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Chembiochem: a European Journal of Chemical Biology

Hye Jin Lee, Emily Bernadette Ehlerding, Weibo Cai
Chronic inflammatory diseases are often progressive, resulting not only in physical damage to patients but also social and economic burdens, making early diagnosis of them very critical. Nuclear medicine techniques can enhance the detection of inflammation by providing functional as well as anatomical information when combined with other modalities such as magnetic resonance imaging, computed tomography or ultrasonography. While small molecules and peptides were mainly used for the treatment and imaging of chronic inflammatory diseases in the past, antibodies and their fragments have also been emerging for chronic inflammatory diseases since they show high specificity to their targets and can have various biological half-lives depending on how they are engineered...
September 21, 2018: Chembiochem: a European Journal of Chemical Biology
Shang-Cheng Hung, Che-Jui Yeh, Chiao-Chu Ku, Wei-Chen Lin, Chiao-Yuan Fan, Medel Zulueta, Yoshiyuki Manabe, Koichi Fukase, Yaw-Kuen Li
Many circulating cancer-related proteins, such as fibroblast growth factors (FGFs), associate with glycosaminoglycans, particularly heparan sulfate, in the cell surface. Disaccharide analogues of heparan sulfate were previously identified as the shortest component of the sugar that bind to FGF-1 and FGF-2. Herein we conceived per-O-sulfonated analogues of such disaccharides taking note of the typical pose of L-iduronic acid and devised a single-step per-O-sulfonation and 1,6-anhydro-bridge formation of unprotected sugars to achieve such compounds by directly using SO3·Et3N as sulfonation reagent and dimethylformamide as solvent...
September 21, 2018: Chembiochem: a European Journal of Chemical Biology
Trishaladevi Durgannavar, Se Jeong Kwon, Amar B T Ghisaidoobe, Kyungmin Rho, Ju Hwan Kim, Sun-Young Yoon, Hyo Jin Kang, Sang Jeon Chung
A highly selective detection method of native protein tyrosine phosphatase 1B (PTP1B) is described using a target specific probe equipped with 1-naphthylamine (Ex = 330 nm, Em = 445 nm). Irradiation of a mixture of PTP1B and Probe 1 with ultraviolet light of 280 nm (correspon6ding to PTP1B excitation maximum) resulted in significant fluorescence increase at 445 nm, following FRET characteristics. This phenomenon does not occur with other closely related phosphatases or cellular abundant alkaline phosphatase (APP)...
September 20, 2018: Chembiochem: a European Journal of Chemical Biology
Christian Wiraja, David C Yeo, Daniel Lio, Mengjia Zheng, Chenjie Xu
Timely monitoring and assessment of human health plays a crucial role in maintaining our well-being. Besides medical tools and devices, suitable probe agents are critical tools to facilitate monitoring, either through passive or active functionality (i.e. sensor) through inducible signals. In this review, we highlight recent developments in activatable optical sensors. In particular, we focus on the role and advantages of nucleic acid sensors. Sensing mechanism and bio-applications of these nucleic acid sensors in ex vivo assays, intracellular or in vivo settings are described herein...
September 19, 2018: Chembiochem: a European Journal of Chemical Biology
Yonghui Xie, Xin Wen, Dongmei Zhao, Congwei Niu, Yuefang Zhao, Haoman Qi, Zhen Xi
Acetohydroxyacid synthase (AHAS), which catalyzes the first step in the biosynthesis of branched-chain amino acids, is a target of several types of potent herbicides and antimicrobials. AHAS contains the catalytic subunit (CS) and the regulatory subunit (RS). AHAS RS is usually composed of ACT domains and C-terminal domains. Herein, we reported that the ACT domain of AHAS RS from different species could efficiently activate its respective CS. Moreover, we discovered the universal cross-activation between the CSs and the ACT domains of RSs across species...
September 17, 2018: Chembiochem: a European Journal of Chemical Biology
Choi Yi Li, Simon J de Veer, Ruby H P Law, James C Whisstock, David Craik, Joakim E Swedberg
Urokinase-type plasminogen activator (uPA) and tissue-type plasminogen activator (tPA) are two serine proteases that contribute to initiating fibrinolysis by activating plasminogen. uPA is also an important tumour-associated protease due to its role in extracellular matrix remodelling. Overexpression of uPA has been identified in several different cancers and uPA inhibition has been reported as a promising therapeutic strategy. Although several peptide-based uPA inhibitors have been developed, the extent to which uPA tolerates different tetrapeptide sequences that span the P1-P4 positions remains to be thoroughly explored...
