ChemBioChem

Cover image for ChemBioChem

June 6, 2005

Volume 6, Issue 6

Pages 933–1134

    1. Cover Picture: Quantum Dots Protected with Tiopronin: A New Fluorescence System for Cell-Biology Studies (ChemBioChem 6/2005) (page 933)

      Jesus M. de la Fuente, Manuela Fandel, Catherine C. Berry, Mathis Riehle, Leroy Cronin, Gregor Aitchison and Adam S. G. Curtis

      Version of Record online: 30 MAY 2005 | DOI: 10.1002/cbic.200590019

      The cover picture shows the synthesis scheme for water-soluble CdS nanocrystals that are protected with tiopronin, by using a straightforward and economical methodology. The chemical functionality of this capping agent provides a very high stability for the nanocrystals and has allowed us to functionalize quantum dots (QDs) with a HIV-1 Tat protein-derived peptide sequence. These nanocrystals are biocompatible with hTERT-BJ1 human fibroblasts. Also shown is an overlay of the fluorescence (green; bottom left) and phase contrast images of hTERT-BJ1 human fibroblasts incubated with CdS@tiopronin-Tat. The functionalization of QDs with the translocation peptide permits them to penetrate the cell membrane and target the nucleus. Detailed information about the synthesis, functionalization and biocompatibility of these nanomaterials is reported by J. M. de la Fuente et al. on p. 989 ff.

    2. Diatom/Copepod Interactions in Plankton: The Indirect Chemical Defense of Unicellular Algae (pages 946–959)

      Georg Pohnert

      Version of Record online: 10 MAY 2005 | DOI: 10.1002/cbic.200400348

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      Watery arms race: Can secondary metabolites from microalgae function as a chemical defense in open water? The rapid release of α,β,γ,δ-unsaturated aldehydes by wounded diatoms (left) is discussed as an indirect chemical defense of these unicellular algae. These metabolites are not directly effective against the herbivores but rather reduce the number of their offspring and interfere with their development (right).

    3. Utilizing the Power of Microbial Genetics to Bridge the Gap Between the Promise and the Application of Marine Natural Products (pages 960–978)

      J. L. Fortman and David H. Sherman

      Version of Record online: 6 MAY 2005 | DOI: 10.1002/cbic.200400428

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      Getting away from the ocean: This review highlights advances in the field of cloning and heterologous expression of microbial secondary-metabolite genes and how these advances may be applied to marine systems to yield reliable and renewable sources of complex bioactive natural products, such as bryostatins 1 (1).

    4. Annonaceous Acetogenins: The Hydroxyl Groups and THF Rings Are Crucial Structural Elements for Targeting the Mitochondria, Demonstration with the Synthesis of Fluorescent Squamocin Analogues (pages 979–982)

      Séverine Derbré, Gaël Roué, Erwan Poupon, Santos A. Susin and Reynald Hocquemiller

      Version of Record online: 28 APR 2005 | DOI: 10.1002/cbic.200400396

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      Track of acetogenins in living cells. Two fluorescent acetogenin probes have been prepared from natural squamocin to clearly demonstrate the crucial role of the polyoxygenated central part as a locus for mitochondria targeting. Reliable synthetic tools, such as radical decarboxylation and catalytic triazole formation, were exploited for the design of the molecules.

    5. Bacterial Cell Penetration by β3-Oligohomoarginines: Indications for Passive Transfer through the Lipid Bilayer (pages 982–985)

      Birgit Geueke, Kenji Namoto, Irina Agarkova, Jean-Claude Perriard, Hans-Peter E. Kohler and Dieter Seebach

      Version of Record online: 25 APR 2005 | DOI: 10.1002/cbic.200400394

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      Uptake of fluorescently labeled β-oligohomoarginines amides by bacteria was examined with confocal laser scanning microscopy and fluorescence quenching assays. The results indicate that microorganisms, which have no endocytotic mechanisms for transmembrane transport, internalize the peptides through an unidentified alternative pathway (see micrograph).

