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Chembiochem: a European Journal of Chemical Biology

Ke-Feng Wang, Chun-Lei Liu, Kun-Yan Sui, Chen Guo, Chun-Zhao Liu
2,5-Furandicarboxylic acid (FDCA) is a biobased platform chemical for the production of polyesters. The magnetic laccase catalyst with TEMPO as the mediator has the remarkable capability of oxidizing HMF to 2,5-furandicarboxylic acid (FDCA). Under optimal reaction conditions, a quantitative yield (90.2%) of FDCA with complete HMF conversion was obtained after 96 h of reaction. More importantly, the magnetic laccase catalyst exhibited good recyclability and stability, maintaining 84.8% of its original activity following 6 reuse cycles...
January 15, 2018: Chembiochem: a European Journal of Chemical Biology
Tingting Zou, Seiichiro Kizaki, Hiroshi Sugiyama
Capillary electrophoresis coupled with DNA 5 Texas Red labeling was used to investigate the ability of duocarmycin B2, Fe(II) peplomycin, and MNase to access the nucleosome. Distinct accessibility patterns of these species to the nucleosome were observed. Duocarmycin B2 was able to enter and react at the core region, although its alkylating efficiency decreased significantly. Intercalation of peplomycin in the nucleosomal core region was highly suppressed, but reaction sites located at the ends of the nucleosomal core remained accessible, which implied the flexibility of the core DNA end...
January 15, 2018: Chembiochem: a European Journal of Chemical Biology
Tobias Betke, Jun Higuchi, Philipp Rommelmann, Keiko Oike, Taiji Nomura, Yasuo Kato, Yasuhisa Asano, Harald Gröger
Nitriles belong to the product classes, which are mostly needed and produced by the chemical industry, playing a major role in various industry segments ranging from high-volume low-price sectors such as polymers to low-volume high-price sectors such as the chiral pharma drugs. A common industrial technology for nitrile production is ammonoxidation as a gas phase reaction at high temperature. A further popular approach are substitution or addition reactions with hydrogen cyanide or derivatives thereof. A major drawback, however, is the very high toxicity of cyanide...
January 14, 2018: Chembiochem: a European Journal of Chemical Biology
Siamak Semsary, Ivana Crnovčić, Ronja Driller, Joachim Vater, Bernhard Loll, Ullrich Keller
X-type actinomycins (Acms) contain 4-hydroxyproline (Acm X0) or 4-oxoproline (Acm X2) in their ß-pentapeptide lactone rings whereas their α-ring contains proline. We demonstrate that these Acms are formed through asymmetric condensation of Acm half molecules (Acm halves) containing proline with 4-hydroxyproline- or 4-oxo-proline-containing Acm halves. In turn we show - using an artificial Acm half analogue (PPL 1) with proline in its peptide chain - its conversion into the 4-hydroxyproline and 4-oxoproline-containing Acm halves, PPL 0 and PPL 2, in mycelial suspensions of Streptomyces antibioticus...
January 12, 2018: Chembiochem: a European Journal of Chemical Biology
Cécile Gasse, Marwa Zaarour, Sam Noppen, Mikhail Abramov, Philippe Marlière, Sandra Liekens, Bart De Strooper, Piet Herdewijn
A modified DNA aptamer was developed that binds BACE1, a therapeutic target involved in Alzheimer's disease. This ssXNA not only tightly binds to BACE1 but also inhibits its protease activity in vitro in the same range as a previously described unmodified aptamer. We report the in vitro selection of functional oligonucleotides using two nucleobase modifications: 5-chlorouracil and 7-deazaadenine. The nucleoside analog 5-chloro-2'-deoxyuridine has already been explored to replace thymidine in a chemically modified genome of a bacterium...
January 11, 2018: Chembiochem: a European Journal of Chemical Biology
Danith H Ly, Raman Bahal, Arunava Manna, Wei-Che Hsieh, Shivaji A Thadke, Gopalsamy Sureshkumar
Template-directed synthesis offers several distinct benefits over conventional laboratory creation, including unsurpassed reaction rate and selectivity. While it is central to many biological processes, such an approach has rarely been applied to the in-situ synthesis and recognition of biomedically relevant target. Towards this goal, we report the development of a three-codon nucleic acid probe containing C-terminal thioester and N-terminal cysteine that is capable of undergoing template-directed oligomerization in the presence of RNA target, and self-deactivation in its absence...
January 11, 2018: Chembiochem: a European Journal of Chemical Biology
Nozomi Ishii, Chie Sunaga, Kanae Sano, Chengcheng Huang, Kenta Iino, Yuji Matsuzaki, Tadashi Suzuki, Ichiro Matsuo
We developed a fluorescence-quenching-based assay system to determine the hydrolysis activity of endo-β-N-acetylglucosaminidases (ENGases). The pentasaccharide derivative 1 was labeled with an N-methylanthraniloyl group as a reporter dye at the non-reducing end and a 2,4-dinitrophenyl group as a quencher molecule at the reducing end. This derivative is hydrolyzed by ENGase, resulting in an increase of fluorescence intensity. Thus, the fluorescence signal is directly proportional to the amount of the tetrasaccharide derivative, allowing ENGase activity to be evaluated easily and quantitatively...
