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https://www.readbyqxmd.com/read/28685529/expression-of-cell-mitotic-progression-proteins-and-keratinocyte-markers-in-porcine-buccal-pouch-mucosal-cells-during-short-term-real-time-primary-culture
#1
A Bryja, M Dyszkiewicz-Konwińska, J Budna, S Ciesiółka, W Kranc, S Borys, M Jeseta, O Urbaniak, D Bukowska, P Antosik, M Bruska, M Nowicki, M Zabel, B Kempisty
The porcine model is often used in clinical trials. The pig has many fundamental anatomic, physiological and nutritional similarities to humans. Additionally, the European Medicines Agency (EMA) demands the use large animals in clinical studies. Oral mucosa has received special attention due to its regenerative properties. Oral tissue is composed of several types of cells including fibroblasts and keratinocytes. The porcine oral mucosa/buccal pouch mucosa has a cellular structure with defined proliferation and differentiated capability...
April 2017: Journal of Biological Regulators and Homeostatic Agents
https://www.readbyqxmd.com/read/28680090/pan-cancer-emt-signature-identifies-rbm47-down-regulation-during-colorectal-cancer-progression
#2
Matjaz Rokavec, Markus Kaller, David Horst, Heiko Hermeking
Epithelial-mesenchymal transition (EMT) plays an important role in tumor invasion and metastasis. A comprehensive, bioinformatics analysis of CCLE and TCGA datasets of seven tumor types allowed us to identify a novel pan-cancer EMT-associated gene expression signature consisting of 16 epithelial and 4 mesenchymal state-associated mRNAs. Among the identified epithelial cell state-associated factors, down-regulation of the RBM47 (RNA binding motif protein 47) mRNA displayed the most significant association with metastasis and poor survival in multiple cohorts of colorectal cancer (CRC) patients...
July 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28584151/discovery-and-characterization-of-a-novel-cd4-binding-adnectin-with-potent-anti-hiv-activity
#3
David Wensel, Yongnian Sun, Zhufang Li, Sharon Zhang, Caryn Picarillo, Thomas McDonagh, David Fabrizio, Mark Cockett, Mark Krystal, Jonathan Davis
A novel fibronectin-based protein (Adnectin) HIV-1 inhibitor was generated using in vitro selection. This inhibitor binds to human CD4 with high affinity (3.9 nM) and inhibits viral entry at a step post-CD4 engagement and preceding membrane fusion. The progenitor sequence of this novel inhibitor was selected from a library of trillions of Adnectin variants using mRNA display, then further optimized for improved anti-viral and physical properties. The final optimized inhibitor exhibited full potency against a panel of 124 envelope (gp160) proteins spanning 11 subtypes, indicating broad spectrum activity...
June 5, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28572907/linker-free-incorporation-of-carbohydrates-into-in-vitro-displayed-macrocyclic-peptides
#4
S A K Jongkees, S Umemoto, H Suga
We report a strategy for efficient post-translational modification of a library of ribosomally-translated peptides by activation and elimination of cysteine to dehydroalanine then conjugate addition of a range of exogenous thiols, with an emphasis on carbohydrates. These reactions are selective for cysteine, and do not interfere with amplification of the nucleic acid component of an mRNA-displayed peptide. Furthermore, these reactions are shown to be compatible with two different macrocyclisation chemistries, and when applied to a peptide containing an N-terminal cysteine give a ketone that can be functionalised in an orthogonal manner...
February 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28522832/the-fragment-hmga2-sh-3p20-from-hmga2-mrna-3-utr-promotes-the-growth-of-hepatoma-cells-by-upregulating-hmga2
#5
Yuan Wang, Fuquan Chen, Zhe Yang, Man Zhao, Shuqin Zhang, Yuen Gao, Jinyan Feng, Guang Yang, Weiying Zhang, Lihong Ye, Xiaodong Zhang
High mobility group A2 (HMGA2) plays a crucial role in the development of cancer. However, the mechanism by which HMGA2 promotes the growth of hepatocellular carcinoma (HCC) remains unclear. Here, we explore the hypothesis that HMGA2 may enhance the growth of hepatoma cells through a fragment based on the secondary structure of HMGA2 mRNA 3'-untranslated region (3'UTR). Bioinformatics analysis showed that HMGA2 mRNA displayed a hairpin structure within its 3'UTR, termed HMGA2-sh. Mechanistically, RNA immunoprecipitation assays showed that the microprocessor Drosha or DGCR8 interacted with HMGA2 mRNA in hepatoma cells...
