regulators of physiological processes in plants.Methods were developed for the analysis of phytohormones in samples from Norway spruce (Picea abies (L.) Karst.) and Scots pine (Pinus sylvestris (L.) Karst»). Identification of abscisic acid, 3-indoleacetic acid, gibbe-rellin Ag and the conjugate N-(3-indoleacetyl)aspartic acid was performed by GC-MS as their methyl esters. A quantitative determination of abscisic acid was made by GC-ECD and this method was also applied to anther samples of Anemone canadensis. 3-Indole-acetic acid and N-(3-indoleacetyl)aspartic acid were quantified by reversed-phase HPLC and spectrofluorimetric detection. Dichlorophene, used as a growth regulator in containerized seedlings of pine and spruce, was analysed by GC-MID in peat and paper.

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  • 12.
    Andersson, David C.
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Martinez, N.
    Zeller, D.
    Rondahl, S. H.
    Koza, M. M.
    Frick, B.
    Ekstrom, F.
    Peters, J.
    Linusson, Anna
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Changes in dynamics of alpha-chymotrypsin due to covalent inhibitors investigated by elastic incoherent neutron scattering2017Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 19, nr 37, s. 25369-25379Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    An essential role of enzymes is to catalyze various chemical reactions in the human body and inhibition of the enzymatic activity by small molecules is the mechanism of action of many drugs or tool compounds used to study biological processes. Here, we investigate the effect on the dynamics of the serine protease alpha-chymotrypsin when in complex with two different covalently bound inhibitors using elastic incoherent neutron scattering. The results show that the inhibited enzyme displays enhanced dynamics compared to the free form. The difference was prominent at higher temperatures (240-310 K) and the type of motions that differ include both small amplitude motions, such as hydrogen atom rotations around a methyl group, and large amplitude motions, such as amino acid side chain movements. The measurements were analyzed with multivariate methods in addition to the standard univariate methods, allowing for a more in-depth analysis of the types of motions that differ between the two forms. The binding strength of an inhibitor is linked to the changes in dynamics occurring during the inhibitor-enzyme binding event and thus these results may aid in the deconvolution of this fundamental event and in the design of new inhibitors.

  • 13.
    Andersson, Hans
    Umeå universitet, Teknisk-naturvetenskaplig fakultet, Kemi.
    Reaction Between Grignard reagents and Heterocyclic N-oxides: Synthesis of Substituted Pyridines, Piperidines and Piperazines2009Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    This thesis describes the development of new synthetic methodologies for preparation of bioactive interesting compounds, e.g. substituted pyridines, piperidines or piparazines. Thesecompounds are synthesized from commercially available, cheap and easily prepared reagents, videlicet the reaction between Grignard reagents and heterocyclic N-oxides.

     The first part of this thesis deals with an improvement for synthesis of dienal-oximes and substituted pyridines. This was accomplished by a rapid addition of Grignard reagents to pyridine N-oxides at rt. yielding a diverse set of substituted dienal-oximes. During these studies, it was observed that the obtained dienal-oxmies are prone to ring-close upon heating. By taking advantage of this, a practical synthesis of substituted pyridines was developed.

    In the second part, an ortho-metalation of pyridine N-oxides using Grignard reagents is discussed. The method can be used for incorporation of a range of different electrophiles, including aldehydes, ketones and halogens. Furthermore, the importance for incorporation of halogens are exemplified through a Suzuki–Miyaura coupling reaction of 2-iodo pyridine N-oxides and different boronic acids. Later it was discovered that if the reaction temperature is kept below -20 °C, the undesired ringopening can be avoided. Thus, the synthesis of 2,3-dihydropyridine N-oxide, by reacting Grignard reagents with pyridine N-oxides at -40 °C followed by sequential addition of aldehyde or ketone, was accomplished. The reaction provides complete regio- and stereoselectivity yielding trans-2,3-dihydropyridine N-oxides in good yields. These intermediate products could then be used for synthesis of either substituted piperidines, by reduction, or reacted in a Diels–Alder cycloaddtion to give the aza-bicyclo compound.

    In the last part of this thesis, the discovered reactivity for pyridine N-oxides, is applied on pyrazine N-oxides in effort to synthesize substituted piperazines. These substances are obtained by the reaction of Grignard reagents and pyrazine N-oxides at -78 °C followed by reduction and protection, using a one-pot procedure. The product, a protected piperazine, that easily can be orthogonally deprotected, allowing synthetic modifications at either nitrogens in a fast and step efficient manner. Finally, an enantioselective procedure using a combination of PhMgCl and (-)-sparteine is discussed, giving opportunity for a stereoselective synthesis of substituted piperazines.

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  • 14.
    Andersson, Hans
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Gustafsson, Magnus
    Olsson, Roger
    Almqvist, Fredrik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Selective synthesis of 2-substituted pyridine N-oxides via directed ortho-metallation using Grignard reagents2008Ingår i: Tetrahedron Letters, ISSN 0040-4039, E-ISSN 1359-8562, Vol. 49, nr 48, s. 6901-3Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Addition of i-PrMgCl to pyridine N-oxides in THF at −78 °C generates selectively an ortho-metallated species, which can be trapped with various electrophiles to generate 2-substituted pyridine N-oxides. Furthermore, by applying a double metal-catalyzed cross-coupling, direct arylation of the pyridine N-oxides is achieved.

  • 15.
    Andersson, Ida E.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Modified Glycopeptides Targeting Rheumatoid Arthritis: Exploring molecular interactions in class II MHC/glycopeptide/T-cell receptor complexes2011Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Rheumatoid arthritis (RA) is an autoimmune inflammatory disease that leads to degradation of cartilage and bone mainly in peripheral joints. In collagen-induced arthritis (CIA), a mouse model for RA, activation of autoimmune CD4+ T cells depends on a molecular recognition system where T-cell receptors (TCRs) recognize a complex between the class II MHC Aq protein and CII259-273, a glycopeptide epitope from type II collagen (CII). Interestingly, vaccination with the Aq/CII259-273 complex can relieve symptoms and cause disease regression in mice. This thesis describes the use of modified glycopeptides to explore interactions important for binding to the Aq protein and recognition by autoimmune T-cell hybridomas obtained from mice with CIA.

    The CII259-273 glycopeptide was modified by replacement of backbone amides with different amide bond isosteres, as well as substitution of two residues that anchor the glycopeptide in prominent pockets in the Aq binding site. A three-dimensional structure of the Aq/glycopeptide complex was modeled to provide a structural basis for interpretation of the modified glycopeptide’s immunological activities. Overall, it was found that the amide bond isosteres affected Aq binding more than could be explained by the static model of the Aq/glycopeptide complex. Molecular dynamics (MD) simulations, however, revealed that the introduced amide bond isosteres substantially altered the hydrogen-bonding network formed between the N-terminal 259-265 backbone sequence of CII259-273 and Aq. These results indicated that the N-terminal hydrogen-bonding interactions follow a cooperative model, where the strength and presence of individual hydrogen bonds depended on the neighboring interactions.

    The two important anchor residues Ile260 and Phe263 were investigated using a designed library of CII259-273 based glycopeptides with substitutions by different (non-)natural amino acids at positions 260 and 263. Evaluation of binding to the Aq protein showed that there was scope for improvement in position 263 while Ile was preferred in position 260. The obtained SAR understanding provided a valuable basis for future development of modified glycopeptides with improved Aq binding. Furthermore, the modified glycopeptides elicited varying T-cell responses that generally could be correlated to their ability to bind to Aq. However, in several cases, there was a lack of correlation between Aq binding and T-cell recognition, which indicated that the interactions with the TCRs were determined by other factors, such as presentation of altered epitopes and changes in the kinetics of the TCR’s interaction with the Aq/glycopeptide complex.

