Selektiv deblockierbare Diamino-D-Galactose-Scaffolds f��r die kombinatorische Synthese potentieller RNA-Liganden

Die Aufkl��rung der Schl��sselrolle der RNA in zahlreichen biologischen Prozessen, die sich aus ihren selektiven Wechselwirkungen mit anderen RNA-Molek��len, Proteinen, Peptiden bzw. Antibiotika ergibt, ist f��r die Wirkstoffforschung von gro��er Bedeutung. Die Aminoglycoside und Antibiotika, die durch eine Hemmung der Proteinbiosynthese schon seit l��ngerem bekannt sind, dienen als Leitstrukuren f��r die Synthese von weiteren Wirkstoffen. Die meisten Aminoglycosid-Antibiotika beinhalten Aminozucker, die mit dem rn2-Desoxystreptamin-Ger��st verbunden sind. Die stereochemische Vielfalt der Substitutionsstellen f��r Amino- und Hydroxylgruppen in diesem Ger��st und deren beschr��nkte konformative Flexibilit��t bieten vielseitige M��glichkeiten, um potenzielle RNA-Liganden so zu gestalten, dass es zu einer spezifischen Erkennung von RNA-Strukturen kommen kann. Ein wichtiger Vertreter dieser Antibiotika, Neomycin B, von dessen Struktur die Entwicklung des Diaminogalactose-Templates abgeleitet wurde, wurde in dieser Arbeit als Leitstruktur gew��hlt. Die Synthese von Diaminogalactose-Scaffolds wurde zun��chst in L��sung durchgef��hrt. Anschlie��end wurden die Bausteine 2 und 4 an einen polymeren Tr��ger gebunden.rnNach Pr��fung der orthogonalen Stabilit��t der Schutzgruppen wurde mit den Scaffolds 2 und 4 eine Bibliothek von 65 Verbindungen hergestellt. Mit 42 dieser Verbindungen wurden anschlie��end Zellassays im Rahmen des Sonderforschungsbereichs 579 (RNA-Liganden-Wechselwirkungen) durchgef��hrt, um ihre Cytotoxizit��t zu pr��fen. F��r einzelne Verbindungen konnten die optimalen Konzentrationen bestimmt werden, bei denen zuk��nftige Tests f��r die Tat/TAR Wechselwirkung ohne st��rende cytotoxische Effekte durchgef��hrt werden k��nnen.rn

Selektiv deblockierbare 2,6-Diamino-2,6-didesoxy-D-glucose-Scaffolds f��r die kombinatorische Synthese potentieller RNA-Liganden

Aminoglydosid-Antibiotika wie Neomycin B oder Cyclopeptid-Antibiotike wie Viaomycin sind daf��r bekannt, da�� sie selektiv an RNA binden k��nnen. Diese Interaktionen beruhen sowohl auf elektrostatischen Wechselwirkungen als auch auf H-Br��cken-Bindungen. Des weiteren ist die definierte r��umliche Anordnung von Donor- und Akzeptor-Resten in den Strukturen der RNA-Liganden wichtig f��r die Affinit��t. Eine M��glichkeit nat��rliche RNA-Liganden zu imitieren ist der Einsatz polyfunktioneller Template wie zum Beispiel das 2,6-Diamino-2,6-didesoxy-D-glucose-Scaffold. Mit Hilfe dieser Scaffolds k��nnen dann verschiedene positv geladene Reste und Donatoren sowie Akzeptoren f��r H-Br��cken-Bindungen oder auch Interkalatoren r��umlich definiert pr��sentiert werden. F��r die unabh��ngige Funktionalisierung einer jeden Position ist ein Satz orthogonal stabiler Schutzgruppen n��tig, wobei eine Hydroxylguppe durch einen Anker ersetzt wird, der eine Anbindung des Scaffolds an einen polymeren Tr��ger erm��glicht. Das neu entwickelte 2,6-Diamino-2,6-didesoxy-D-glucose-Scaffold ist das erste Monosaccharid-Templat, das in allen f��nf Positionen mit orthogonal stabilen Schutzgruppen blockiert ist. Alle Positionen k��nne in beliebiger Reihenfolge selektiv deblockiert und anschlie��end derivatisiert werden. Das Scaffold kann mit Aminos��uren, Guanidinen oder Interkalatoren umgesetzt werden, um so nat��rlich vorkommende RNA-bindende Aminoglycoside oder Peptide zu imitieren. Aufbauend auf diesem Monosaccharid-Templat wurde eine Bibliothek von ��ber 100 potentiellen RNA-Liganden synthetisiert, die im Rahmen des Sonderforschungsbereichs 579 (RNA-Liganden-Wechselwirkungen) in Zellassays auf ihre F��higkeit zur Hemmung der Tat/TAR-Wechselwirkung untersucht wurden, wobei bis jetzt 9 Verbindungen mit einer hemmenden Wirkung im micromolaren Bereich gefunden wurden.