September 17, 2018: Chembiochem: a European Journal of Chemical Biology
Shubhendu Palei, Kira-Sophie Becher, Christian Nienberg, Joachim Jose, Henning D Mootz
Semi-synthetic cyclic peptides containing both non-proteinogenic building blocks as the synthetic part and a genetically encoded sequence amenable to DNA-based randomization hold great potential to expand the chemical space in the quest for novel bioactive peptides. Key to an efficient selection of novel binders to biomacromolecules is a robust method to link their genotype and phenotype. We have developed a novel bacterial cell surface display technology to present cyclic peptides composed of a synthetic and a genetically encoded fragment in their backbones...
September 14, 2018: Chembiochem: a European Journal of Chemical Biology
Christopher Allan, Miroslav Kosar, Christina V Burr, Colin Logan Mackay, Rory R Duncan, Alison Nicola Hulme
The tyrosine side chain is amphiphilic leading to significant variations in the surface exposure of tyrosine residues in the folded structure of a native sequence protein. This variability can be exploited to give residue-selective functionalization of a protein substrate by using a highly reactive diazonium group tethered to an agarose-based resin. This novel catch-and-release approach to protein modification has been demonstrated for proteins with accessible tyrosine residues, which are compared with a control group of proteins in which there are no accessible tyrosine residues...
September 13, 2018: Chembiochem: a European Journal of Chemical Biology
Ilaria Furlan, Ivana Domljanovic, Jesper Uhd, Kira Astakhova
Nucleic acid hybridisation plays a key role in many biological processes including transcription, translation and regulation of gene expression. Several sophisticated applications rely on this fundamental interaction, including the polymerase chain reaction and gene therapy. To specifically target a nucleic acid sequence, synthetic oligonucleotides with a suitable affinity and specificity towards the target need to be designed. The affinity of potential probes or therapeutic agents to their target sequence is generally investigated by melting experiments, which break the hydrogen bonding and stacking interactions that stabilise the double helix, to form two single strands...
September 13, 2018: Chembiochem: a European Journal of Chemical Biology
Bimal Koirala, Jingjun Lin, Gee W Lau, Yftah Tal-Gan
Streptococcus pneumoniae (pneumococcus) is a prevalent human pathogen responsible for a variety of diseases, including pneumonia, bacteremia, sepsis, meningitis and otitis media, with a death toll of >22,000 a year in the United States alone. Pneumococcus utilizes the competence regulon and its associated signaling peptide, the competence stimulating peptide (CSP), to initiate its attack on the host and establish an infection. In this work, we set to: 1) develop a pan-group QS inhibitor that can effectively interact with both the pneumococcus ComD1 and ComD2 receptors; and 2) evaluate the utility of dominant-negative CSPs (dnCSPs) in attenuating pneumococcus infectivity...
September 13, 2018: Chembiochem: a European Journal of Chemical Biology
Leena Penttinen, Chiara Rutanen, Janne Jänis, Juha Rouvinen, Nina Hakulinen
Catechol oxidases and tyrosinases are coupled binuclear copper enzymes that oxidize various o-diphenolic compounds to corresponding o-quinones. Tyrosinases have an additional monooxygenation ability to hydroxylate monophenol to o-diphenol. It is still not clear what causes the difference in the catalytic activities. We solved a complex structure of Aspergillus oryzae catechol oxidase with resorcinol bound into the active site. Catalytic activity of A. oryzae catechol oxidase was studied, for the first time, by high-resolution FT-ICR mass spectrometry to shed light on the reaction mechanism...
September 11, 2018: Chembiochem: a European Journal of Chemical Biology
Boris Bauwens, Jef Rozenski, Piet Herdewijn, Johan Robben
Deoxyxylonucleic acid (dxNA) is a synthetic polymer which may have the potential of heredity and evolution. Because of its unusual backbone geometry, sequence information stored in dxNA is presumed to be inaccessible to natural nucleic acids or proteins. Despite a large structural similarity with natural nucleotides, 2'-deoxyxylonucleotide (dxNT) incorporation by polymerases is limited. We present the identification of a mutant of DNA polymerase Therminator with increased tolerance to deoxyxylose-induced backbone distortions...
September 11, 2018: Chembiochem: a European Journal of Chemical Biology
Chia-Wei Hu, Matthew Worth, Hao Li, Jiaoyang Jiang
The O-linked N-acetylglucosamine (O-GlcNAc) modification is an essential component in cell regulation. A single pair of human enzymes conducts this modification dynamically on a broad variety of proteins: O-GlcNAc transferase (OGT) adds the GlcNAc residue and O-GlcNAcase (OGA) hydrolyzes it. This modification is dysregulated in many diseases, but its exact role on particular substrates remains unclear. In addition, no apparent sequence motif was found in the modified proteins and the factors controlling the substrate specificity of OGT and OGA are largely unknown...