    6. Development of a Lectin Microarray for the Rapid Analysis of Protein Glycopatterns (pages 985–989)

      Kanoelani T. Pilobello, Lakshmipriya Krishnamoorthy, Deepika Slawek and Lara K. Mahal

      Version of Record online: 30 MAR 2005 | DOI: 10.1002/cbic.200400403

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      Glycosylation plays a role in a wide variety of biological processes including bacterial pathogenesis, tumor cell metastasis and inflammation. Despite the importance of carbohydrates, few techniques exist for the rapid and systematic evaluation of protein glycosylation. This paper describes a lectin microarray for the rapid analysis of protein glycopatterns (see scheme).

    7. Quantum Dots Protected with Tiopronin: A New Fluorescence System for Cell-Biology Studies (pages 989–991)

      Jesus M. de la Fuente, Manuela Fandel, Catherine C. Berry, Mathis Riehle, Leroy Cronin, Gregor Aitchison and Adam S. G. Curtis

      Version of Record online: 25 APR 2005 | DOI: 10.1002/cbic.200500071

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      Water-soluble CdS nanocrystals functionalized with tiopronin have been developed by using a straightforward and economical methodology. These quantum dots are biocompatible with hTERT-BJ1 human fibroblasts. The functionalization of the quantum dots with a translocation peptide has allowed them to penetrate the cell membrane and target the nucleus (see scheme).

    8. 2′/3′-O-peptidyl Adenosine as a General Base Catalyst of its Own External Peptidyl Transfer: Implications for the Ribosome Catalytic Mechanism (pages 992–996)

      Mohamed M. Changalov, Gabriela D. Ivanova, Miroslav A. Rangelov, Parag Acharya, Sandipta Acharya, Noriaki Minakawa, András Földesi, Ivanka B. Stoineva, Vihra M. Yomtova, Christo D. Roussev, Akira Matsuda, Jyoti Chattopadhyaya and Dimiter D. Petkov

      Version of Record online: 5 APR 2005 | DOI: 10.1002/cbic.200400349

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      A physical organic study reveals general base catalysis by the 2′-oxyanion of the peptidyl adenosine ethanolysis; this implies a proton-shuttle role for the 2′-OH of peptidyl tRNA A76 in the ribosome substrate-assisted catalytic mechanism.

    9. From Virtual to Real Screening for D3 Dopamine Receptor Ligands (pages 997–999)

      Evgeny Byvatov, Britta C. Sasse, Holger Stark and Gisbert Schneider

      Version of Record online: 25 APR 2005 | DOI: 10.1002/cbic.200400400

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      Even in the absence of receptor-structure information, iterative virtual screening cycles with support vector machines (SVM) offer a rapid way to identify novel leads with minimal experimental effort. First, an SVM is trained for prediction of D3 receptor-selective ligands. Based on the prediction of this virtual filter, compounds are tested for binding affinity at D2 and D3 receptors. Second, a similarity search is performed with the most promising candidate from round one. Four out of five compounds from the final hit list exhibited nanomolar affinity at the D3 receptor including a novel scaffold structure. The Ki value of the best molecule (1) was 40±6 nM.

    10. Regulating Enzyme Activities in a Multiple-Enzyme Complex (pages 999–1002)

      Yi Chen and Chengde Mao

      Version of Record online: 25 APR 2005 | DOI: 10.1002/cbic.200400445

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      Off and on. This paper reports a general strategy (strand displacement) to isothermally, individually, and reversibly regulate each DNA enzyme in a multiple-enzyme complex. The graph shows the time course of the codigestion of two substrate strands (Sa and Sb) with the sequential addition of inhibitor (I) and remover (R) strands.