Dynamics of carbohydrate��lectin interaction The interaction p-nitrophenyl-����-D-galactose with a lectin from Ricinius communis

L&in-induced agglutination is a complex process determined by several factprs such as the nature of lectin (valency, binding constant) the properties of cell membrane (fluidity, distribution of lectin receptor sites) and the metabolic state of the cell (microvilli, microtubules, microfilament) [l-3].

Synthesis of Specifically Deuteriated Derivatives of D-Galactose and D-Galactosamine

Simple and convenient methods for introducing deuterium label at C-3 and C-6 position of N-acetyl-D-galactosamine and D-galactose, respectively, are described. For the synthesis of 2-acetamido-2-deoxy-D-3-[2H] galactopyranose, benzyl 2-acetamido-2-deoxy-4,6-O-benzylidene-agr-D-galactopyranoside was oxidized with dimethyl sulfoxide- acetic anhydride and the product was reduced with sodium borodeuteride to introduce the deuterium at C-3. After benzylidene reduction, the mixture was subjected to hydrogenolysis and purified by column chromatography. 1,2:3,4-di-O-isopropylidene-agr-D-galactopyranoside was oxidized followed by reduction with sodium borodeuteride and deprotection to yield D-6-[2H] galactose.

Computer modelling approach to study the modes of binding of alpha- and beta-anomers of D-galactose, D-fucose and D-glucose to L-arabinose-binding protein

The modes of binding of alpha- and beta-anomers of D-galactose, D-fucose and D-glucose to L-arabinose-binding protein (ABP) have been studied by energy minimization using the low resolution (2.4 A) X-ray data of the protein. These studies suggest that these sugars preferentially bind in the alpha-form to ABP, unlike L-arabinose where both alpha- and beta-anomers bind almost equally. The best modes of binding of alpha- and beta-anomers of D-galactose and D-fucose differ slightly in the nature of the possible hydrogen bonds with the protein. The residues Arg 151 and Asn 232 of ABP from bidentate hydrogen bonds with both L-arabinose and D-galactose, but not with D-fucose or D-glucose. However in the case of L-arabinose, Arg 151 forms hydrogen bonds with the hydroxyl group at the C-4 atom and the ring oxygen, whereas in case of D-galactose it forms bonds with the hydroxyl groups at the C-4 and C-6 atoms of the pyranose ring. The calculated conformational energies also predict that D-galactose is a better inhibitor than D-fucose and D-glucose, in agreement with kinetic studies. The weak inhibitor D-glucose binds preferentially to one domain of ABP leading to the formation of a weaker complex. Thus these studies provide information about the most probable binding modes of these sugars and also provide a theoretical explanation for the observed differences in their binding affinities.

