ChemBioChem

Cover image for Vol. 15 Issue 13

Early View (Online Version of Record published before inclusion in an issue)

Editor: Peter Gölitz; Editorial Board Chairs: Thomas Carell, Donald Hilvert, Barbara Imperiali

Online ISSN: 1439-7633

Associated Title(s): ChemCatChem, ChemMedChem, ChemPhysChem, ChemSusChem

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  1. 1 - 32
  1. Minireviews

    1. Biological Applications of Expanded Genetic Codes

      Xiang Li and Prof. Dr. Chang C. Liu

      Article first published online: 29 AUG 2014 | DOI: 10.1002/cbic.201402159

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      Why stop at 20? Expanded genetic codes allow the direct addition of new chemistries into proteins in living organisms. We discuss the applications and possibilities of expanded genetic codes in protein, cell, synthetic, and evolutionary biology.

  2. Full Papers

    1. Thermophiles as Potential Source of Novel Endotoxin Antagonists: the Full Structure and Bioactivity of theLipo-oligosaccharide from Thermomonas hydrothermalis

      Dr. Flaviana Di Lorenzo, Dr. Ida Paciello, Dr. Luigi Lembo Fazio, Dr. Luciana Albuquerque, Dr. Luisa Sturiale, Prof. Milton S. da Costa, Prof. Rosa Lanzetta, Prof. Michelangelo Parrilli, Prof. Domenico Garozzo, Prof. Maria Lina Bernardini, Dott. Alba Silipo and Prof. Antonio Molinaro

      Article first published online: 29 AUG 2014 | DOI: 10.1002/cbic.201402233

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      Bacterial life at high temperature implies modifications of cell-wall components to resist to the hostile habitats. Structural elucidation of the lipo-oligosaccharide from the thermophile Thermomonas hydrothermalis confirmed this paradigm, highlighting a new lipo-oligosaccharide with low immunopotential and able to antagonize E. coli lipopolysaccharide activity.

    2. Short Antimicrobial Lipo-α/γ-AA Hybrid Peptides

      Yaqiong Li, Christina Smith, Haifan Wu, Peng Teng, Yan Shi, Shruti Padhee, Torey Jones, Anh-My Nguyen, Chuanhai Cao, Hang Yin and Jianfeng Cai

      Article first published online: 28 AUG 2014 | DOI: 10.1002/cbic.201402264

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      Best of both worlds: We developed short lipo-α/γ-AA hybrid peptides that display potent, broad-spectrum activity against medicinally relevant Gram-positive and Gram-negative bacteria. These hybrids are easier to synthesize and more selective than previously developed lipo-γ-AA peptides and therefore have potential for developing a new class of antibiotics to combat drug resistance.

  3. Communications

    1. Engineering of Highly Selective Variants of Parvibaculum lavamentivorans Alcohol Dehydrogenase

      Dominik Spickermann, Dr. Sascha Hausmann, Dr. Christian Degering, Prof. Ulrich Schwaneberg and Dr. Christian Leggewie

      Article first published online: 28 AUG 2014 | DOI: 10.1002/cbic.201402216

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      Improved enzymes: We describe the development of highly selective Parvibaculum lavamentivorans alcohol dehydrogenase variants to produce the useful product (R)-3-quinuclidinol. The enantiomeric excess in the biocatalytic production was increased from 84.3 % (wild-type) to ≥99 %, and the conversion rate was enhanced by 43.5 %.

    2. Enzyme Toolbox: Novel Enantiocomplementary Imine Reductases

      Philipp N. Scheller, Silvia Fademrecht, Sebastian Hofelzer, Prof. Dr. Jürgen Pleiss, Dr. Friedemann Leipold, Prof. Dr. Nicholas J. Turner, Dr. Bettina M. Nestl and Prof. Dr. Bernhard Hauer

      Article first published online: 27 AUG 2014 | DOI: 10.1002/cbic.201402213

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      Let's transfer hydrides to imines. Biocatalytic preparation of chiral amines by imine reductases is an emerging technology but is limited to few described enzymes. Several hundred additional enantiocomplementary imine reductases sequences were collected in a database, and the biochemical potentials of three of them are reported. Site-directed mutagenesis revealed key amino acid residues for catalysis and stereoselectivity.