May 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28368002/macrocycle-peptides-delineate-locked-open-inhibition-mechanism-for-microorganism-phosphoglycerate-mutases
#6
Hao Yu, Patricia Dranchak, Zhiru Li, Ryan MacArthur, Matthew S Munson, Nurjahan Mehzabeen, Nathan J Baird, Kevin P Battalie, David Ross, Scott Lovell, Clotilde K S Carlow, Hiroaki Suga, James Inglese
Glycolytic interconversion of phosphoglycerate isomers is catalysed in numerous pathogenic microorganisms by a cofactor-independent mutase (iPGM) structurally distinct from the mammalian cofactor-dependent (dPGM) isozyme. The iPGM active site dynamically assembles through substrate-triggered movement of phosphatase and transferase domains creating a solvent inaccessible cavity. Here we identify alternate ligand binding regions using nematode iPGM to select and enrich lariat-like ligands from an mRNA-display macrocyclic peptide library containing >10(12) members...
April 3, 2017: Nature Communications
https://www.readbyqxmd.com/read/28358987/highly-selective-targeting-of-hepatic-stellate-cells-for-liver-fibrosis-treatment-using-a-d-enantiomeric-peptide-ligand-of-fn14-identified-by-mirror-image-mrna-display
#7
Luying Huang, Jing Xie, Qiuyan Bi, Zhuoxuan Li, Sha Liu, Qing Shen, Chong Li
Although liver fibrosis is a major public health issue, there is still no effective drug therapy in the clinic. Fibroblast growth factor-inducible 14 (Fn14), a membrane receptor highly specifically expressed in activated hepatic stellate cells (HSCs), is the key driver of liver fibrosis, and thus, it has a great potential as a novel target for the development of effective treatment. Here, we identified a d-enantiomeric peptide ligand of Fn14 through mirror-image mRNA display. This included the chemical synthesis of a d-enantiomer of the target protein (extracellular domain of Fn14), identification of an l-peptide ligand of d-Fn14 using a constructed mRNA peptide library, and identification of a d-enantiomer of the l-peptide, which is a ligand of the natural Fn14 for reasons of symmetry...
April 12, 2017: Molecular Pharmaceutics
https://www.readbyqxmd.com/read/28319812/exploring-sequence-space-harnessing-chemical-and-biological-diversity-towards-new-peptide-leads
#8
REVIEW
Richard Obexer, Louise J Walport, Hiroaki Suga
From their early roots in natural products, peptides now represent an expanding class of novel drugs. Their modular structures make them ideal candidates for pooled library screening approaches. Key technologies for library generation and screening, such as SICLOPPS, phage display and mRNA display, give unparalleled access to tight binding peptides. Through combination with genetic code reprogramming and chemical modifications, access to more natural product-like libraries, spanning non-canonical peptide space, is readily achievable...
June 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28302013/multicyclic-peptides-as-scaffolds-for-the-development-of-tumor-targeting-agents
#9
Anastasia Loktev, Uwe Haberkorn, Walter Mier
The lack of specificity of traditional cytotoxic drugs triggers the development of anticancer agents with high selectivity to tumor-specific proteins. The unveiling of target structures such as EGFR or Her2 allows the focused development of novel therapies and has strongly advanced tumor treatment. Tumor-specific high-affinity ligands can be identified by using display techniques such as phage, yeast surface, ribosome and mRNA display. These techniques enable the screening of huge libraries, consequently providing a valuable alternative to rational drug development...
March 16, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/28275529/enhanced-mrna-protein-fusion-efficiency-of-a-single-domain-antibody-by-selection-of-mrna-display-with-additional-random-sequences-in-the-terminal-translated-regions
#10
Kazuki Takahashi, Masato Sunohara, Takuya Terai, Shigefumi Kumachi, Naoto Nemoto
In vitro display technologies such as mRNA and cDNA display are powerful tools to create and select functional peptides. However, in some cases, efficiency of mRNA-protein fusion is very low, which results in decreased library size and lower chance of successful selection. In this study, to improve mRNA-protein fusion efficiency, we prepared an mRNA display library of a protein with random N- and C-terminal coding regions consisting of 12 nucleotides (i.e. four amino acids), and performed an electrophoresis mobility shift assay (EMSA)-based selection of successfully formed mRNA display molecules...