Comparative Characterisation of 3-D Hydroxyapatite Scaffolds Developed via Replication of Synthetic Polymer Foams and Natural Marine Sponges

The production of complex inorganic forms, based on naturally occurring scaffolds offers an exciting avenue for the construction of a new generation of ceramic-based bone substitute scaffolds. The following study reports an investigation into the architecture (porosity, pore size distribution, pore interconnectivity and permeability), mechanical properties and cytotoxic response of hydroxyapatite bone substitutes produced using synthetic polymer foam and natural marine sponge performs. Infiltration of polyurethane foam (60 pores/in2) using a high solid content (80wt %), low viscosity (0.126Pas) hydroxyapatite slurry yielded 84-91% porous replica scaffolds with pore sizes ranging from 50��m - 1000��m (average pore size 577��m), 99.99% pore interconnectivity and a permeability value of 46.4 x10-10m2. Infiltration of the natural marine sponge, Spongia agaricina, yielded scaffolds with 56- 61% porosity, with 40% of pores between 0-50��m, 60% of pores between 50-500��m (average pore size 349 ��m), 99.9% pore interconnectivity and a permeability value of 16.8 x10-10m2. The average compressive strengths and compressive moduli of the natural polymer foam and marine sponge replicas were 2.46��1.43MPa/0.099��0.014GPa and 8.4��0.83MPa /0.16��0.016GPa respectively. Cytotoxic response proved encouraging for the HA Spongia agaricina scaffolds; after 7 days in culture medium the scaffolds exhibited endothelial cells (HUVEC and HDMEC) and osteoblast (MG63) attachment, proliferation on the scaffold surface and penetration into the pores. It is proposed that the use of Spongia agaricina as a precursor material allows for the reliable and repeatable production of ceramic-based 3-D tissue engineered scaffolds exhibiting the desired architectural and mechanical characteristics for use as a bone 3 scaffold material. Moreover, the Spongia agaricina scaffolds produced exhibit no adverse cytotoxic response.

Osteogenic cell response to 3-D hydroxyapatite scaffolds developed via replication of natural marine sponges

Bone tissue engineering may provide an alternative to autograft, however scaffold optimisation is required to maximize bone ingrowth. In designing scaffolds, pore architecture is important and there is evidence that cells prefer a degree of non-uniformity. The aim of this study was to compare scaffolds derived from a natural porous marine sponge (Spongia agaricina) with unique architecture to those derived from a synthetic polyurethane foam. Hydroxyapatite scaffolds of 1 cm3 were prepared via ceramic infiltration of a marine sponge and a polyurethane (PU) foam. Human foetal osteoblasts (hFOB) were seeded at 1x105 cells/scaffold for up to 14 days. Cytotoxicity, cell number, morphology and differentiation were investigated. PU-derived scaffolds had 84-91% porosity and 99.99% pore interconnectivity. In comparison marine sponge-derived scaffolds had 56-61% porosity and 99.9% pore interconnectivity. hFOB studies showed that a greater number of cells were found on marine sponge-derived scaffolds at than on the PU scaffold but there was no significant difference in cell differentiation. X-ray diffraction (XRD) and inductively coupled plasma mass spectrometry (ICP-MS) showed that Si ions were released from the marine-derived scaffold. In summary, three dimensional porous constructs have been manufactured that support cell attachment, proliferation and differentiation but significantly more cells were seen on marine-derived scaffolds. This could be due both to the chemistry and pore architecture of the scaffolds with an additional biological stimulus from presence of Si ions. Further in vivo tests in orthotopic models are required but this marine-derived scaffold shows promise for applications in bone tissue engineering.

