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cyclization peptides

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https://www.readbyqxmd.com/read/28608830/a-simple-defined-medium-for-the-production-of-true-diketopiperazines-in-xylella-fastidiosa-and-their-identification-by-ultra-fast-liquid-chromatography-electrospray-ionization-ion-trap-mass-spectrometry
#1
Michelli Massaroli da Silva, Moacir Dos Santos Andrade, Anelize Bauermeister, Marcus Vinícius Merfa, Moacir Rossi Forim, João Batista Fernandes, Paulo Cezar Vieira, Maria Fátima das Graças Fernandes da Silva, Norberto Peporine Lopes, Marcos Antônio Machado, Alessandra Alves de Souza
Diketopiperazines can be generated by non-enzymatic cyclization of linear dipeptides at extreme temperature or pH, and the complex medium used to culture bacteria and fungi including phytone peptone and trypticase peptone, can also produce cyclic peptides by heat sterilization. As a result, it is not always clear if many diketopiperazines reported in the literature are artifacts formed by the different complex media used in microorganism growth. An ideal method for analysis of these compounds should identify whether they are either synthesized de novo from the products of primary metabolism and deliver true diketopiperazines...
June 13, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28598597/azapeptide-synthesis-methods-for-expanding-side-chain-diversity-for-biomedical-applications
#2
Ramesh Chingle, Caroline Proulx, William D Lubell
Mimicry of bioactive conformations is critical for peptide-based medicinal chemistry because such peptidomimetics may augment stability, enhance affinity, and increase specificity. Azapeptides are peptidomimetics in which the α-carbon(s) of one or more amino acid residues are substituted by nitrogen. The resulting semicarbazide analogues have been shown to reinforce β-turn conformation through the combination of lone pair-lone pair repulsion of the adjacent hydrazine nitrogen and urea planarity. Substitution of a semicarbazide for an amino amide residue in a peptide may retain biological activity and add benefits such as improved metabolic stability...
June 9, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28578648/synthetic-peptide-drugs-for-targeting-skin-cancer-malignant-melanoma-and-melanotic-lesions
#3
Alex Eberle, Bhimsen Rout, Mei Bigliardi Qi, Paul L Bigliardi
Peptides play decisive roles in the skin, ranging from host defense responses to various forms of neuroendocrine regulation of cell and organelle function. Synthetic peptides conjugated to radionuclides or photosensitizers may serve to identify and treat skin tumors and their metastatic forms in other organs of the body. In the introductory part of his review, the role and interplay of the different peptides in the skin is briefly summarized, including their potential application for the management of frequently occurring skin cancers...
June 4, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/28561582/interplay-of-stereochemistry-conformational-rigidity-and-ease-of-synthesis-for-13-membered-cyclic-peptidomimetics-containing-apc-residues
#4
Dongyue Xin, Andrew Jeffries, Kevin Burgess
As part of a program to design small molecules that bind proteins, we require cyclic peptides (or peptidomimetics) that are severely constrained such that they adopt one predominant conformation in solution. This paper describes syntheses of the 13-membered cyclic tetrapeptides 1 containing aminopyrrolidine carboxyl (APC) residues. A linear precursor was prepared and used to determine optimal conditions for cyclization of that substrate. A special linker was prepared to enable cyclization of similar linear peptidomimetics on a solid phase, and the solution-phase cyclization conditions were shown to be appropriate for this too...
May 31, 2017: ACS Combinatorial Science
https://www.readbyqxmd.com/read/28544675/cyclotides-overview-and-biotechnological-applications
#5
REVIEW
Andrew Gould, Julio A Camarero
Cyclotides are globular microproteins with a unique head-to-tail cyclized backbone, stabilized by three disulfide bonds forming a cystine knot. This unique circular backbone topology and knotted arrangement of three disulfide bonds makes them exceptionally stable to chemical, thermal, and biological degradation compared to other peptides of similar size. In addition, cyclotides have been shown to be highly tolerant to sequence variability, aside from the conserved residues forming the cystine knot. Cyclotides can also cross cellular membranes and are able to modulate intracellular protein-protein interactions, both in vitro and in vivo...
May 24, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28541045/orally-absorbed-cyclic-peptides
#6
Daniel S Nielsen, Nicholas E Shepherd, Weijun Xu, Andrew J Lucke, Martin J Stoermer, David P Fairlie
Peptides and proteins are not orally bioavailable in mammals, although a few peptides are intestinally absorbed in small amounts. Polypeptides are generally too large and polar to passively diffuse through lipid membranes, while most known active transport mechanisms facilitate cell uptake of only very small peptides. Systematic evaluations of peptides with molecular weights above 500 Da are needed to identify parameters that influence oral bioavailability. Here we describe 125 cyclic peptides containing four to thirty-seven amino acids that are orally absorbed by mammals...