  4. Full Papers

    1. A Coenzyme-Independent Decarboxylase/Oxygenase Cascade for the Efficient Synthesis of Vanillin

      Dr. Toshiki Furuya, Misa Miura and Prof. Dr. Kuniki Kino

      Article first published online: 27 AUG 2014 | DOI: 10.1002/cbic.201402215

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      Vanillin, a valuable building block and flavor, was efficiently synthesized from ferulic acid, which is available from renewable resources. A new biocatalysis, that is, a “coenzyme-independent decarboxylase/oxygenase cascade”, allows high-yield production of vanillin in one pot.

  5. Communications

    1. Multiplexed Programmable Release of Captured DNA

      Julia Kennedy-Darling, Matthew T. Holden, Dr. Michael R. Shortreed and Prof. Lloyd M. Smith

      Article first published online: 26 AUG 2014 | DOI: 10.1002/cbic.201402343

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      Where the red fern glows: Toehold-mediated branch migration enables the rapid and selective elution of desired subsets of captured DNA sequences from solid supports. This approach allowed for the multiplexed release of crosslinked chromatin regions and revealed hidden images in DNA microarrays.

    2. PNA-Encoded Synthesis (PES) of a 10 000-Member Hetero-Glycoconjugate Library and Microarray Analysis of Diverse Lectins

      Dr. Alexandre Novoa, Takuya Machida, Dr. Sofia Barluenga, Dr. Anne Imberty and Prof. Nicolas Winssinger

      Article first published online: 26 AUG 2014 | DOI: 10.1002/cbic.201402280

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      Carbohydrate arrays: We report a highly miniaturized synthetic format to access a nucleic-acid-encoded hetero-glycoconjugate libraries with an unprecedented diversity in the combinations of carbohydrates, linkers, and capping groups. Novel information about plant and bacterial lectin specificity was obtained after conversion of this library to a microarray format.

  6. Full Papers

    1. Probing Ambiguous Base-Pairs by Genetic Transformation with XNA Templates

      Dr. Valérie Pezo, Guy Schepers, Dr. Catia Lambertucci, Dr. Philippe Marlière and Prof. Piet Herdewijn

      Article first published online: 26 AUG 2014 | DOI: 10.1002/cbic.201402226

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      An anhydrohexitol backbone bearing ambiguous bases functions as template for in vivo DNA synthesis. The greatest ambiguity was achieved by a 5-nitroindazole base. Such heterocycles stand as promising candidates for generating random DNA sequences in E. coli.

    2. Chemically Synthesized 58-mer LysM Domain Binds Lipochitin Oligosaccharide

      Dr. Kasper K. Sørensen, Dr. Jens B. Simonsen, Dr. Nicolai N. Maolanon, Prof. Jens Stougaard and Prof. Knud J. Jensen

      Article first published online: 26 AUG 2014 | DOI: 10.1002/cbic.201402125

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      A nod is as good as sugar: The L. japonicus LysM2 domain binds to the nod factor from M. loti, thereby causing a conformational change in the LysM2 domain. A glycan microarray was used to demonstrate preferential binding over oligosaccharides, and CD spectroscopy detected conformational changes.

    3. Repositioning the Substrate Activity Screening (SAS) Approach as a Fragment-Based Method for Identification of Weak Binders

      Rafaela Gladysz, Matthias Cleenewerck, Dr. Jurgen Joossens, Prof. Dr. Anne-Marie Lambeir, Prof. Dr. Koen Augustyns and Prof. Dr. Pieter Van der Veken

      Article first published online: 25 AUG 2014 | DOI: 10.1002/cbic.201402192

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      The best of both worlds: Screening of a substrate activity screening (SAS) library first for inhibitors and then for substrates generates complementary data sets. Combined, these provide coherent SAR data that can be used both for fragment-based construction of noncovalent small molecules and for the production of inhibitors with covalent warheads.

    4. Synergistic Actions of Tailoring Enzymes in Pradimicin Biosynthesis

      Kandy Napan, Dr. Shuwei Zhang, Whitney Morgan, Thomas Anderson, Prof. Dr. Jon Y. Takemoto and Prof. Dr. Jixun Zhan

      Article first published online: 22 AUG 2014 | DOI: 10.1002/cbic.201402306

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      Synergistic actions: Three tailoring enzymes in pradimicin (Pdm) biosynthesis were investigated. PdmW was characterized as a dedicated C-6 hydroxylase, amino acid ligase PdmN had relaxed specificity toward aa acceptor substrates, and the C-5 hydroxylase PdmJ worked synergistically with PdmW to yield dihydroxylated products. Several new pradimicin analogues were produced through combinatorial biosynthesis.