The key enzyme in galactose metabolism, UDP-galactose-4-epimerase, affects cell-wall integrity and morphology in Candida albicans even in the absence of galactose

The enzyme UDP-galactose-4-epimerase (GAL10) catalyzes a key step in galactose metabolism converting UDP-galactose to UDPglucose which then can get metabolized through glycolysis and TCA cycle thus allowing the cell to use galactose as a carbon and energy source. As in many fungi, a functional homolog of GAL10 exists in Candida albicans. The domainal organization of the homologs from Saccharomyces cerevisiae and C albicans show high degree of homology having both mutarotase and an epimerase domain. The former is responsible for the conversion of beta-D-galactose to alpha-D-galactose and the hitter for epimerization of UDP-galactose to UDP-glucose. Absence of C albicans GAL10 (CaGAL10) affects cell-wall organization, oxidative stress response, biofilm formation and filamentation. Cagal10 mutant cells tend to flocculate extensively as compared to the wild-type cells. The excessive filamentation in this mutant is reflected in its irregular and wrinkled colony morphology. Cagal10 strain is more susceptible to oxidative stress when tested in presence of H2O2. While the S. cerevsiae GAL10 (ScGAL10), essential for survival in the presence of galactose, has not been reported to have defects in the absence of galactose, the C albicans homolog shows these phenotypes during growth in the absence of galactose. Thus a functional CaGal10 is required not only for galactose metabolism but also for normal hyphal morphogenesis, colony morphology, maintenance of cell-wall integrity and for resistance to oxidative stress even in the absence of galactose. (c) 2006 Elsevier Inc. All rights reserved.

Diabetic-like loss of corneal sensitivity in the 50% galactose fed rat is ameliorated with topical administration of an aldose reductase inhibitor

Purpose: To investigate the temporal course of corneal sensitivity loss & the role of aldose reductase inhibitors (ARI) in an animal model of diabetic ocular complications. Methods: Weanling male S-D rats were randomly grouped to received ad libitum water & diet consisting of Purina (#5001) w/ either: 50% starch (CON,n=15) or 50% D-galactose (GAL,n=30). Half the galactosemic rats (ARI,n=15) received topical 0.25% CT-112 (3x daily, 20��l, Senju Pharmaceutical Co., Japan). Control & remaining half of the galactosemic animals received equivalent doses of saline eyedrops. Rats were restrained w/o medication during sensitivity measurements conducted w/ a Cochet-Bonnet Aesthesiometer mounted on a micromanipulator. The end of the filament (0.012mm dia.), which applied a mean pressure of 0.96 g/mm perpendicular to the corneal surface at center, was in the plane of focus of a slit-lamp biomicroscope. Measurements were conducted by two investigators which were masked to the treatment group. The average blink-responses from 10 consecutive stimuli to each cornea were expressed as a percent. Results: Mean (��SD) baseline corneal sensitivity in all groups were similar (CON 73%��11, GAL 71%��15, ARI 74%��16). Corneal sensitivity in the galactosemic rat was decreased (p

Synthese und Konformationsanalyse von Glycopeptiden aus der homophilen Erkennungsregion des LI-Cadherins