January 11, 2018: Chembiochem: a European Journal of Chemical Biology
Monita Muralidharan, Rajdeep Das, Vijay Bhat, Amit Kumar Mandal
Electrostatic attraction between α and β globin chains hold the subunits together in tetrameric human hemoglobin molecule (α₂β₂). Compared to normal globin chains, the affinity of a mutant chain to its partner globin in genetic variants of hemoglobin might be different. This leads to an unequal abundance of normal and variant hemoglobin in heterozygous sample, even though the rates of synthesis of both normal and variant chains are same. The aforementioned affinities across various globin chains might be assessed by the quantification of different forms of tetramers present in a variant hemoglobin sample...
January 8, 2018: Chembiochem: a European Journal of Chemical Biology
Makoto Hashimoto, Hikaru Kato, Ayako Katsuki, Sachiko Tsukamoto, Isao Fujii
Himeic acid A, produced by the marine fungus Aspergillus japonicus MF275, is a specific inhibitor of the ubiquitin-activating enzyme E1 in the ubiquitin-proteasome system. To elucidate the mechanism of himeic acid biosynthesis, we first carried out feeding experiments with labeled precursors. The long fatty acyl side chain attached to the pyrone ring was confirmed to be of polyketide origin, while the amide substituent was found to be derived from leucine. These results suggest that a polyketide synthase-non-ribosomal peptide synthase (PKS-NRPS) is involved in himeic acid biosynthesis...
January 5, 2018: Chembiochem: a European Journal of Chemical Biology
Dorien Van Lysebetten, Stefania Felissati, Eirini Antonatou, Lieselot Carrette, Pieter Espeel, Evelien Foquet, Filip Du Prez, Annemieke Madder
The development of straightforward and versatile peptide cyclisation methods is highly desired in order to meet the demand for more stable peptide based drugs. In this paper, a new method for the synthesis of side chain-to-tail cyclic peptides with simultaneous introduction of a N-terminal handle based on the introduction of a N-terminal thiolactone building block, is described. A primary amine liberates a homocysteine analogue from the thiolactone building block which further enables cyclisation of the peptide through disulfide bond formation with a C-terminal cysteamine...
January 4, 2018: Chembiochem: a European Journal of Chemical Biology
Russell Judge, Victoria Scott, Gricelda Simler, Steve Pratt, Marian Namovic, Brent Putman, Ana Aguirre, Vincent Stoll, Mulugeta Mamo, Steve Swann, Adrian D Hobson
We describe the design, synthesis and SAR of a series of 2-aminobenzothiazole inhibitors of Rho Kinase (ROCK) 1 and 2 which were optimized to low nanomolar potencies using structure-based design. Protein Kinase A was used as a surrogate protein structure to guide compound design. A subset of these molecules also showed robust activity in a myosin phosphatase cell based assay and in a mechanical hyperalgesia in vivo pain model.
January 4, 2018: Chembiochem: a European Journal of Chemical Biology
Ge Qu, Richard Lonsdale, Peiyuan Yao, Guangyue Li, Beibei Liu, Manfred T Reetz, Zhoutong Sun
Directed evolution of stereo- or regioselective enzymes as catalysts in asymmetric transformations is of particular interest in organic synthesis. Upon evolving these biocatalysts, screening is the bottleneck. To beat the numbers problem most effectively, methods and strategies for building "small but smart" mutant libraries have been developed. Herein, we compared two different strategies regarding the application of triple-code saturation mutagenesis (TCSM) at multiresidue sites of the Thermoanaerobacter brockii alcohol dehydrogenase by using distinct reduced amino-acid alphabets...
January 4, 2018: Chembiochem: a European Journal of Chemical Biology
Min Wu, Xiaoai Wu, Yayue Wang, Lei Gu, Jiao You, Haoxing Wu, Ping Feng
Strongly fluorogenic BODIPY-tetrazine probes have been obtained by introducing an alkoxy-tetrazine fragment at the boron center. The fluorescence signal from these probes strongly increases by up to 225-fold after reaction with bioorthogonal coupling partners, and the hydrophilicity of probes is improved which is suitable for live-cell imaging.