    Several of the modified glycopeptides were also found to bind well to the human RA-associated DR4 protein and elicit strong responses with T-cell hybridomas obtained from transgenic mice expressing DR4 and the human CD4 co-receptor. This encourages future investigations of modified glycopeptides that can be used to further probe the MHC/glycopeptide/TCR recognition system and that also constitute potential therapeutic vaccines for treatment of RA. As a step towards this goal, three modified glycopeptides presented in this thesis have been identified as candidates for vaccination studies using the CIA mouse model.

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  • 16.
    Andréasson, Måns
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Umeå University.
    Redefining the essential molecular aspects that drive interactions between small molecules and G-quadruplex DNA2023Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    G-Quadruplex (G4) structures are secondary nucleic acid structures located in guanine-rich regions of DNA and RNA sequences, involved in gene regulation and cellular maintenance. Efforts to target G4s in a therapeutic setting are scarce, mainly due to vague details about the binding interactions between the ligands and the G4 structure combined with the lack of emphasis on drug-like properties early in the ligand development process. Furthermore, the ability to target specific G4 structures with small drug-like molecules remains a big challenge to overcome in the field. In this thesis, extensive organic synthesis developments coupled with computational-aided design and orthogonal in vitro assays has been used in tandem to reveal in-depth knowledge about ligand-to-G4 interactions. First, a macrocyclic approach was applied to design and discover novel G4 ligands which showed that macrocycles offer a solid foundation for ligand design. Next, computational tools to optimise the macrocyclic molecular conformation were used based on the macrocycles' abilities to stack on the G4 surface. In addition, macrocyclic, and non-macrocyclic ligands that bound G4 with high potency were shown to correlate with electron-deficient electrostatic potential (ESP) maps. The frequent inclusion of cationic residues in G4 ligands and their enhancement on ligand-to-G4 binding was, thereof, ascribed to their impact on the electrostatic character of the ligands' arene-arene interactions with the G4 surface, and not through direct electrostatic ionic interactions. In addition, the dispersion energetic component in the arene-arene interactions between the G4 ligand and the G4 was discovered to be paramount for ligand-to-G4 binding. The implementation of these descriptors in practice resulted in the discovery of potent G4 binders with adequate pharmacokinetic (PK) properties, accentuating the significance of understanding the molecular interactions between ligands and G4s in rational ligand design. Finally, a G4 ligand conjugated to an oligonucleotide was demonstrated as a modular approach to achieve selective binding of a ligand to a specific G4 structure. 

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  • 17.
    Andréasson, Måns
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Bhuma, Naresh
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Pemberton, Nils
    AstraZeneca, Mölndal, Gothenburg, Sweden.
    Chorell, Erik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Using Macrocyclic G-Quadruplex Ligands to Decipher the Interactions Between Small Molecules and G-Quadruplex DNA2022Ingår i: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 28, nr 65, artikel-id e202202020Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    This study aims to deepen the knowledge of the current state of rational G4-ligand design through the design and synthesis of a novel set of compounds based on indoles, quinolines, and benzofurans and their comparisons with well-known G4-ligands. This resulted in novel synthetic methods and G4-ligands that bind and stabilize G4 DNA with high selectivity. Furthermore, the study corroborates previous studies on the design of G4-ligands and adds deeper explanations to why a) macrocycles offer advantages in terms of G4-binding and -selectivity, b) molecular pre-organization is of key importance in the development of strong novel binders, c) an electron-deficient aromatic core is essential to engage in strong arene-arene interactions with the G4-surface, and d) aliphatic amines can strengthen interactions indirectly through changing the arene electrostatic nature of the compound. Finally, fundamental physicochemical properties of selected G4-binders are evaluated, underscoring the complexity of aligning the properties required for efficient G4 binding and stabilization with feasible pharmacokinetic properties.

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  • 18.
    Andréasson, Måns
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Donzel, Maxime
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Abrahamsson, Alva
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Berner, Andreas
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Doimo, Mara
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Quiroga, Anna
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Pemberton, Nils
    AstraZeneca, Gothenburg, Sweden.
    Wanrooij, Sjoerd
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Chorell, Erik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    The Synergism of the Dispersion and Electrostatic Components in the Arene-Arene Interactions Between Ligands and G4 DNAManuskript (preprint) (Övrigt vetenskapligt)
  • 19.
    Anugwom, I.
    et al.
    Laboratory of Industrial Chemistry and Reaction Engineering, Process Chemistry Centre, Åbo Akademi University, Åbo-Turku, Finland.
    Mäki-Arvela, P.
    Laboratory of Industrial Chemistry and Reaction Engineering, Process Chemistry Centre, Åbo Akademi University, Åbo-Turku, Finland.
    Eta, V.
    Laboratory of Industrial Chemistry and Reaction Engineering, Process Chemistry Centre, Åbo Akademi University, Åbo-Turku, Finland.
    Virtanen, P.
    Laboratory of Industrial Chemistry and Reaction Engineering, Process Chemistry Centre, Åbo Akademi University, Åbo-Turku, Finland.
    Mikkola, Jyri-Pekka
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Laboratory of Industrial Chemistry and Reaction Engineering, Process Chemistry Centre, Åbo Akademi University, Åbo-Turku, Finland.
    Towards optimal treatment procedure upon fractionation of Nordic lignocelluloses using novel alkanol amine – superbase ionic liquid system2012Ingår i: NWBC 2012: 4th Nordic Wood Biorefinery Conference, VTT , 2012, s. 320-322Konferensbidrag (Refereegranskat)
  • 20. Artemenko, A.
    et al.
    Shchukarev, Andrey
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Štenclová, P.
    Wågberg, Thomas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.
    Segervald, Jonas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.
    Jia, X.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.
    Kromka, A.
    Reference XPS spectra of amino acids2021Konferensbidrag (Refereegranskat)
    Abstract [en]

    In this report we present XPS data for five amino acids (AAs) (tryptophan, methionine, glutamine, glutamic acid, and arginine) with different side chain groups measured in solid state (powder form). The theoretically and experimentally obtained chemical structure of AAs are compared. Here, we analyse and discuss C 1 s, N 1 s, O 1s and S 2p core level binding energies, FWHMs, atomic concentrations of the functional groups in AAs. The experimentally obtained and theoretically calculated ratio of atomic concentrations are compared. The zwitterionic nature of methionine and glutamine in solid state was determined from protonated amino groups in N 1s peak and deprotonated carboxylic groups in the C 1s spectrum. The obtained XPS results for AAs well correspond with previously reported data.

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  • 21. Asgari, Parham
    et al.
    Hua, Yuanda
    Bokka, Apparao
    Thiamsiri, Chanachon
    Prasitwatcharakorn, Watcharapon
    Karedath, Ashif
    Chen, Xin
    Sardar, Sinjinee
    Yum, Kyungsuk
    Leem, Gyu
    Pierce, Brad S.
    Nam, Kwangho
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Gao, Jiali
    Jeon, Junha
    Catalytic hydrogen atom transfer from hydrosilanes to vinylarenes for hydrosilylation and polymerization2019Ingår i: Nature Catalysis, ISSN 2520-1158, Vol. 2, nr 2, s. 164-173Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Because of the importance of hydrogen atom transfer (HAT) in biology and chemistry, there is increased interest in new strategies to perform HAT in a sustainable manner. Here, we describe a sustainable, net redox-neutral HAT process involving hydrosilanes and alkali metal Lewis base catalysts-eliminating the use of transition metal catalysts-and report an associated mechanism concerning Lewis base-catalysed, complexation-induced HAT. The catalytic Lewis base-catalysed, complexation-induced HAT is capable of accessing both branch-specific hydrosilylation and polymerization of vinylarenes in a highly selective fashion, depending on the Lewis base catalyst used. In this process, the Earth-abundant, alkali metal Lewis base catalyst plays a dual role. It first serves as a HAT initiator and subsequently functions as a silyl radical stabilizing group, which is critical to highly selective cross-radical coupling. An electron paramagnetic resonance study identified a potassiated paramagnetic species, and multistate density functional theory revealed a high HAT character, yet multiconfigurational nature in the transition state of the reaction.