��ber die Sekund��rstruktur von LI-Cadherin ist bislang wenig bekannt. Es gibt keine R��ntgenanalysen und keine NMR-spektroskopische Untersuchungen. Man kann nur aufgrund der Sequenzhomologien zu den bereits untersuchten klassischen Cadherinen vermuten, da�� im LI-Cadherin ��hnliche Verh��ltnisse in der entscheidenden Wechselwirkungsdom��ne vorliegen. In Analogie zum E-Cadherin wurde angenommen, da�� es im LI-Cadherin eine ���homophile Erkennungsregion��� gibt, die in einer typischen beta-Turn-Struktur mit anschlie��enden Faltblattbereichen vorliegen sollte. Um den Einflu�� verschiedener Saccharid-Antigene auf die Turn-Bildung zu untersuchen, wurden im ersten Teil der vorliegenden Arbeit verschiedene Saccharid-Antigen-Bausteine synthetisiert, mit denen dann im zweiten Teil der Arbeit durch sequentielle Festphasensynthese entsprechende Glycopeptidstrukturen aus dieser Region des LI-Cadherins aufgebaut wurden. Zur Synthese s��mtlicher Antigen-Bausteine ging man von D-Galactose aus, die ��ber das Galactal und eine Azidonitratisierung in vier Stufen zum Azidobromid umgesetzt wurde. In einer Koenigs-Knorr-Glycosylierung wurde dieses dann auf die Seitenkette eines gesch��tzten Serin-Derivats ��bertragen. Reduktion und Schutzgruppenmanipulationen lieferten den TN Antigen-Baustein. Ein TN-Antigen-Derivat war Ausgangspunkt f��r die Synthesen der weiteren Glycosyl-Serin-Bausteine. So lie�� sich mittels der Helferich-Glycosylierung der T Antigen-Baustein herstellen, und der STN-Antigen-Baustein wurde durch eine Sialylierungsreaktion und weitere Schutzgruppenmanipulationen erhalten. Da die Route ��ber das T-Antigen-Derivat den Hauptsyntheseweg f��r die weiteren komplexeren Antigene bildete, wurden verschiedene Schutzgruppenmuster getestet. Darauf aufbauend lie��en sich durch verschiede Glycosylierungsreaktionen und Schutzgruppenmanipulationen der komplexe (2->6)-ST-Antigen-Baustein, (2->3)-Sialyl-T- und Glycophorin-Antigen-Baustein synthetisieren. Im n��chsten Abschnitt der Doktorarbeit wurden die synthetisierten Saccharid-Antigen-Serin-Konjugate in Festphasen-Glycopeptidsynthesen eingesetzt. Zun��chst wurde ein mit dem TN Antigen glycosyliertes Tricosapeptid hergestellt. Mittels NMR-spektroskopischen Untersuchungen und folgenden Energieminimierungsberechnungen konnte eine dreidimensionale Struktur ermittelt werden. Die Peptidsequenz des Turn-bildenden Bereichs wurde f��r die folgenden Synthesen gew��hlt. Die Abfolge der einzelnen Reaktionsschritte f��r die Festphasensynthesen mit den verschiedenen Saccharid-Antigen-Bausteinen war ��hnlich. Insgesamt verlief die Festphasen-Glycopeptidsynthese in starker Abh��ngigkeit vom sterischen Anspruch der Saccharid-Bausteine. S��mtliche so synthetisierten Glycopeptide wurden NMR spektroskopisch charakterisiert und mittels NOE-Experimenten hinsichtlich ihrer Konformation untersucht. Durch diese Bestimmung der r��umlichen Protonen-Protonen-Kontakte konnte mittels Rechnungen zur Energieminimierung, basierend auf MM2 Kraftfeldern, eine dreidimensionale Struktur f��r die Glycopeptide postuliert werden. S��mtliche synthetisierten Glycopeptide weisen eine schleifenartige Konformation auf. Der Einflu�� der Saccharid-Antigene ist unterschiedlich, und l����t sich in drei Gruppen einteilen.

Conservation of the RNA Transport Machineries and Their Coupling to Translation Control across Eukaryotes

Restriction of proteins to discrete subcellular regions is a common mechanism to establish cellular asymmetries and depends on a coordinated program of mRNA localization and translation control. Many processes from the budding of a yeast to the establishment of metazoan embryonic axes and the migration of human neurons, depend on this type of cell polarization. How factors controlling transport and translation assemble to regulate at the same time the movement and translation of transported mRNAs, and whether these mechanisms are conserved across kingdoms is not yet entirely understood. In this review we will focus on some of the best characterized examples of mRNA transport machineries, the "yeast locasome" as an example of RNA transport and translation control in unicellular eukaryotes, and on the Drosophila Bic-D/Egl/Dyn RNA localization machinery as an example of RNA transport in higher eukaryotes. This focus is motivated by the relatively advanced knowledge about the proteins that connect the localizing mRNAs to the transport motors and the many well studied proteins involved in translational control of specific transcripts that are moved by these machineries. We will also discuss whether the core of these RNA transport machineries and factors regulating mRNA localization and translation are conserved across eukaryotes.