  7. Communications

    1. Traceless Semisynthesis of a Set of Histone 3 Species Bearing Specific Lysine Methylation Marks

      Zhonglei Chen, Adrian T. Grzybowski and Prof. Alexander J. Ruthenburg

      Article first published online: 22 AUG 2014 | DOI: 10.1002/cbic.201402313

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      Without a trace: Advanced protein-ligation methodologies, optimized protein-engineering strategies, and radical-mediated desulfurization were coupled to generate native-like histone 3, bearing all five of its most studied methyllysines. We demonstrated that these semisynthetic histones, in the context of nucleosomes, are valuable reagents for unbiased binding partner discovery.

    2. Site-Specific Modification of the Anticancer and Antituberculosis Polyether Salinomycin by Biosynthetic Engineering

      Hanna Luhavaya, Simon R. Williams, Dr. Hui Hong, Prof. Luciana Gonzaga de Oliveira and Prof. Peter F. Leadlay

      Article first published online: 22 AUG 2014 | DOI: 10.1002/cbic.201402300

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      Redirecting polyether biosynthesis: The origin of the unusual cis double bond in the polyether ionophore salinomycin has been revealed. Deletion of a gene encoding a previously unknown dehydratase diverts oxidative cyclization to produce analogues specifically modified in the trioxaspiroacetal core.

  8. Full Papers

    1. Ribosylhopane, a Novel Bacterial Hopanoid, as Precursor of C35 Bacteriohopanepolyols in Streptomyces coelicolor A3(2)

      Wenjun Liu, Elias Sakr, Dr. Philippe Schaeffer, Dr. Helen M. Talbot, Janina Donisi, Thomas Härtner, Dr. Elmar Kannenberg, Prof. Eriko Takano and Prof. Michel Rohmer

      Article first published online: 22 AUG 2014 | DOI: 10.1002/cbic.201402261

      Thumbnail image of graphical abstract

      The last missing intermediate in the biosynthetic pathway leading to the widespread bacterial triterpenes of the hopane series was ribosylhopane. Deletion of genes encoding a putative nucleosidase and a putative transaminase resulted in the accumulation of intermediates and thus elucidation of this pathway.

    2. Synthesis of Cholesterol Analogues Bearing BODIPY Fluorophores by Suzuki or Liebeskind–Srogl Cross-Coupling and Evaluation of Their Potential for Visualization of Cholesterol Pools

      Dr. Zheng Liu, Dr. Seth G Thacker, Dr. Sara Fernandez-Castillejo, Dr. Edward B. Neufeld, Prof. Dr. Alan T. Remaley and Prof. Dr. Robert Bittman

      Article first published online: 22 AUG 2014 | DOI: 10.1002/cbic.201402042

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      All roads lead to BODIPY: Versatile BODIPY–cholesterol conjugates were synthesized in which the key steps were Suzuki or Liebeskind–Srogl cross-coupling of cholesterol phenyl moieties with structurally diverse BODIPY scaffolds (blue). These conjugates were used to enable the simultaneous tracking of different cellular cholesterol pools by confocal microscopy and flow cytometry.

  9. Highlights

    1. Fast Reversibility of Dimeriser System enables Quantification of Signal Molecule Turnover

      Dr. Merel J. W. Adjobo-Hermans

      Article first published online: 21 AUG 2014 | DOI: 10.1002/cbic.201402294

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      The design of a brake: Chemical induced dimerisation systems have revolutionised signal transduction research by allowing fast activation of specific proteins. A recent report describes the design of tools that enable the rapid switching off of the induced signal, thereby enabling quantification of signal molecule turnover.

  10. Full Papers

    1. Peptidyl Succinimidyl Peptides as Taspase 1 Inhibitors

      Johannes van den Boom, Marija Mamić, Daniele Baccelliere, Dr. Susanne Zweerink, Dr. Farnusch Kaschani, Prof. Dr. Shirley Knauer, Prof. Dr. Peter Bayer and Prof. Dr. Markus Kaiser

      Article first published online: 21 AUG 2014 | DOI: 10.1002/cbic.201402108

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      Mechanism-based Taspase 1 inhibitors: Based on the proposed asparaginase-like substrate cleavage mechanism, peptidyl succinimidyl peptides were designed and found to act as Taspase 1 inhibitors. These showed high inhibition against purified Taspase 1, but were not effective against Taspase 1 in cell lysate.