    11. Identification of Novel Anthrax Lethal Factor Inhibitors Generated by Combinatorial Pictet–Spengler Reaction Followed by Screening in situ (pages 1002–1006)

      Mehdi M. D. Numa, Lac V. Lee, Che-Chang Hsu, Kristen E. Bower and Chi-Huey Wong

      Version of Record online: 6 MAY 2005 | DOI: 10.1002/cbic.200500009

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      Potent library. Anthrax lethal factor (LF) is a zinc-dependent metalloprotease involved in the rapid development of the deadly infection caused by Bacillus anthracis. Blocking its action is a plausible method to mitigate the deleterious effects of late stage infection. We report the inhibition of LF by tetrahydro-isoquinoline polyphenolic compounds, such as 5 a, which were identified by screening a combinatorial library that was generated by Pictet–Spengler reaction. We also report the identification of commercially available polyphenolic inhibitors against LF.

    12. New Methods for the Generation of Carbohydrate Arrays on Glass Slides and Their Evaluation (pages 1007–1015)

      Moritz B. Biskup, Jan U. Müller, Ralf Weingart and Richard R. Schmidt

      Version of Record online: 28 APR 2005 | DOI: 10.1002/cbic.200400300

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      On the spot attachment. New types of carbohydrate arrays were obtained by reductive amination or PyBOP-mediated amide-bond formation. The covalency and the stability of the linkage were investigated by using fluorescence-labeled 1 a and 1 b. Carbohydrate arrays of these types were employed to study the interactions of carbohydrate epitopes with lectins.

    13. Biosynthetic Precursors of Fungal Pyrrolizidines, the Loline Alkaloids (pages 1016–1022)

      Jimmy D. Blankenship, Justin B. Houseknecht, Sitaram Pal, Lowell P. Bush, Robert B. Grossman and Christopher L. Schardl

      Version of Record online: 28 APR 2005 | DOI: 10.1002/cbic.200400327

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      Loline origins. Loline alkaloids are fungal pyrrolizidines that are synthesized by a pathway distinct from that of plant pyrrolizidines (necines). Results from feeding experiments with isotopically labeled precursors suggest that lolines are derived from L-proline and the aminopropyl moiety of L-homoserine, which were apparently linked by a novel N-alkylation reaction (see scheme).

      Corrected by:

      Corrigendum: Biosynthetic Precursors of Fungal Pyrrolizidines, the Loline Alkaloids

      Vol. 7, Issue 3, 404, Version of Record online: 1 MAR 2006

    14. Kanamycin A-Derived Cationic Lipids as Vectors for Gene Transfection (pages 1023–1033)

      Matthieu Sainlos, Michelle Hauchecorne, Noufissa Oudrhiri, Samia Zertal-Zidani, Abderrahim Aissaoui, Jean-Pierre Vigneron, Jean-Marie Lehn and Pierre Lehn

      Version of Record online: 10 MAY 2005 | DOI: 10.1002/cbic.200400344

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      Aminoglycosides for nonviral gene delivery. A new class of synthetic vectors for gene delivery, by using an aminoglycoside—kanamycin A—as cationic headgroup, has been characterised with regard to its members' physicochemical properties and their transfection efficiencies. The various data collected have been exploited to provide insights into the key factors influencing their transfection activity.

    15. “Parallel” and “Antiparallel Tail-Clamps” Increase the Efficiency of Triplex Formation with Structured DNA and RNA Targets (pages 1034–1042)

      Anna Nadal, Ramon Eritja, Teresa Esteve and Maria Pla

      Version of Record online: 4 MAY 2005 | DOI: 10.1002/cbic.200400358

      Hold on! The secondary structure of the target might have an inhibitory effect on triplex formation with clamp molecules. We describe a new type of clamp: “tail-clamps” (both parallel and antiparallel) that efficiently forms triple helices with structured DNA and RNA targets and allows the capture and recovery of target sequences.

    16. Chemical Synthesis of Triple-Labelled Three-Helix Bundle Binding Proteins for Specific Fluorescent Detection of Unlabelled Protein (pages 1043–1050)

      Torun Engfeldt, Björn Renberg, Harry Brumer, Per Åke Nygren and Amelie Eriksson Karlström

      Version of Record online: 4 MAY 2005 | DOI: 10.1002/cbic.200400388

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      Make your mark. Three-helix bundle proteins with three different incorporated reporter groups (see graphic) have been prepared by solid-phase peptide synthesis by using an orthogonal protection scheme. The synthetic proteins were used as fluorescent biosensors for the detection of human IgG and IgA.