  • 22.
    Badea, Silviu-Laurentiu
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Danet, Andrei-Florin
    Enantioselective stable isotope analysis (ESIA) - A new concept to evaluate the environmental fate of chiral organic contaminants2015Ingår i: Science of the Total Environment, ISSN 0048-9697, E-ISSN 1879-1026, Vol. 514, s. 459-466Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Since 2011, the enantiospecific stable carbon isotope analysis (ESIA) has emerged as an innovative technique to assess the environmental fate of chiral emerging compounds by combining in one experimental technique both compound specific isotope analysis (CSIA) and enantioselective analysis. To date, the ESIA was applied for four classes of compounds: alpha-hexachlorocyclohexane (alpha-HCH), polar herbicides (phenoxy acids), synthetic polycyclic musk galaxolide (HHCB), and phenoxyalkanoic methyl herbicides. From an analytical point of view there are factors that are hindering the application of ESIA methods for the field samples: (i.e. amounts of target analyte, matrix effects, GC resolution) and overcoming these factors is challenging. While ESIA was shown as a mature technique for the first three abovementioned class of compounds, no isotope analysis of individual enantiomers could be performed for phenoxyalkanoic methyl herbicides. With respect to field studies, one study showed that ESIA might be a promising tool to distinguish between biotic and abiotic transformation pathways of chiral organic contaminants and even to differentiate between their aerobic and anaerobic biotransformation pathways. The development of ESIA methods for new chiral emerging contaminants in combination with development of multi-element isotope analysis will contribute to a better characterization of transformation pathways of chiral organic contaminants. (C) 2015 Elsevier B.V. All rights reserved.

  • 23.
    Barange, Deepak Kumar
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Johnson, Magnus T.
    Cairns, Andrew G.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Olsson, Roger
    Almqvist, Fredrik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Regio- and Stereoselective Alkylation of Pyridine-N-oxides: Synthesis of Substituted Piperidines and Pyridines2016Ingår i: Organic Letters, ISSN 1523-7060, E-ISSN 1523-7052, Vol. 18, nr 24, s. 6228-6231Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Regio- and stereoselective addition of alkyl Grignard reagents to pyridine-N-oxides gave C2-alkylated N-hydroxy-1,2,5,6-tetrahydropyridines and trans-2,3-disubstituted N-hydroxy-1,2,5,6-tetrahydropyridines in good to excellent yields. These intermediates were aromatized or alternatively reduced in one-pot methodologies for efficient syntheses of alkylpyridines or piperidines, respectively. These reactions have a broad substrate scope and short reaction times.

  • 24.
    Barzegar, Hamid Reza
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.
    Nitze, Florian
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.
    Malolepszy, Artur
    Stobinski, Leszek
    Tai, Cheuk-Wai
    Wågberg, Thomas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.
    Water assisted growth of C60 rods and tubes by liquid-liquid interfacial precipitation method2012Ingår i: Molecules, ISSN 1431-5157, E-ISSN 1420-3049, Vol. 17, nr 6, s. 6840-6853Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    C60 nanorods with hexagonal cross sections are grown using a static liquid-liquid interfacial precipitation method in a system of C60/m-dichlorobenzene solution and ethanol. Adding water to the ethanol phase leads instead to C60 tubes where both length and diameter of the C60 tubes can be controlled by the water content in the ethanol. Based on our observations we find that the diameter of the rods/tubes strongly depends on the nucleation step. We propose a liquid-liquid interface growth model of C60 rods and tubes based on the diffusion rate of the good C60 containing solvent into the poor solvent as well as on the size of the crystal seeds formed at the interface between the two solvents. The grown rods and tubes exhibit a hexagonal solvate crystal structure with m-dichlorobenzene solvent molecules incorporated into the crystal structure, independent of the water content. An annealing step at 200 °C at a pressure <1 kPa transforms the grown structures into a solvent-free face centered cubic structure. Both the hexagonal and the face centered cubic structures are very stable and neither morphology nor structure shows any signs of degradation after three months of storage.

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  • 25. Basu, Basudeb
    et al.
    Paul, Susmita
    Kundu, Samir
    Byström, Emil
    Irgum, Knut
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Almqvist, Fredrik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Organic Polymeric Resins Embedded with Pd NPs: Newly Designed, Efficient and Chemoselective Catalyst for Reduction of Nitrobenzenes2017Ingår i: Current Organocatalysis, ISSN 2213-3372, Vol. 4, nr 1, s. 48-61Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background: Organic polymer supported palladium nanoparticles (NPs) are important for use as heterogeneous catalyst in various organic reactions. This works describes Pd Nps immobilized on to polystyrene-based ion-exchange resin surface for use as catalyst in the reduction of nitrobenzenes. The heterogeneous catalyst was found useful for hydrogenation of nitro group under both catalytic transfer hydrogenation (CTH) as well as by using molecular hydrogen (H2).

    Methods: The catalyst was prepared from Amberlite IRA 900 Cl after rinsing with formic acid (10%) and subsequent treatment with Na2PdCl4 in DMF. The resulting Pd Nps immobilized resins was designated as VersaCat Pd and used for CTH of nitrobenzenes in the presence of H-donors (sodium formate, formic acid, hydrazine hydrate) and also for hydrogenation with H2 gas. The catalyst was characterized by FT-IR, MAS-NMR, SEM, TEM and XPS and surface morphologies were studied before and after the reaction.

    Results: Hydrogenations of nitrobenzenes under CTH using different H-source and direct use of H2 gas were achieved successfully with good to excellent yields. Reactions were performed under mild conditions and high degree of chemoselectivity was also observed. The catalyst was recyclable, used for six consecutive runs with appreciable conversions and showed higher activity (> 3 times) in terms of metalcontent than commercially available Pd/C (10%) in the hydrogenation of nitrobenzenes using H2 gas. The TEM images showed that Pd Nps are evenly distributed with size 50-200 mm on polymeric matrices and there was no significant changes observed after the first catalytic run. However, considerable rupture of the polymeric surface occurred after six runs, as seen from SEM studies.

    Conclusion: The present study establishes high catalytic efficiency and chemoselectivity of the newly developed organic polystyrene-based resin-soaked Pd NPs (VersaCat Pd) in the reduction of nitrobenzenes. Both CTH and hydrogenation using H2 gas were successfully done. Interestingly, hydrazine hydrate offered excellent control over chemoselectivity under CTH conditions and allowed clean conversion from nitro to amine, while keeping a chloro substitutent unaffected. Hydrogenation using molecular H2 gave maximum TOF. Easy preparation, high efficacy, TOF, chemoselectivity, and versatile applications are notable features for this heterogeneous palladium catalyst (VersaCat Pd). These features are often required in chemical industries.

  • 26. Beckmann, Katrin
    et al.
    Uchtenhagen, Hannes
    Berggren, Gustav
    Anderlund, Magnus F
    Thapper, Anders
    Messinger, Johannes
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Styring, Stenbjörn
    Kurz, Philipp
    Formation of stoichiometrically 18O-labelled oxygen from the oxidation of 18O-enriched water mediated by a dinuclear manganese complex-a mass spectrometry and EPR study2008Ingår i: Energy & Environmental Science, ISSN 1754-5692, E-ISSN 1754-5706, Vol. 1, s. 668-76Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Oxygen formation was detected for the oxidations of various multinuclear manganese complexes by oxone (HSO5-) in aqueous solution. To determine to what extent water was the source of the evolved O2, H218O isotope-labelling experiments coupled with membrane inlet mass spectrometry (MIMS) were carried out. We discovered that during the reaction of oxone with [Mn2(OAc)2(bpmp)]+ (1), stoichiometrically labelled oxygen (18O2) was formed. This is the first example of a homogeneous reaction mediated by a synthetic manganese complex where the addition of a strong chemical oxidant yields 18O2 with labelling percentages matching the theoretically expected values for the case of both O-atoms originating from water. Experiments using lead acetate as an alternative oxidant supported this finding. A detailed investigation of the reaction by EPR spectroscopy, MIMS and Clark-type oxygen detection enabled us to propose potential reaction pathways.