  11. Communications

    1. Biofilm-Eradicating Properties of Quaternary Ammonium Amphiphiles: Simple Mimics of Antimicrobial Peptides

      Megan C. Jennings, Laura E. Ator, Thomas J. Paniak, Prof. Dr. Kevin P. C. Minbiole and Prof. Dr. William M. Wuest

      Article first published online: 21 AUG 2014 | DOI: 10.1002/cbic.201402254

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      EradiCATION: By combining key features of polyamines and antimicrobial peptides, we demonstrated for the first time that hybrid compounds are capable of eradicating bacterial biofilms at low concentrations. This work provides insight toward the minimum chemical scaffold required to eradicate biofilms.

    2. Heterologous Production of Glidobactins/Luminmycins in Escherichia coli Nissle Containing the Glidobactin Biosynthetic Gene Cluster from Burkholderia DSM7029

      Dr. Xiaoying Bian, Dr. Fan Huang, Dr. Hailong Wang, Thorsten Klefisch, Prof. Dr. Rolf Müller and Prof. Dr. Youming Zhang

      Article first published online: 21 AUG 2014 | DOI: 10.1002/cbic.201402199

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      Production of proteasome inhibitors in­ E. coli: We directly cloned the glidobactin gene cluster (glb) from Burkholderia and successfully detected glidobactins/luminmycins in E. coli Nissle. We also improved the yield of glidobactin A tenfold by promoter change. In addition, identification of new acyclic biosynthetic intermediates implies substrate specificity of the TE domain for cyclization.

    3. Chemoenzymatic Synthesis of Trehalose Analogues: Rapid Access to Chemical Probes for Investigating Mycobacteria

      Bailey L. Urbanek, Douglas C. Wing, Krystal S. Haislop, Chelsey J. Hamel, Dr. Rainer Kalscheuer, Prof. Peter J. Woodruff and Prof. Benjamin M. Swarts

      Article first published online: 19 AUG 2014 | DOI: 10.1002/cbic.201402288

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      Trehalose tools for TB: A one-step chemoenzymatic method for the rapid and efficient synthesis of trehalose analogues was developed. This method enabled facile preparation and administration of a trehalose-based probe for detecting mycobacteria, which might enable the development of new diagnostic tools for tuberculosis (TB) research.

  12. Full Papers

    1. Photobleaching Reveals Heterogeneous Stoichiometry for Equinatoxin II Oligomers

      Dr. Matthew A. B. Baker, Dr. Nejc Rojko, Dr. Bríd Cronin, Prof. Gregor Anderluh and Prof. Mark I. Wallace

      Article first published online: 19 AUG 2014 | DOI: 10.1002/cbic.201300799

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      Poring over the data: Equinatoxin II (EqtII) is known to oligomerize to form pores that spontaneously insert into membranes. Single-molecule photobleaching of fluorescently labeled EqtII was used to determine the stoichiometry of EqtII oligomers in supported lipid bilayers, which suggests that there is a large variation in the number of subunits in individual pores.

    2. Lactose-Functionalized Dendrimers Arbitrate the Interaction of Galectin-3/MUC1 Mediated Cancer Cellular Aggregation

      Anna K. Michel, Dr. Pratima Nangia-Makker, Dr. Avraham Raz and Dr. Mary J. Cloninger

      Article first published online: 19 AUG 2014 | DOI: 10.1002/cbic.201402134

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      How sweet it is: PAMAM-based glycodendrimers (pink sphere) were used to re-pattern galectin-3 at the surface of cancer cells (aqua spheres). One glycodendrimer was found to effectively prohibit galectin-3 mediated cellular aggregation, and another glycodendrimer was found to readily induce cellular aggregation.

    3. Low-Resolution Structures of OmpA⋅DDM Protein–Detergent Complexes

      Dr. Jørn Døvling Kaspersen, Dr. Christian Moestrup Jessen, Dr. Brian Stougaard Vad, Prof. Dr. Esben Skipper Sørensen, Dr. Kell Kleiner Andersen, Prof. Dr. Marianne Glasius, Prof. Dr. Cristiano Luis Pinto Oliveira, Prof. Dr. Daniel Erik Otzen and Prof. Dr. Jan Skov Pedersen

      Article first published online: 19 AUG 2014 | DOI: 10.1002/cbic.201402162

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      SAXS studies of membrane proteins: The use of small-angle X-ray scattering to determine low-resolution structures of the outer-membrane protein OmpA (from E. coli ) solubilized by the surfactant dodecyl maltoside has provided valuable information about how membrane proteins are embedded in amphiphilic environments.