    17. Creating Space for Large Secondary Alcohols by Rational Redesign of Candida antarctica Lipase B (pages 1051–1056)

      Anders O. Magnusson, Johanna C. Rotticci-Mulder, Alberto Santagostino and Karl Hult

      Version of Record online: 10 MAY 2005 | DOI: 10.1002/cbic.200400410

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      Enlarged pocket fits larger substrates. The size of the stereospecificity pocket was increased by changing Trp104 for smaller amino acids. An Ala (pale green) at this position liberated the volume in dark green. The Trp104Ala mutant had a specificity constant of 830 s−1M−1 towards nonan-5-ol, 5500 times larger than that of the wild-type.

    18. Examples of Peptide–Peptoid Hybrid Serine Protease Inhibitors Based on the Trypsin Inhibitor SFTI-1 with Complete Protease Resistance at the P1[BOND]P1′ Reactive Site (pages 1057–1061)

      Maciej Stawikowski, Roma Stawikowska, Anna Jaśkiewicz, Ewa Zabłotna and Krzysztof Rolka

      Version of Record online: 10 MAY 2005 | DOI: 10.1002/cbic.200400412

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      Catch me if you can. By incorporating N-substituted glycine residues (peptoid monomers, shown) at the P1 position of sunflower trypsin inhibitor (SFTI-1), we have obtained strong, competitive and selective peptide–peptoid hybrid serine protease inhibitors that are completely protease resistant at their P1[BOND]P1′ reactive sites.

    19. Multiplex-PCR-Based Recombination as a Novel High-Fidelity Method for Directed Evolution (pages 1062–1067)

      Thorsten Eggert, Susanne Aileen Funke, Nalam M. Rao, Priyamvada Acharya, Holger Krumm, Manfred T. Reetz and Karl-Erich Jaeger

      Version of Record online: 6 MAY 2005 | DOI: 10.1002/cbic.200400417

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      Directed evolution has matured during the last decade to become a key technology in the field of molecular enzyme engineering. We present a novel in vitro recombination method called multiplex-PCR-based recombination (MUPREC) which can be used to recombine single point mutations previously generated by error-prone PCR or complete saturation mutagenesis (see graphic).

    20. Chemoenzymatic Synthesis of HIV-1 gp41 Glycopeptides: Effects of Glycosylation on the Anti-HIV Activity and α-Helix Bundle-Forming Ability of Peptide C34 (pages 1068–1074)

      Lai-Xi Wang, Haijing Song, Shuwen Liu, Hong Lu, Shibo Jiang, Jiahong Ni and Hengguang Li

      Version of Record online: 10 MAY 2005 | DOI: 10.1002/cbic.200400440

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      Glycosylation and HIV-1. Chemoenzymatic synthesis of glycoforms of HIV-1 gp41 C34 peptide (see figure), a region essential for HIV-1 membrane fusion, and the effects of glycosylation on the inhibitory activity and the helix-bundle forming ability of the gp41 C-peptide are described. The results have valuable implications for both HIV-1 inhibitor design and vaccine development.

    21. Discrimination of Single-Nucleotide Alterations by G-Specific Fluorescence Quenching (pages 1075–1081)

      Chikara Dohno and Isao Saito

      Version of Record online: 25 APR 2005 | DOI: 10.1002/cbic.200400325

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      Minor groove/helix interior switching: A pyrenyl group attached at the sugar C4′-position of thymidine (4′PyT) intercalates within the DNA helix in mismatched duplexes while locating to the minor groove in matched duplexes. Oligodeoxynucleotides containing 4′PyT exhibit enhanced fluorescence only upon hybridization with their fully complementary targets, since the pyrenyl fluorophore is then positioned away from the quenching guanine moieties in the DNA helix.