January 3, 2018: Chembiochem: a European Journal of Chemical Biology
Almog Bregman-Cohen, Batel Deri, Shiran Maimon, Yael Pazy, Ayelet Fishman
2-Hydroxybiphenyl 3-monooxygenase (HbpA) is a flavin-containing NADH-dependent aromatic hydroxylase that oxidizes a broad range of 2-substituted phenols. In order to modulate its activity and selectivity, several residues in the active site pocket were investigated by saturation mutagenesis. Variant M321A demonstrated altered regioselectivity by oxidizing for the first time 3-hydroxybiphenyl, thus enabling the production of a new antioxidant, 3,4-dihydroxybiphenyl, with similar ferric reducing capacity as the well-studied piceatannol...
January 3, 2018: Chembiochem: a European Journal of Chemical Biology
Małgorzata Sierant, Katarzyna Kulik, Elzbieta Sochacka, Rafal Szewczyk, Milena Sobczak, Barbara Nawrot
The 5-substituted 2-thiouridines (R5S2U) present in the first (wobble) position of the anticodons of transfer RNAs (tRNAs) contribute to accuracy in reading mRNA codons and tune protein synthesis. Previously, we have shown that, under oxidative stress conditions in vitro, R5S2Us are sensitive to hydrogen peroxide (H2O2), and their oxidative desulfuration produces 5-substituted uridines (R5Us) and 4-pyrimidinone nucleosides (R5H2Us) at a ratio that depends on pH and an R5 substituent. Here, we demonstrate that the desulfuration of 2-thiouridines, either alone or within an RNA/tRNA chain, is catalyzed by cytochrome C (cyt C)...
December 29, 2017: Chembiochem: a European Journal of Chemical Biology
Carsten Schmuck, Martin Ehlers, Jean-Noel Grad, Sumit Mittal, David Bier, Marcel Mertel, Ludwig Ohl, Maria Bartel, Jeroen Briels, Marius Heimann, Christian Ottmann, Elsa Sanchez-Garcia, Daniel Hoffmann
14-3-3 proteins play a central role in signaling pathways in cells: they interact as gatekeeper proteins with a huge number of binding partners. Their function as hub for intracellular communication can explain why these adapter proteins are associated with a wide range of diseases. How they control the various cellular mechanisms is still unclear, but it is assumed that the dimeric nature of the 14-3-3 proteins plays a key role in their activity. Here we present, to the best of our knowledge, the first example of a small molecule binding to the 14-3-3ζ dimerization interface...
December 28, 2017: Chembiochem: a European Journal of Chemical Biology
Gloria Saab-Rincon, Hanan Alwaseem, Valeria Guzmán-Luna, Leticia Olvera, Rudi Fasan
The multi-domain, catalytically self-sufficient cytochrome P450 BM-3 from Bacillus megaterium (P450BM3) constitutes a versatile enzyme for the oxyfunctionalization of organic molecules and natural products. However, the limited stability of the diflavin reductase domain limits the utility of this enzyme for synthetic applications. In this work, a consensus-guided mutagenesis approach was applied to enhance the thermal stability of the reductase domain of P450BM3. Upon phylogenetic analysis of a set of distantly related P450s (% identity > 38%), a total of 14 amino acid substitutions were identified and evaluated in terms of their stabilizing effect relative to the wild-type reductase domain...
December 24, 2017: Chembiochem: a European Journal of Chemical Biology
David E Mortenson, Dale F Kreitler, Nicole C Thomas, Ilia A Guzei, Samuel H Gellman, Katrina T Forest
β-Amino acids have a backbone that is expanded by one carbon atom relative to α-amino acids, and β residues have been widely investigated as subunits in protein-like molecules that adopt discrete and predictable conformations. Two classes of β residue have been widely explored in the context of generating α-helix-like conformations: β3-amino acids, which are homologous to α-amino acids and bear a side chain on the backbone carbon adjacent to nitrogen; and residues constrained by a five-membered ring, such as the one derived from trans-2-aminocyclopentanecarboxylic acid (ACPC)...
December 22, 2017: Chembiochem: a European Journal of Chemical Biology
Ruben Ragg
The broader, the better! ChemBioChem had a successful year in 2017 receiving its 10 000 th submission. By broadening the journal scope through the addition of biomaterials, ChemBioChem will help to intertwine chemistry and biology even further. Also up next in 2018, a young chemists Special Issue, so gather up ChemBioTalents!
December 21, 2017: Chembiochem: a European Journal of Chemical Biology
Ansgar Rühlmann, Georg Groth, Vlada B Urlacher
Previous studies on cytochrome P450 monooxygenases (CYP) from the family 154 reported on their substrate promiscuity and high activity. Hence, in this study we describe the uncharacterized family member CYP154F1. Screening of more than 100 organic compounds revealed that CYP154F1 preferably accepts small linear molecules with a carbon chain length of 8-10 atoms. In contrast to the thoroughly characterized CYP154E1, CYP154F1 has a much narrower substrate spectrum and low activity. A structural alignment of homology models of CYP154F1 and CYP154E1 revealed few differences in active sites of both family members...
December 19, 2017: Chembiochem: a European Journal of Chemical Biology
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