2017: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/28240181/recent-advances-in-synthesis-and-identification-of-cyclic-peptides-for-bioapplications
#11
Yong Siang Ong, Liqian Gao, Karunakaran A Kalesh, Zhiqiang Yu, Jigang Wang, Chengcheng Liu, Yiwen Li, Hongyan Sun, Su Seong Lee
Cyclic peptides, owing to their good stability, high resistance to exo- and to some extent endo-peptidases, enhanced binding affinity and selectivity towards target biomolecules, are actively investigated as biochemical tools and therapeutic agents. In this review, we discuss various commonly utilized synthetic strategies for cyclic peptides and peptoids (peptidomimetics), their important screening methods to identify the bioactive cyclic peptides and peptoids such as combinatorial bead-based peptide library, phage display, mRNA display etc...
February 24, 2017: Current Topics in Medicinal Chemistry
https://www.readbyqxmd.com/read/28146347/highly-constrained-bicyclic-scaffolds-for-the-discovery-of-protease-stable-peptides-via-mrna-display
#12
David E Hacker, Jan Hoinka, Emil S Iqbal, Teresa M Przytycka, Matthew C T Hartman
Highly constrained peptides such as the knotted peptide natural products are promising medicinal agents because of their impressive biostability and potent activity. Yet, libraries of highly constrained peptides are challenging to prepare. Here, we present a method which utilizes two robust, orthogonal chemical steps to create highly constrained bicyclic peptide libraries. This technology was optimized to be compatible with in vitro selections by mRNA display. We performed side-by-side monocyclic and bicyclic selections against a model protein (streptavidin)...
March 17, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/27865780/rasins-genetically-encoded-intrabodies-of-activated-ras-proteins
#13
Mehmet Cetin, William E Evenson, Garrett G Gross, Farzad Jalali-Yazdi, Daniel Krieger, Don Arnold, Terry T Takahashi, Richard W Roberts
K- and H-Ras are the most commonly mutated genes in human tumors and are critical for conferring and maintaining the oncogenic phenotype in tumors with poor prognoses. Here, we design genetically encoded antibody-like ligands (intrabodies) that recognize active, GTP-bound K- and H-Ras. These ligands, which use the 10th domain of human fibronectin as their scaffold, are stable inside the cells and when fused with a fluorescent protein label, the constitutively active G12V mutant H-Ras. Primary selection of ligands against Ras with mRNA display resulted in an intrabody (termed RasIn1) that binds with a KD of 2...
February 17, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27862752/improving-the-binding-affinity-of-in-vitro-evolved-cyclic-peptides-by-inserting-atoms-into-the-macrocycle-backbone
#14
Jonas Wilbs, Simon J Middendorp, Christian Heinis
Cyclic peptides binding to targets of interest can be generated efficiently with powerful in vitro display techniques, such as phage display or mRNA display. The cyclic peptide libraries screened with these methods are generated by altering in a combinatorial fashion the amino acid sequence of the peptides, the number of amino acids in the macrocycle rings, and the cyclization chemistry. A structural element that cannot easily be varied in the cyclic peptides is the backbone, which is built from amino acids, each of which contributes three atoms to the macrocyclic ring structure...
December 14, 2016: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/27624596/endoplasmic-reticulum-directed-recombinant-mrna-displays-subcellular-localization-equal-to-endogenous-mrna-during-transient-expression-in-cho-cells
#15
Thomas Beuchert Kallehauge, Stefan Kol, Mikael Rørdam Andersen, Christian Kroun Damgaard, Gyun Min Lee, Helene Faustrup Kildegaard
When expressing pharmaceutical recombinant proteins in mammalian cells, the protein is commonly directed through the secretory pathway, in a signal peptide-dependent manner, to acquire specific post-translational modifications and to facilitate secretion into the culture medium. One key premise for this is the direction of the mRNA encoding the recombinant protein to the surface of the endoplasmic reticulum (ER) for subsequent protein translocation into the secretory pathway. To evaluate the efficiency of this process in Chinese hamster ovary (CHO) cells, the subcellular localization of recombinant mRNA encoding the therapeutic proteins, erythropoietin (EPO) and Rituximab, was determined...