  • 27.
    Behren, Sandra
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Development and Evaluation of Tools to Explore Posttranslational HexNAc-Tyrosine and Mucin-Type O-Glycosylation2021Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Glycosylation is the most abundant form of post-translational modification (PTM). Recently, O-glycosylation attracted much attention in the glycoproteomic field due to its association with various diseases, such as pathogenic infections and cancer. However, glycoproteomic analysis of O-linked glycosylation is highly challenging due its structural diversity and complexity. New and efficient methods need to be developed to obtain a better understanding of the biological functions of O-glycans. In the presented thesis, glycopeptide microarrays were used as tools to explore the role of mucin type O-glycosylation in cancer, bacterial adhesion processes and galectin recognition on a molecular level, and to get insights into a new group of tyrosine O-glycosylation. A better understanding of these carbohydrate-protein interactions on a molecular level could facilitate the development of glycomimetic inhibitors to fight bacterial infections or block glycan binding proteins involved in cancer progression, or improve the design of novel carbohydrate-based cancer vaccines.

    In the first part of this work, tools were developed to elucidate the role of a novel group of PTMs, where N-acetylhexosamine (HexNAc = α-GalNAc, α- or β-GlcNAc) was found to modify the hydroxyl group of tyrosine. Synthetic glycopeptides carrying this new modification, as well as glycopeptide microarray libraries were prepared to evaluate the abilities of plant lectins (carbohydrate-binding proteins) to detect HexNAc-O-Tyr modifications. These lectins are commonly used in glycoproteomic work flows to detect and enrich glycopeptides and -proteins. Additionally, HexNAc-O-Tyr-specific rabbit antibodies were raised and immunologically analyzed by enzyme-linked immunosorbent assays, western blot and microarray binding studies.

    In the second part of the presented thesis, synthetic mucin glycopeptide microarray libraries were prepared and employed to explore carbohydrate-protein interactions of galectins, bacterial lectins and tumor specific antibodies. Mucin glycoproteins are part of the mucus barrier that protects the host against invading pathogens. However, bacteria and viruses have co-evolved with the human host and have developed strategies to promote virulence, for example by adhering to glycans on the host cell-surface. To combat bacterial infections, their virulence and pathogenicity must be understood on a molecular level. In this work, mucin glycopeptides were enzymatically modified with different fucose motifs and used to determine the fine binding specificities of fucose-recognizing lectins LecB from Pseudomonas aeruginosa and the Clostridium difficile toxin A. Furthermore, a synthesis strategy was developed to generate simplified mucin core glycopeptides that could be used as scaffolds to enzymatically generate LacdiNAc modified glycopeptides. They could be used in microarray binding studies to evaluate the glycan binding preferences of various proteins, including the Helicobacter pylori lectin LabA and human galectins, which play roles in cancer development and progression. Aberrant glycosylation of mucin glycoproteins has been associated with various types of cancer. Tumor specific carbohydrate antigens on mucins represent attractive antigenic targets for the development of effective anti-cancer vaccines. In this work, antibodies induced by tumor-associated MUC1 glycopeptide-bacteriophage Qβ vaccine conjugates were immunologically analyzed using MUC1 glycopeptide microarray libraries.

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  • 28.
    Behren, Sandra
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Delgado, Sandra
    Arda, Ana
    Jiménez-Barbero, Jesús
    Westerlind, Ulrika
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Binding Specificities of Human Galectins toward Mucin Glycopeptide LibrariesManuskript (preprint) (Övrigt vetenskapligt)
  • 29.
    Behren, Sandra
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Funder, Tobias
    Westerlind, Ulrika
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Synthesis of Simplified Mucin Cores 1-4 MUC1 and MUC5AC Glylcopeptides for Enzymatic Modification with LacdiNAc MotifsManuskript (preprint) (Övrigt vetenskapligt)
  • 30.
    Behren, Sandra
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Leibniz-Institut für Analytische Wissenschaften, Dortmund, Germany.
    Schorlemer, Manuel
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Leibniz-Institut für Analytische Wissenschaften, Dortmund, Germany.
    Schmidt, Gudula
    Institut für Experimentelle und Klinische Pharmakologie und Toxikologie, Universität Freiburg, Freiburg, Germany.
    Westerlind, Ulrika
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Leibniz-Institut für Analytische Wissenschaften, Dortmund, Germany.
    Aktories, Klaus
    Institut für Experimentelle und Klinische Pharmakologie und Toxikologie, Universität Freiburg, Freiburg, Germany.
    Antibodies directed against GalNAc- and GlcNAc-O-Tyrosine posttranslational modifications – a new tool for glycoproteomic detection2023Ingår i: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 29, nr 29, artikel-id e202300392Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In the last decade, it was discovered that protein mucin-type O-glycosylation and O-GlcNAcylation modify Tyr residues besides the well explored Thr and Ser amino acids. Several glycoproteomic studies have identified α-GalNAc-O-Tyr modifications, and studies propose that β-GlcNAc-O-Tyr also exists as a new group of posttranslational modifications (PTMs). Specific bacterial toxins have further been identified to modify host GTPases with α-GlcNAc-O-Tyr to promote bacterial virulence. Despite being identified on numerous proteins, the biological roles, biosynthesis and expression of GalNAc- and GlcNAc-O-Tyr modifications are poorly understood. A major obstacle is the lack of tools to specifically detect and identify proteins containing these modifications. With this in mind, we prepared vaccine constructs and raised antibodies to enable selective detection of proteins carrying these new PTMs. The obtained polyclonal antibody sera were evaluated using ELISA and glycopeptide microarrays and were found to be highly selective for GlcNAc- and GalNAc-O-Tyr glycopeptides over the corresponding Ser- and Thr-modifications. For microarray analysis, synthetic GlcNAc- and GalNAc-O-Tyr Fmoc-amino acids were prepared and applied in Fmoc-SPPS to obtain an extensive O-glycopeptide library. After affinity purification, the antibodies were applied in western blot analysis and showed specific detection of α-GlcNAc-O-Tyr modified RhoA GTPase.

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  • 31.
    Behren, Sandra
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Schorlemer, Manuel
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Xiao, Yao
    Woods, Robert J.
    Marcelo, Filipa
    Westerlind, Ulrika
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Deciphering the Molecular Recognition of GalNAc- and GlcNAc-O-Tyrosine Glycopeptides by Plant LectinsManuskript (preprint) (Övrigt vetenskapligt)
  • 32.
    Behren, Sandra
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Westerlind, Ulrika
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Novel approaches to design glycan-based antibacterial inhibitors2023Ingår i: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, Vol. 26, nr 1, artikel-id e202200795Artikel, forskningsöversikt (Refereegranskat)
    Abstract [en]

    The interactions between bacterial lectins and carbohydrates on the host cell surface can mediate bacterial adhesion, invasion, and immune evasion. Multivalency plays a key role in these binding events. However, additional molecular mechanisms greatly impact multivalent binding recognition. To develop specific and effective bacterial inhibitors, a deeper understanding of the complex underlying mechanisms of bacterial adhesion processes is necessary. By interfering with bacterial adhesion, synthetic multivalent glycoconjugates do not only have the potential to improve or replace antibiotic treatments, but also represent useful tools to study carbohydrate-pathogen interactions. In this review, we highlight a few recent advances in the synthesis and application of synthetic glycan-based scaffolds to uncover the nature of glycan-bacteria interactions and to design efficient bacterial inhibitors.