September 10, 2018: Chembiochem: a European Journal of Chemical Biology
Mehmet V Yigit, Nidhi Nandu, Mustafa Salih Hizir, Neil M Roberston, Birol Ozturk
MoS2 nanoparticles (2D-nps) exhibit artificial enzyme properties which can be regulated at the bio-nano interfaces. We have discovered that protein lipase is able to tune the peroxidase-like activity of the MoS2 2D-nps offering low nanomolar label-free detection and identification in samples with unknown identity. The inhibition of the peroxidase-like activity of the MoS2 2D-nps was demonstrated to be concentration-dependent and as low as 5 nM of lipase was detected with this approach. The results were compared with several other proteins which did not display any significant interference with the nanozyme behavior of the MoS2 2D-nps...
September 9, 2018: Chembiochem: a European Journal of Chemical Biology
Siddhant Sethi, Nozomi Honda, Licheng Wan, Shigetaka Nakamura, Kenzo Fujimoto
Genes are the blue prints for the architecture of the living organisms as they provide the backbone of the information required for formation of proteins. Changes in genes leads to disorders and these disorders could be rectified by reversing the mutation which caused it. Current photo-chemical methods for site-directed mutagenesis use 3-cyanovinylcarbazole (CNVK) incorporated in the oligodeoxyribonucleotide (ODN). The major drawback of this method, requirement of high temperature, has been addressed and the deamination has been achieved at 37ºC but with low efficiency...
September 8, 2018: Chembiochem: a European Journal of Chemical Biology
Woojoo Kim, Ashay Patel, Gene Hur, Peter Tufar, Michael Wuo, Andrew J McCammon, Michael D Burkart
Nonribosomal peptide synthetases (NRPSs) are responsible for the synthesis of a variety of bioactive natural products with clinical and economic significance. Interestingly, these large multimodular enzyme machineries incorporate nonproteinogenic D-amino acids through the use of auxiliary epimerization domains, converting L-amino acids into D-amino acids, which impart into the resulting natural products unique bioactivity and resistance to proteases. Due to the large and complex nature of NRPSs, several questions remain unanswered about the mechanism of the catalytic domain reactions...
September 8, 2018: Chembiochem: a European Journal of Chemical Biology
Venkat Gopalan, Seth E Lyon, Tien-Hao Chen, Andrew J Wallace, Katie L Adib
Chemo-enzymatic approaches are important for generating site-specific, chemically-modified RNAs, a cornerstone for RNA structure-function correlation studies. T7 RNA polymerase (T7RNAP)-mediated in vitro transcription (IVT) of a DNA template containing the G-initiating class III Φ6.5 promoter is typically used to generate 5'-chemically-modified RNAs by including a guanosine analog (G-analog) initiator in the IVT. However, the yield of 5'-G-analog-initiated RNA is often poor and variable due to the high ratios of G-analog:GTP used in IVTs...
September 8, 2018: Chembiochem: a European Journal of Chemical Biology
Georg T Höfler, Elena Fernández-Fueyo, Milja Pesic, Sabry Younes, Eun-Gyu Choi, Yong H Kim, Vlada Urlacher, Isabel Arends, Frank Hollmann
A photoenzymatic NADH regeneration system was established. The combination of deazariboflavin as photocatalyst with putidaredoxin reductase enables selective reduction of NAD+ into the enzyme-active 1,4-NADH to promote an alcohol dehydrogenase-catalysed stereospecific reduction reaction. Catalytic turnover of all reaction components was demonstrated. Factors influencing the efficiency of the overall system were identified.
September 7, 2018: Chembiochem: a European Journal of Chemical Biology
Lei Liu
Histone ubiquitination and deubiquitination processes and the mechanisms of their regulation are greatly relevant to the field of epigenetics. Recently, the deubiquitinating enzyme USP51 was reported to selectively cleave ubiquitination on histone H2A at K13 or K15 (i.e. H2AK13Ub and H2AK15Ub) but not at K119 (i.e. H2AK119Ub) in nucleosomes in vivo. To elucidate the mechanism for the selectivity of USP51, we built structurally well-defined in vitro protein systems bearing a ubiquitin modification at precise sites...
September 7, 2018: Chembiochem: a European Journal of Chemical Biology
Ryuji Tsunekawa, Kazuhiro Katayama, Kengo Hanaya, Shuhei Higashibayashi, Yoshikazu Sugimoto, Takeshi Sugai
3',4',7-Trimethoxyflavone (TMF) has been reported to show a potent reversal effect on breast cancer resistance protein (BCRP/ABCG2)-mediated drug resistance. In this study, we designed and synthesized five derivatives with either a hydroxy group or fluorine atom at C-5 and several kinds of capping moiety at the C-7 hydroxy group, on the same 3',4'-dimethoxy substituted flavone skeleton. We subsequently evaluated the efficacies of these compounds against BCRP-expressing human leukemia K562/BCRP cells. Reversal of drug resistance was expressed as the concentration of compound causing a two-fold reduction in drug sensitivity (RI50)...
September 6, 2018: Chembiochem: a European Journal of Chemical Biology
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