October 2016: Biotechnology Journal
https://www.readbyqxmd.com/read/27576167/region-specific-alterations-of-a-to-i-rna-editing-of-serotonin-2c-receptor-in-the-cortex-of-suicides-with-major-depression
#16
D Weissmann, S van der Laan, M D Underwood, N Salvetat, L Cavarec, L Vincent, F Molina, J J Mann, V Arango, J F Pujol
Brain region-specific abnormalities in serotonergic transmission appear to underlie suicidal behavior. Alterations of RNA editing on the serotonin receptor 2C (HTR2C) pre-mRNA in the brain of suicides produce transcripts that attenuate 5-HT2CR signaling by impairing intracellular G-protein coupling and subsequent intracellular signal transduction. In brain, the distribution of RNA-editing enzymes catalyzing deamination (A-to-I modification) shows regional variation, including within the cerebral cortex. We tested the hypothesis that altered pre-mRNA 5-HT2CR receptor editing in suicide is region-specific...
August 30, 2016: Translational Psychiatry
https://www.readbyqxmd.com/read/27465925/directed-evolution-of-scanning-unnatural-protease-resistant-supr-peptides-for-in-vivo-applications
#17
Stephen V Fiacco, Lindsay E Kelderhouse, Amanda Hardy, Yonatan Peleg, Biliang Hu, Argentina Ornelas, Peiying Yang, Seth T Gammon, Shannon M Howell, Pin Wang, Terry T Takahashi, Steven W Millward, Richard W Roberts
Peptides typically have poor biostabilities, and natural sequences cannot easily be converted into drug-like molecules without extensive medicinal chemistry. We have adapted mRNA display to drive the evolution of highly stable cyclic peptides while preserving target affinity. To do this, we incorporated an unnatural amino acid in an mRNA display library that was subjected to proteolysis prior to selection for function. The resulting "SUPR (scanning unnatural protease resistant) peptide" showed ≈500-fold improvement in serum stability (t1/2 =160 h) and up to 3700-fold improvement in protease resistance versus the parent sequence...
September 2, 2016: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/27464514/cloning-and-characterization-of-lxr-and-srebp1-and-their-potential-roles-in-regulation-of-lc-pufa-biosynthesis-in-rabbitfish-siganus-canaliculatus
#18
Qinghao Zhang, Cuihong You, Fang Liu, Wendi Zhu, Shuqi Wang, Dizhi Xie, Óscar Monroig, Douglas R Tocher, Yuanyou Li
Rabbitfish Siganus canaliculatus was the first marine teleost demonstrated to have the ability to biosynthesize C20-22 long-chain polyunsaturated fatty acid (LC-PUFA) from C18 PUFA precursors, which is generally absent or low in marine teleosts. Thus, understanding the molecular basis of LC-PUFA biosynthesis in rabbitfish will contribute to efforts aimed at optimizing LC-PUFA biosynthesis in teleosts, especially marine species. In the present study, the importance of the transcription factors liver X receptor (Lxr) and sterol regulatory element-binding protein 1 (Srebp1) in regulation of LC-PUFA biosynthesis in rabbitfish was investigated...
September 2016: Lipids
https://www.readbyqxmd.com/read/27411326/use-of-peptide-libraries-for-identification-and-optimization-of-novel-antimicrobial-peptides
#19
REVIEW
Martin Ashby, Asya Petkova, Jurnorain Gani, Ralf Mikut, Kai Hilpert
The increasing rates of resistance among bacteria and to a lesser extent fungi have resulted in an urgent need to find new molecules that hold therapeutic promise against multidrug-resistant strains. Antimicrobial peptides have proven very effective against a variety of multidrug-resistant bacteria. Additionally, the low levels of resistance reported towards these molecules are an attractive feature for antimicrobial drug development. Here we summarise information on diverse peptide libraries used to discover or to optimize antimicrobial peptides...
2017: Current Topics in Medicinal Chemistry
https://www.readbyqxmd.com/read/27385640/peptide-synthesis-on-a-next-generation-dna-sequencing-platform
#20
Nina Svensen, Olve B Peersen, Samie R Jaffrey
Methods for displaying large numbers of peptides on solid surfaces are essential for high-throughput characterization of peptide function and binding properties. Here we describe a method for converting the >10(7) flow cell-bound clusters of identical DNA strands generated by the Illumina DNA sequencing technology into clusters of complementary RNA, and subsequently peptide clusters. We modified the flow-cell-bound primers with ribonucleotides thus enabling them to be used by poliovirus polymerase 3D(pol) ...
September 2, 2016: Chembiochem: a European Journal of Chemical Biology
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