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  • 33.
    Behren, Sandra
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Yu, Jin
    Imperial College, London.
    Pett, Christian
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Schorlemer, Manuel
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Heine, Viktoria
    RWTH Aachen University.
    Fischöder,, Thomas
    RWTH Aachen University.
    Elling, Lothar
    RWTH Aachen University.
    Westerlind, Ulrika
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Bacteria Lectin Recognition Towards Fucose Binding Motifs Highlights the Impact of Presenting Mucin Core GlycopeptidesManuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    Mucin glycoproteins are essential components of the mucosal protective barrier, which constantly senses and clears the host from pathogens. Throughout evolution, bacteria and virus have developed strategies to modulate and penetrate the mucosal barrier and cause virulence by interacting with the glycans of membrane-bound mucins at the epithelial cell-surface. These interactions may promote bacteria cell-adhesion, biofilm formation, protein toxin delivery, or cause an inflammatory environment. O-fucosylated glycan epitopes are commonly found on mucin glycoproteins, and are key ligands of many bacterial and viral lectins (glycan binding proteins). Herein we describe a chemoenzymatic synthesis strategy to efficiently prepare an extensive library of fucosylated mucin core tandem repeats glycopeptides to elucidate the fine fucose-binding specificities of the Pseudomonas aeruginosa lectin LecB and the Clostridium difficile toxin A. Therefore, glycan core structures were decorated with terminal Lewis and H-antigens, which play critical roles in infection biology. The fucosylated mucin glycopeptides were applied in microarray binding studies to explore the importance of the glycan and peptide backbone presentation of these terminal antigens in binding interactions with the two bacterial lectins. 

  • 34.
    Berglin, Ewa
    et al.
    Umeå universitet, Medicinska fakulteten, Institutionen för odontologi, Oral mikrobiologi.
    Edlund, Maj-Britt K.
    Umeå universitet, Medicinska fakulteten, Institutionen för odontologi, Oral mikrobiologi.
    Nyberg, Göran K.
    Umeå universitet, Medicinska fakulteten, Institutionen för odontologi, Oral mikrobiologi.
    Carlsson, Jan
    Umeå universitet, Medicinska fakulteten, Institutionen för odontologi, Oral mikrobiologi.
    Potentiation by L-cysteine of the bactericidal effect of hydrogen peroxide in Escherichia coli1982Ingår i: Journal of Bacteriology, ISSN 0021-9193, E-ISSN 1098-5530, Vol. 152, nr 1, s. 81-88Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Under anaerobic conditions an exponentially growing culture of Escherichia coli K-12 was exposed to hydrogen peroxide in the presence of various compounds. Hydrogen peroxide (0.1 mM) together with 0.1 mM L-cysteine or L-cystine killed the organisms more rapidly than 10 mM hydrogen peroxide alone. The exposure of E. coli to hydrogen peroxide in the presence of L-cysteine inhibited some of the catalase. This inhibition, however, could not fully explain the 100-fold increase in hydrogen peroxide sensitivity of the organism in the presence of L-cysteine. Of other compounds tested only some thiols potentiated the bactericidal effect of hydrogen peroxide. These thiols were effective, however, only at concentrations significantly higher than 0.1 mM. The effect of L-cysteine and L-cystine could be annihilated by the metal ion chelating agent 2,2'-bipyridyl. DNA breakage in E. coli K-12 was demonstrated under conditions where the organisms were killed by hydrogen peroxide.

  • 35.
    Berglin, Ewa H.
    et al.
    Umeå universitet, Medicinska fakulteten, Institutionen för odontologi, Oral mikrobiologi.
    Carlsson, Jan
    Umeå universitet, Medicinska fakulteten, Institutionen för odontologi, Oral mikrobiologi.
    Potentiation by sulfide of hydrogen peroxide-induced killing of Escherichia coli1985Ingår i: Infection and Immunity, ISSN 0019-9567, E-ISSN 1098-5522, Vol. 49, nr 3, s. 538-543Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    L-Cysteine potentiates 100-fold the hydrogen peroxide-induced killing of a growing culture of Escherichia coli K-12 (Berglin et al., J. Bacteriol. 152:81-88). In the present study it is shown that hydrogen sulfide is formed from L-cysteine and that sodium sulfide could substitute for L-cysteine in the potentiation of hydrogen peroxide-induced killing of E. coli K-12. Addition of an amino acid, L-leucine, L-valine, or L-alanine, to an L-cysteine-containing medium with a growing culture of E. coli K-12 inhibited hydrogen sulfide formation and the potentiation of hydrogen peroxide-induced killing. These amino acids did not inhibit hydrogen sulfide formation from L-cysteine by a cell extract, and they did not inhibit the potentiation by sulfide of hydrogen peroxide-induced killing. This indicated that the amino acids protected the culture from L-cysteine-potentiated, hydrogen peroxide-induced killing by inhibiting the transport of L-cysteine into the cell. The potentiation by sodium sulfide of hydrogen peroxide-induced killing was abolished by the metal ion chelator 2,2'-bipyridyl. This indicated that metal ions, in addition to sulfide, were involved in the killing. Toxic effects of hydrogen peroxide are often presumed to be mediated by hydroxyl radicals formed in iron-catalyzed reactions. It was demonstrated that iron sulfide was more efficient than ferrous iron in catalyzing the formation of hydroxyl radicals from hydrogen peroxide. It was suggested that hydrogen sulfide formed in polymicrobial infections may play an important role in the host defense by potentiating the antimicrobial effect of hydrogen peroxide produced by phagocytic cells.

  • 36.
    Bergqvist, Per-Anders
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Zaliauskiene, Audrone
    Field study considerations in the use of passive sampling devices in water monitoring2007Ingår i: Passive Sampling Techniques in Environmental Monitoring / [ed] R. Greenwood, G. Mills and B. Vrana, Amsterdam: Elsevier, 2007, s. 311-328Kapitel i bok, del av antologi (Övrigt vetenskapligt)
    Abstract [en]

    Semipermeable membrane devices (SPMDs) are passive monitors that are being increasingly used by monitoring agencies and wastewater dischargers to measure the contents of lipophilic organic chemicals that may adversely affect water quality. This chapter addresses the most frequently asked questions regarding the use of SPMDs for water monitoring and other questions related to the field application of SPMDs. It provides a sound understanding of the applicability and limitations of SPMDs for obtaining reliable monitoring data. The chapter discusses under field study considerations: pre-exposure considerations; SPMD storage considerations; and precautions/procedures during deployment and retrieval of SPMDs. In environmental monitoring projects using SPMDs, quality control (QC) procedures for sampling and analysis are applied to ensure that the data are of high quality. Appropriate QC samples are prepared to quantify possible sampler contamination during transport, deployment, retrieval, storage, processing, enrichment, fractionation operations and analyte recovery. In general, two groups of quality assurance measures are implemented: replicate QC and sampling device control.