  13. Communications

    1. Proteasome Inhibitors with Photocontrolled Activity

      Mickel J. Hansen, Willem A. Velema, Gerjan de Bruin, Prof. Herman S. Overkleeft, Dr. Wiktor Szymanski and Prof. Ben L. Feringa

      Article first published online: 14 AUG 2014 | DOI: 10.1002/cbic.201402237

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      Photoswitchable chemotherapeutic agents: Photoswitchable proteasome inhibitors were synthesized, and the changes in their biological activities were determined. Substantial differences in proteasome inhibitory activity in cell extracts were observed before and after irradiation with light. The results of this study show the potential of photopharmacology in anticancer therapy and research.

  14. Full Papers

    1. Functional Chromatography Reveals Three Natural Products that Target the Same Protein with Distinct Mechanisms of Action

      Dr. Min Jin Kang, Dr. Tongde Wu, Dr. E. M. Kithsiri Wijeratne, Eric C. Lau, Damian J. Mason, Celestina Mesa, Joseph Tillotson, Prof. Dr. Donna D. Zhang, Prof. Dr. A. A. Leslie Gunatilaka, Dr. James J. La Clair and Prof. Dr. Eli Chapman

      Article first published online: 14 AUG 2014 | DOI: 10.1002/cbic.201402258

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      Picking p97's pockets: Functional chromatography was used to identify natural products that bind to p97. Application of this method to a panel of fungal and plant extracts identified rheoemodin, 1-hydroxy-dehydroherbarin, and phomapyrrolidinone A, each with a unique mechanism of p97 modulation. This strongly supports the application of functional chromatography to discover discrete protein modulators.

  15. Book Reviews

  16. Communications

    1. Bottom-up Design of Small Molecules that Stimulate Exon 10 Skipping in Mutant MAPT Pre-mRNA

      Dr. Yiling Luo and Prof. Dr. Matthew D. Disney

      Article first published online: 12 AUG 2014 | DOI: 10.1002/cbic.201402069

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      Bottoms up! A rational design strategy enabled by an understanding of RNA–small-molecule interactions identified a small molecule that controls the alternative pre-mRNA splicing of mutant MAPT, which causes Parkinsonism. The small molecule that affects pre-mRNA splicing by directly binding a pre-mRNA, reverses destabilization caused by the DDPAC mutation in the hairpin stem at the exon 10–intron junction.

    2. Highly Efficient Fluorescent Interstrand Photo-crosslinking of DNA Duplexes Labeled with 5-Fluoro-4-thio-2′-O-methyluridine

      Dr. Joanna Nowak-Karnowska, Ziad Chebib, Prof. Jan Milecki, Prof. Stefan Franzen and Prof. Bohdan Skalski

      Article first published online: 8 AUG 2014 | DOI: 10.1002/cbic.201402182

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      Always cross(link) at the light: Selective photoexcitation of 5-fluoro-4-thio-2′-O-methyluridine (FSU) between two adenosines in oligonucleotide duplexes results in highly efficient crosslinking of the two strands by formation of a fluorescent adduct (P) with thymidine.

    3. Rapid Reconstitution of Biosynthetic Machinery for Fungal Metabolites in Aspergillus oryzae: Total Biosynthesis of Aflatrem

      Koichi Tagami, Dr. Atsushi Minami, Ryuya Fujii, Dr. Chengwei Liu, Dr. Mizuki Tanaka, Prof. Dr. Katsuya Gomi, Prof. Dr. Tohru Dairi and Prof. Dr. Hideaki Oikawa

      Article first published online: 1 AUG 2014 | DOI: 10.1002/cbic.201402195

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      Rapid and simple: Reconstitution of indole diterpene aflatrems in Aspergillus oryzae was demonstrated with only two rounds of transformations applying “tandem transformation” method. From a total of seven heterologously expressed genes, aflatrem was synthesized.

  17. Book Reviews

    1. Hydroxamic Acids: A Unique Family of Chemicals with Multiple Biological Activities. Edited by Satya P. Gupta.

      Timothy Bugg

      Article first published online: 4 JUN 2014 | DOI: 10.1002/cbic.201402188

      Springer, Berlin 2013, X+312 pp., hardcover, € 139.09.—ISBN 978-3-642-38110-2

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