    22. PIGA (N,N-Di-n-butyl-5-chloro-2-(4-chlorophenyl)indol-3-ylglyoxylamide), a New Mitochondrial Benzodiazepine-Receptor Ligand, Induces Apoptosis in C6 glioma Cells (pages 1082–1088)

      Beatrice Chelli, Leonardo Rossi, Eleonora Da Pozzo, Barbara Costa, Francesca Spinetti, Mariarosa Rechichi, Alessandra Salvetti, Annalisa Lena, Francesca Simorini, Renato Vanacore, Fabrizio Scatena, Federico Da Settimo, Vittorio Gremigni and Claudia Martini

      Version of Record online: 10 MAY 2005 | DOI: 10.1002/cbic.200400350

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      Therapeutic potential against glial tumours. The selective mBzR ligand PIGA induced apoptosis in rat C6 glioma cells, dissipated mitochondrial transmembrane potential and caused cytosolic accumulation of cytochrome c. Characteristic features of apoptotic cell death, such as caspase-3 activation and DNA fragmentation, were detected in PIGA-treated cells.

    23. Domain-Selective Ligand-Binding Modes and Atomic Level Pharmacophore Refinement in Angiotensin I Converting Enzyme (ACE) Inhibitors (pages 1089–1103)

      Andreas G. Tzakos and Ioannis P. Gerothanassis

      Version of Record online: 10 MAY 2005 | DOI: 10.1002/cbic.200400386

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      Tailoring the molecular key to its biological lock: the case of ACE inhibitors. The figure shows the molecular “keys” lisinopril (left) and RXP407 (right) in their biological “locks”.

    24. On the in vitro and in vivo Properties of Four Locked Nucleic Acid Nucleotides Incorporated into an Anti-H-Ras Antisense Oligonucleotide (pages 1104–1109)

      Kees Fluiter, Miriam Frieden, Jeroen Vreijling, Christoph Rosenbohm, Marit B. De Wissel, Signe M. Christensen, Troels Koch, Henrik Ørum and Frank Baas

      Version of Record online: 28 APR 2005 | DOI: 10.1002/cbic.200400419

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      Stable and sticky. Locked nucleic acid (LNA) monomers are ideally suited for use in antisense oligonucleotides. The biological properties of antisense oligonucleotides that contain the four LNAs shown were evaluated. The pharmacokinetic parameters of an oligonucleotide can be altered by the choice of LNA chemistry. α-L-LNA is the most promising member of the LNA family, pairing good efficacy with specificity.

    25. Molecular Basis of the Interaction Specificity between the Human Glucocorticoid Receptor and Its Endogenous Steroid Ligand Cortisol (pages 1110–1118)

      Johannes von Langen, Karl-Heinrich Fritzemeier, Stephan Diekmann and Alexander Hillisch

      Version of Record online: 10 MAY 2005 | DOI: 10.1002/cbic.200400361

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      Steroid simulation: Molecular dynamics simulations of the glucocorticoid receptor protein (see molecular model) were used to explain measured binding affinities of this receptor for cortisol and four cortico- and sex steroids. Our approach is able to discriminate strongly and weakly binding compounds and explains the binding properties of several steroids at a molecular level.

    26. New Inhibitors of the Tat–TAR RNA Interaction Found with a “Fuzzy” Pharmacophore Model (pages 1119–1125)

      Steffen Renner, Verena Ludwig, Oliver Boden, Ute Scheffer, Michael Göbel and Gisbert Schneider

      Version of Record online: 10 MAY 2005 | DOI: 10.1002/cbic.200400376

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      Ligand-based virtual screening: A “fuzzy” pharmacophore model was applied for virtual screening for TAR RNA ligands (see figure). The best hit showed binding behavior ten times (IC50=46 μM) stronger than that of the reference acetylpromazine in a fluorescence resonance energy transfer (FRET) assay.

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      Preview: ChemBioChem 6/2005 (page 1134)

      Version of Record online: 30 MAY 2005 | DOI: 10.1002/cbic.200590018

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