  • 37. Bernardo-Garcia, Noelia
    et al.
    Sánchez-Murcia, Pedro A.
    Espaillat, Akbar
    Umeå universitet, Medicinska fakulteten, Molekylär Infektionsmedicin, Sverige (MIMS). Umeå universitet, Medicinska fakulteten, Umeå Centre for Microbial Research (UCMR). Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten).
    Martínez-Caballero, Siseth
    Cava, Felipe
    Umeå universitet, Medicinska fakulteten, Molekylär Infektionsmedicin, Sverige (MIMS). Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten). Umeå universitet, Medicinska fakulteten, Umeå Centre for Microbial Research (UCMR).
    Hermoso, Juan A.
    Gago, Federico
    Cold-induced aldimine bond cleavage by Tris in Bacillus subtilis alanine racemase2019Ingår i: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 17, nr 17, s. 4350-4358Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Pyridoxal 5'-phosphate (PLP) is a versatile cofactor involved in a large variety of enzymatic processes. Most of PLP-catalysed reactions, such as those of alanine racemases (AlaRs), present a common resting state in which the PLP is covalently bound to an active-site lysine to form an internal aldimine. The crystal structure of BsAlaR grown in the presence of Tris lacks this covalent linkage and the PLP cofactor appears deformylated. However, loss of activity in a Tris buffer only occurred after the solution was frozen prior to carrying out the enzymatic assay. This evidence strongly suggests that Tris can access the active site at subzero temperatures and behave as an alternate racemase substrate leading to mechanism-based enzyme inactivation, a hypothesis that is supported by additional X-ray structures and theoretical results from QM/ MM calculations. Taken together, our findings highlight a possibly underappreciated role for a common buffer component widely used in biochemical and biophysical experiments.

  • 38.
    Bharate, Jaideep B.
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Ådén, Jörgen
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Gharibyan, Anna
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Adolfsson, Dan E.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Jayaweera, Sanduni Wasana
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Singh, Pardeep
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Vielfort, Katarina
    Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten).
    Tyagi, Mohit
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Bonde, Mari
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Bergström, Sven
    Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten).
    Olofsson, Anders
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Almqvist, Fredrik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    K2S2O8-mediated coupling of 6-amino-7-aminomethyl-thiazolino-pyridones with aldehydes to construct amyloid affecting pyrimidine-fused thiazolino-2-pyridones2021Ingår i: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 19, nr 44, s. 9758-9772Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We herein present the synthesis of diversely functionalized pyrimidine fused thiazolino-2-pyridones via K2S2O8-mediated oxidative coupling of 6-amino-7-(aminomethyl)-thiazolino-2-pyridones with aldehydes. The developed protocol is mild, has wide substrate scope, and does not require transition metal catalyst or base. Some of the synthesized compounds have an ability to inhibit the formation of Amyloid-β fibrils associated with Alzheimer's disease, while others bind to mature amyloid-β and α-synuclein fibrils.

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  • 39. Bharate, Jaideep B.
    et al.
    Ådén, Jörgen
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Gharibyan, Anna
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Adolfsson, Dan E.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Jayaweera, Sanduni Wasana
    Vielfort, Katarina
    Umeå universitet, Medicinska fakulteten, Umeå Centre for Microbial Research (UCMR). Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten). Umeå universitet, Medicinska fakulteten, Molekylär Infektionsmedicin, Sverige (MIMS).
    Singh, Pardeep
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Tyagi, Mohit
    Bergström, Sven
    Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten).
    Olofsson, Anders
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Almqvist, Fredrik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Umeå universitet, Medicinska fakulteten, Umeå Centre for Microbial Research (UCMR). Umeå universitet, Medicinska fakulteten, Molekylär Infektionsmedicin, Sverige (MIMS).
    K2S2O8-mediated aerobic oxidative coupling of 6-amino-7-(aminomethyl)-thiazolino-pyridones with aldehydes: Direct access to highly functionalized pyrimidine fused thiazolino-2-pyridones with amyloid fibril binding activity or inhibitors of Amyloid-β fibril formationManuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    We herein present the synthesis of diversely functionalized pyrimidine fused thiazolino-2-pyridones via K2S2O8-mediated oxidative coupling of 6-amino-7-(aminomethyl)- thiazolino-2-pyridones with aldehydes. The developed protocol is mild, has wide substrate scope, and does not require transition metal catalyst or base. Some of the synthesized compounds have the ability to inhibit the formation of Amyloid-β fibrils associated with Alzheimer's disease, while others bind to mature Amyloid-β and α-Synuclein fibrils.

  • 40. Bhattacharjee, Snehasish
    et al.
    Chakraborty, Sandipan
    Chorell, Erik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Sengupta, Pradeep K.
    Bhowmik, Sudipta
    Importance of the hydroxyl substituents in the B-ring of plant flavonols on their preferential binding interactions with VEGF G-quadruplex DNA: Multi-spectroscopic and molecular modeling studies2018Ingår i: International Journal of Biological Macromolecules, ISSN 0141-8130, E-ISSN 1879-0003, Vol. 118, s. 629-639Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    G-quadruplex (G4) structures are known to be promising anticancer drug targets and flavonols (an important class of fiavonoids) are small molecules reported to possess several health-promoting properties including those of anticancer activities. In this work, we explored the interactions of the structurally related plant flavonols kaempferol (KAE; 3,5,7,4'-OH flavone) and morin (MOR; 3,5,7,2',4'-OH flavone) with various G4-DNA sequences along with duplex DNA using a combination of spectroscopic and molecular docking studies. Our results revealed that KAE shows preferential interaction with VEGF G4-DNA in comparison to the other G4 sequences and duplex DNA. Moreover, KAE enhances the thermal stability of VEGF G4-DNA. In contrast, MOR exhibits an appreciably weaker level of interaction with both duplex and various G4-DNAs, with no significant structural specificity. The contrasting DNA binding behaviors suggest a crucial role of the 2'-OH substituent in the Bring of flavonol moiety. While KAE is relatively planar, MOR adopts a significantly non-planar conformation attributable to steric hindrance from the additional 2'-OH substituent. This small structural difference is apparently very important for the ability of KAE and MOR to interact with VEGF G4-DNA. Thus, KAE (but not MOR) appears to be an effective ligand for VEGF G4-DNA, opening up possibilities of its application for regulation of gene expression in cancer cells. 

  • 41.
    Bhowmick, Asmit
    et al.
    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, CA, Berkeley, United States.
    Simon, Philipp S.
    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, CA, Berkeley, United States.
    Bogacz, Isabel
    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, CA, Berkeley, United States.
    Hussein, Rana
    Department of Biology, Humboldt-Universität zu Berlin, Berlin, Germany.
    Zhang, Miao
    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, CA, Berkeley, United States.
    Makita, Hiroki
    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, CA, Berkeley, United States.
    Ibrahim, Mohamed
    Department of Biology, Humboldt-Universität zu Berlin, Berlin, Germany.
    Chatterjee, Ruchira
    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, CA, Berkeley, United States.
    Doyle, Margaret D.
    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, CA, Berkeley, United States.
    Cheah, Mun Hon
    Molecular Biomimetics, Department of Chemistry-Ångström, Uppsala University, Uppsala, Sweden.
    Chernev, Petko
    Molecular Biomimetics, Department of Chemistry-Ångström, Uppsala University, Uppsala, Sweden.
    Fuller, Franklin D.
    Linac Coherent Light Source, SLAC National Accelerator Laboratory, CA, Menlo Park, United States.
    Fransson, Thomas
    Department of Physics, AlbaNova University Center, Stockholm University, Stockholm, Sweden.
    Alonso-Mori, Roberto
    Linac Coherent Light Source, SLAC National Accelerator Laboratory, CA, Menlo Park, United States.
    Brewster, Aaron S.
    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, CA, Berkeley, United States.
    Sauter, Nicolas K.
    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, CA, Berkeley, United States.
    Bergmann, Uwe
    Department of Physics, University of Wisconsin-Madison, WI, Madison, United States.
    Dobbek, Holger
    Department of Biology, Humboldt-Universität zu Berlin, Berlin, Germany.
    Zouni, Athina
    Department of Biology, Humboldt-Universität zu Berlin, Berlin, Germany.
    Messinger, Johannes
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Molecular Biomimetics, Department of Chemistry-Ångström, Uppsala University, Uppsala, Sweden.
    Kern, Jan
    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, CA, Berkeley, United States.
    Yachandra, Vittal K.
    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, CA, Berkeley, United States.
    Yano, Junko
    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, CA, Berkeley, United States.
    Going around the Kok cycle of the water oxidation reaction with femtosecond X-ray crystallography2023Ingår i: IUCrJ, E-ISSN 2052-2525, Vol. 10, nr 6, s. 642-655Artikel, forskningsöversikt (Refereegranskat)
    Abstract [en]