Crystal structure of yeast initiation factor 4A, a DEAD-box RNA helicase

The eukaryotic translation initiation factor 4A (eIF4A) is a member of the DEA(D/H)-box RNA helicase family, a diverse group of proteins that couples an ATPase activity to RNA binding and unwinding. Previous work has provided the structure of the amino-terminal, ATP-binding domain of eIF4A. Extending those results, we have solved the structure of the carboxyl-terminal domain of eIF4A with data to 1.75 ��� resolution; it has a parallel ��-�� topology that superimposes, with minor variations, on the structures and conserved motifs of the equivalent domain in other, distantly related helicases. Using data to 2.8 ��� resolution and molecular replacement with the refined model of the carboxyl-terminal domain, we have completed the structure of full-length eIF4A; it is a ���dumbbell��� structure consisting of two compact domains connected by an extended linker. By using the structures of other helicases as a template, compact structures can be modeled for eIF4A that suggest (i) helicase motif IV binds RNA; (ii) Arg-298, which is conserved in the DEA(D/H)-box RNA helicase family but is absent from many other helicases, also binds RNA; and (iii) motifs V and VI ���link��� the carboxyl-terminal domain to the amino-terminal domain through interactions with ATP and the DEA(D/H) motif, providing a mechanism for coupling ATP binding and hydrolysis with conformational changes that modulate RNA binding.

Electrochemical RNA genosensors for toxic algal species: enhancing selectivity and sensitivity

Harmful algal blooms (HABs) are becoming more frequent as climate changes, with tropical species moving northward. Monitoring programs detecting the presence of toxic algae before they bloom are of paramount importance to protect aquatic ecosystems, aquaculture, human health and local economies. Rapid and reliable species identification methods using molecular barcodes coupled to biosensor detection tools have received increasing attention over the past decade as an alternative to the impractical standard microscopic counting-based techniques. This work reports on a PCR amplification-free electrochemical genosensor for the enhanced selective and sensitive detection of RNA from multiple Mediterranean toxic algal species. For a sandwich hybridization (SHA), we designed longer capture and signal probes for more specific target discrimination against a single base-pair mismatch from closely related species and for reproducible signals. We optimized experimental conditions, viz., minimal probe concentration in the SHA on a screen-printed gold electrode and selected the best electrochemical mediator. Probes from 13 Mediterranean dinoflagellate species were tested under optimized conditions and the format further tested for quantification of RNA from environmental samples. We not only enhanced the selectivity and sensitivity of the state-of-the-art toxic algal genosensors but also increased the repertoire of toxic algal biosensors in the Mediterranean, towards an integral and automatic monitoring system.

Electrochemical RNA genosensors for toxic algal species: enhancing selectivity and sensitivity

Harmful algal blooms (HABs) are becoming more frequent as climate changes, with tropical species moving northward. Monitoring programs detecting the presence of toxic algae before they bloom are of paramount importance to protect aquatic ecosystems, aquaculture, human health and local economies. Rapid and reliable species identification methods using molecular barcodes coupled to biosensor detection tools have received increasing attention over the past decade as an alternative to the impractical standard microscopic counting-based techniques. This work reports on a PCR amplification-free electrochemical genosensor for the enhanced selective and sensitive detection of RNA from multiple Mediterranean toxic algal species. For a sandwich hybridization (SHA), we designed longer capture and signal probes for more specific target discrimination against a single base-pair mismatch from closely related species and for reproducible signals. We optimized experimental conditions, viz., minimal probe concentration in the SHA on a screen-printed gold electrode and selected the best electrochemical mediator. Probes from 13 Mediterranean dinoflagellate species were tested under optimized conditions and the format further tested for quantification of RNA from environmental samples. We not only enhanced the selectivity and sensitivity of the state-of-the-art toxic algal genosensors but also increased the repertoire of toxic algal biosensors in the Mediterranean, towards an integral and automatic monitoring system.