    The water oxidation reaction in photosystem II (PS II) produces most of the molecular oxygen in the atmosphere, which sustains life on Earth, and in this process releases four electrons and four protons that drive the downstream process of CO2 fixation in the photosynthetic apparatus. The catalytic center of PS II is an oxygen-bridged Mn4Ca complex (Mn4CaO5) which is progressively oxidized upon the absorption of light by the chlorophyll of the PS II reaction center, and the accumulation of four oxidative equivalents in the catalytic center results in the oxidation of two waters to dioxygen in the last step. The recent emergence of X-ray free-electron lasers (XFELs) with intense femtosecond X-ray pulses has opened up opportunities to visualize this reaction in PS II as it proceeds through the catalytic cycle. In this review, we summarize our recent studies of the catalytic reaction in PS II by following the structural changes along the reaction pathway via room-temperature X-ray crystallography using XFELs. The evolution of the electron density changes at the Mn complex reveals notable structural changes, including the insertion of OX from a new water molecule, which disappears on completion of the reaction, implicating it in the O-O bond formation reaction. We were also able to follow the structural dynamics of the protein coordinating with the catalytic complex and of channels within the protein that are important for substrate and product transport, revealing well orchestrated conformational changes in response to the electronic changes at the Mn4Ca cluster.

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  • 42.
    Biasi, P.
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Department of Chemical Engineering, Laboratory of Industrial Chemistry and Reaction Engineering, Process Chemistry Centre (PCC), Åbo Akademi University, Åbo-Turku, Finland.
    Salmi, T.
    Department of Chemical Engineering, Laboratory of Industrial Chemistry and Reaction Engineering, Process Chemistry Centre (PCC), Åbo Akademi University, Åbo-Turku, Finland.
    Mikkola, Jyri-Pekka
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Department of Chemical Engineering, Laboratory of Industrial Chemistry and Reaction Engineering, Process Chemistry Centre (PCC), Åbo Akademi University, Åbo-Turku, Finland.
    Tailoring the process of H2O2 direct synthesis: Catalyst design and reaction engineering to reach an industrial feasibility2014Ingår i: 21st International Congress of Chemical and Process Engineering, CHISA 2014 and 17th Conference on Process Integration, Modelling and Optimisation for Energy Saving and Pollution Reduction, PRES 2014, Czech Society of Chemical Engineering , 2014, s. 65-65Konferensbidrag (Refereegranskat)
  • 43.
    Bidleman, Terry F.
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Ericson, Lars
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Liljelind, Per
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Tysklind, Mats
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Drosophilin a methyl ether (DAME) and other chlorinated dimethoxybenzenes in fungi and forest litter from Sweden2023Ingår i: Chemosphere, ISSN 0045-6535, E-ISSN 1879-1298, Vol. 347, artikel-id 140685Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Fungi and substrates undergoing fungal decomposition were collected from forests in northern and southernSweden and analyzed for chlorinated dimethoxybenzenes (DMBs). Specimens were fungi fruiting bodies, rottingwood, forest litter and underlying humus. Targeted compounds were DAME (1,2,4,5-tetrachloro-3,6-DMB) andrelated fungal secondary metabolites. A screening procedure was developed which involved soaking the speci-mens in ethyl acetate followed by analysis by capillary gas chromatography – mass spectrometry with mass selec-tive detection (GC-MSD). DAME was the most frequently found (62% of 47 specimens) and often the most abun-dant target compound, with range and mean ± SD concentrations of <0.0017–3.81 and 0.21 ± 0.63 mg kg−1ww. Based on log-log correlations of partition coefficients of hydrophobic compounds between fungal biomass/water (KD) and octanol/water (KOW), five species of fungi are suggested to produce DAME de novo versus bioaccu-mulation from forest runoff water. Full-scan mass spectra of some high-concentration specimens indicated thepresence of a Cl2DMB and a Cl3DMB, which could not be identified further due to lack of standards, anddrosophilin A (DA = 2,3,5,6-tetrachloro-4-methoxyphenol), the precursor to DAME. Tetrachloroveratrole(TeCV = 1,2,3,4-tetrachloro-5,6-DMB) was found in only a few specimens. This study supports our hypothesis offungi as a source of DAME in terrestrial runoff and indicates that other chlorinated secondary metabolites arepresent. DAME is widely distributed globally, and it would be good to have a better understanding of its sourcesand pathways as a marker of terrestrial organochlorines and their availability for bioaccumulation

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  • 44.
    Bidleman, Terry Frank
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Air Quality Processes Research Section, Environment Canada.
    Jantunen, L. M.
    Hung, H.
    Ma, J.
    Stern, G. A.
    Rosenberg, B.
    Racine, J.
    Annual cycles of organochlorine pesticide enantiomers in Arctic air suggest changing sources and pathways2015Ingår i: Atmospheric Chemistry And Physics, ISSN 1680-7316, E-ISSN 1680-7324, Vol. 15, nr 3, s. 1411-1420Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Air samples collected during 1994-2000 at the Canadian Arctic air monitoring station Alert (82 degrees 30'N, 62 degrees 20'W) were analysed by enantiospecific gas chromatography-mass spectrometry for alpha-hexachlorocyclohexane (alpha-HCH), trans-chlordane (TC) and cis-chlordane (CC). Results were expressed as enantiomer fractions (EF = peak areas of (+)/[(+) + (-)] enantiomers), where EFs = 0.5, <0.5 and >0.5 indicate racemic composition, and preferential depletion of (+) and (-) enantiomers, respectively. Long-term average EFs were close to racemic values for alpha-HCH (0.504 +/- 0.004, n = 197) and CC (0.505 +/- 0.004, n = 162), and deviated farther from racemic for TC (0.470 +/- 0.013, n = 165). Digital filtration analysis revealed annual cycles of lower alpha-HCH EFs in summer-fall and higher EFs in winter-spring. These cycles suggest volatilization of partially degraded alpha-HCH with EF < 0.5 from open water and advection to Alert during the warm season, and background transport of alpha-HCH with EF > 0.5 during the cold season. The contribution of sea-volatilized alpha-HCH was only 11% at Alert, vs. 32% at Resolute Bay (74.68 degrees N, 94.90 degrees W) in 1999. EFs of TC also followed annual cycles of lower and higher values in the warm and cold seasons. These were in phase with low and high cycles of the TC / CC ratio (expressed as F-TC = TC/(TC + CC)), which suggests greater contribution of microbially "weathered" TC in summer-fall versus winter-spring. CC was closer to racemic than TC and displayed seasonal cycles only in 1997-1998. EF profiles are likely to change with rising contribution of secondary emission sources, weathering of residues in the environment, and loss of ice cover in the Arctic. Enantiomer-specific analysis could provide added forensic capability to air monitoring programs.

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  • 45.
    Blomberg, David
    Umeå universitet, Teknisk-naturvetenskaplig fakultet, Kemi.
    Synthesis of β-turn and pyridine based peptidomimetics2007Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Despite the unfavorable pharmacokinetic properties associated with peptides, they are still of great interest in drug development due to a multitude of interesting biological functions. The development of peptidomimetics strives to maintain or improve the biological activity of a peptide concurrently with removing the unwanted properties. This thesis describes two synthetic approaches to peptidomimetics with particular emphasis on secondary structure mimetics.

    First the design, synthesis and evaluation of two beta-turn mimetics incorporated in the endorphin Leu-enkephalin is presented. The beta-turn mimetics were stabilized by replacement of the intramolecular hydrogen bond with an ethylene bridge, and the amide bond between Tyr and Gly was replaced with an ether linkage. Linear analogues of the two mimetics were also synthesized. The peptidomimetics and their linear analogues were evaluated in a competitive binding assay at two opiate receptors, my and delta. One of the cyclized beta-turn mimetics was found to be a delta receptor antagonist with an IC50 value of 160 nM.

    Second a synthetic strategy to a beta-strand mimetic using 2-fluoro-4-iodopyridine as scaffold is described. The synthesis involved a Grignard exchange reaction on the pyridine scaffold using an amino acid derivative as electrophile followed by an SNAr reaction using an amine as nucleophile. The synthesis of a tripeptidomimetic of Leu-Gly-Gly and attempts to introduce chiral building blocks at the C-terminal, as well as studies towards elongated mimetics are presented.

    Two additional studies deal with the synthesis of two classes of potential thrombin inhibitors based on the pyridine scaffold. The first class contain pyridine as central fragment (P2 residue) substituted with a para-amidinobenzylamine group as P1 residue and various benzoyl groups as P3 residues. Three potential thrombin inhibitors were synthesized and found to be microM inhibitors in an enzymatic assay. In the second class, the pyridine ring serves as P3 residue. This class also lacks a strongly basic group in the P1 position. A small library of eight compounds were synthesized and evaluated in the enzymatic assay. Unfortunately, these compounds lacked inhibitory activity.

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  • 46.
    Blomberg, David
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Fex, Tomas
    Xue, Yafeng
    Brickmann, Kay
    Kihlberg, Jan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. AstraZeneca.
    Design, synthesis and biological evaluation of thrombin inhibitors based on a pyridine scaffold2007Ingår i: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 5, nr 16, s. 2599-2605Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A series of 2,4- disubstituted pyridine derivatives has been designed, synthesised and evaluated as thrombin inhibitors. A Grignard exchange reaction was used to introduce various benzoyl substituents in position 4 of the pyridine ring, where they serve as P3 residues in binding to thrombin. In position 2 of the pyridine ring, a para-amidinobenzylamine moiety was incorporated as P1 residue by an SNAr reaction using ammonia as nucleophile followed by a reductive amination. A crystal structure obtained for one of the compounds in the active site of thrombin revealed that the basic amidine group of the inhibitor was anchored to Asp 189 at the bottom of the S1 pocket. A comparison with melagatran, bound in the active site of thrombin, revealed a good shape match but lack of hydrogen bonding possibilities in the S2 - S3 region for the thrombin inhibitors reported in this study.

  • 47. Borah, Raju Kumar
    et al.
    Raul, Prasanta Kumar
    Mahanta, Abhijit
    Shchukarev, Andrey
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Mikkola, Jyri-Pekka
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Industrial Chemistry & Reaction Engineering, Åbo Akademi University, Åbo-Turku, Finland.
    Thakur, Ashim Jyoti
    Copper Oxide Nanoparticles as a Mild and Efficient Catalyst for N-Arylation of Imidazole and Aniline with Boronic Acids at Room Temperature2017Ingår i: Synlett: Accounts and Rapid Communications in Synthetic Organic Chemistry, ISSN 0936-5214, E-ISSN 1437-2096, Vol. 28, nr 10, s. 1177-1182Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The present work describes the excellent catalytic activity of copper(II) oxide nanoparticles (NPs) towards N-arylation of aniline and imidazole at room temperature. The copper(II) oxide NPs were synthesized by a thermal refluxing technique and characterized by FT-IR spectroscopy; powder XRD, SEM, EDX, TEM, TGA, XPS, BET surface area analysis, and particle size analysis. The size of the NPs was found to be around 12 nm having a surface area of 164.180 m(2) g(-1). The catalytic system was also found to be recyclable and could be reused in subsequent catalytic runs without a significant loss of activity.

  • 48.
    Bourajoini, Hasna
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Kordas, K.
    Microelectronics and Materials Physics Laboratories, Department of Electrical Engineering, University of Oulu, University of Oulu, Finland.
    Larsson, W.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Mikkola, Jyri-Pekka
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Laboratory of Industrial Chemistry and Reaction Engineering, Process Chemistry Centre, Åbo Akademi University, Åbo-Turku, Finland.
    Synthesis of calcium manganese oxides - Unravelling the natures secrets2014Ingår i: 21st International Congress of Chemical and Process Engineering, CHISA 2014 and 17th Conference on Process Integration, Modelling and Optimisation for Energy Saving and Pollution Reduction, PRES 2014, Czech Society of Chemical Engineering , 2014, s. 371-371, artikel-id P3.95Konferensbidrag (Refereegranskat)
  • 49. Bui, Hue T B
    et al.
    Vo, Duy D
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Umeå universitet, Medicinska fakulteten, Umeå Centre for Microbial Research (UCMR).
    Chau, Yen N T
    Tu, Cuc T K
    Mai, Hieu V
    Truong, Kiet V
    Facile Synthesis of 4-Oxo-4H-quinolizine-2-carboxamide Derivatives2015Ingår i: Synthetic Communications, ISSN 0039-7911, E-ISSN 1532-2432, Vol. 45, nr 24, s. 2861-2868Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A facile synthetic method for the construction of 2-substituted-4-oxo-4H-quinolizine-based core structure has been successfully developed. The synthesis made use of a one-pot Stobbe condensation followed by cyclization starting from the commercially available 2-pyridinecarbaldehyde. The structure of the formed 4-oxo-4H-quinolizine-2-carboxylate was fully confirmed by mass spectra, H-1 NMR and C-13 NMR, correlation spectrography, heteronuclear multiple bond correlation, and heteronuclear single quantum coherence (HSQC) spectra. The ethyl carboxylate moiety was then further functionalized via direct aminolysis by a range of amines to afford the corresponding 4-oxo-4H-quinolizine-2-carboxamides 4a-i in moderate to good yields.

  • 50. Bui, Hue Thi Buu
    et al.
    Ha, Quy Thi Kim
    Oh, Won Keun
    Vo, Duy Duc
    Umeå universitet, Medicinska fakulteten, Umeå Centre for Microbial Research (UCMR). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Chau, Yen Nguyen Tram
    Tu, Cuc Thi Kim
    Pham, Em Canh
    Tran, Phuong Thao
    Tran, Loan Thi
    Mai, Hieu Van
    Microwave assisted synthesis and cytotoxic activity evaluations of new benzimidazole derivatives2016Ingår i: Tetrahedron Letters, ISSN 0040-4039, E-ISSN 1359-8562, Vol. 57, nr 8, s. 887-891Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Twelve new 2-quinolizinylbenzimidazole and 2-naphthalylbenzimidazole derivatives with various 5- and 6-positioned substituents (aza, H, CH3, Cl, NO2, NH2, OCH3), have been synthesized in moderate to excellent yields via the condensation of 4-oxo-4H-quinolizinecarbaldehyde or naphthalenecarbaldehyde with substituted o-phenylenediamines, o-nitroaniline, and 2,3-pyridinediamine using sodium metabisulfite or sodium hydrosulfite under microwave irradiation. The new benzimidazole derivatives were screened for their cytotoxic activity against the human breast cancer cell line (MCF-7). The results showed on one hand that 2-(substituted quinolizinyl)-1H-benzimidazoles (12bf) were less active (3–6 fold) than the positive control Tamoxifen (CC50 = 6.52 μM), and on the other hand, among the 2-(substituted naphthalyl)-1H-benzimidazoles series (13af), compounds 6,7,8-trimethoxy-3-(5-chloro-1H-benzo[d]imidazol-2-yl)naphthalen-1-ol (13c) (CC50 = 7.48 μM) and 6,7,8-trimethoxy-3-(5-methoxy-1H-benzo[d]imidazol-2-yl)naphthalen-1-ol (13f) (CC50 = 6.43 μM) were found to be as active as Tamoxifen.

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