May 25, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28538738/solid-phase-synthesis-cyclization-and-site-specific-functionalization-of-aziridine-containing-tetrapeptides
#7
Benjamin K W Chung, Christopher J White, Andrei K Yudin
Cyclic tetrapeptides comprise a potent and selective class of molecules with a wide range of biological activities, including the phytotoxic activity of tentoxin and the histone deacetylase (HDAC) inhibitory effects of chlamydocin. The incorporation of a functional aziridine group within cyclic peptides enables their conformational control and allows for late-stage and site-selective functionalization of these molecules, thereby creating the potential for covalent protein labeling. This protocol describes the solid-phase synthesis, cyclization, and site-specific structural modification of aziridine-containing tetrapeptides...
June 2017: Nature Protocols
https://www.readbyqxmd.com/read/28536266/two-proteins-for-the-price-of-one-structural-studies-of-the-dual-destiny-preproalbumin-with-sunflower-trypsin-inhibitor-1
#8
Bastian Franke, Amy M James, Mehdi Mobli, Michelle L Colgrave, Joshua S Mylne, K Johan Rosengren
Seed storage proteins are both an important source of nutrition for humans and essential for seedling establishment. Interestingly, unusual napin-type 2S seed storage albumin precursors in sunflower contain a sequence that is released as a macrocyclic peptide during post-translational processing. The mechanism by which such peptides emerge from linear precursors proteins has received increased attention, however the structural characterization of intact precursor proteins has been limited. Here we report the 3D NMR structure of the Helianthus annuus PreproAlbumin With Sunflower trypsin inhibitor-1 (PawS1), and provide new insights into the processing of this remarkable dual-destiny protein...
May 23, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28534477/decoding-and-reprogramming-fungal-iterative-nonribosomal-peptide-synthetases
#9
Dayu Yu, Fuchao Xu, Shuwei Zhang, Jixun Zhan
Nonribosomal peptide synthetases (NRPSs) assemble a large group of structurally and functionally diverse natural products. While the iterative catalytic mechanism of bacterial NRPSs is known, it remains unclear how fungal NRPSs create products of desired length. Here we show that fungal iterative NRPSs adopt an alternate incorporation strategy. Beauvericin and bassianolide synthetases have the same C1-A1-T1-C2-A2-MT-T2a-T2b-C3 domain organization. During catalysis, C3 and C2 take turns to incorporate the two biosynthetic precursors into the growing depsipeptide chain that swings between T1 and T2a/T2b with C3 cyclizing the chain when it reaches the full length...
May 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28520410/proteolytically-stable-cyclic-decapeptide-for-breast-cancer-cell-targeting
#10
Yogita Raghuwanshi, Hashem Etayash, Rania Soudy, Igor Paiva, Afsaneh Lavasanifar, Kamaljit Kaur
Starting with a previously reported linear breast cancer targeting decapeptide WxEAAYQkFL, here we report the synthesis of a novel cyclic peptide analogue cyclic WXEAAYQkFL. The N- to C-terminus amide cyclized peptide with one d-amino acid (k) displayed higher uptake by breast cancer cells, with minimal uptake by the noncancerous cells compared to the linear peptide with two d-amino acids (x and k), and was stable toward proteolytic degradation. When immobilized on gold microcantilever surface, the cyclic peptide was able to capture breast cancer cells specifically and sense samples with ≥25 cancer cells/mL...
June 6, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28504677/%C3%AE-lactone-formation-during-product-release-from-a-nonribosomal-peptide-synthetase
#11
Jason E Schaffer, Margaret R Reck, Neha K Prasad, Timothy A Wencewicz
Nonribosomal peptide synthetases (NRPSs) are multidomain modular biosynthetic assembly lines that polymerize amino acids into a myriad of biologically active nonribosomal peptides (NRPs). NRPS thioesterase (TE) domains employ diverse release strategies for off-loading thioester-tethered polymeric peptides from termination modules typically via hydrolysis, aminolysis, or cyclization to provide mature antibiotics as carboxylic acids/esters, amides, and lactams/lactones, respectively. Here we report the enzyme-catalyzed formation of a highly strained β-lactone ring during TE-mediated cyclization of a β-hydroxythioester to release the antibiotic obafluorin (Obi) from an NRPS assembly line...
July 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28498670/palladium-catalyzed-aminocarbonylation-in-solid-phase-peptide-synthesis-a-method-for-capping-cyclization-and-isotope-labeling
#12
Anna Skogh, Stig D Friis, Troels Skrydstrup, Anja Sandström
A new synthetic approach for introducing N-capping groups onto peptides attached to a solid support, combining aminocarbonylation under mild conditions using a palladacycle precatalyst and solid-phase peptide synthesis, is reported. The use of a silacarboxylic acid as an in situ CO-releasing molecule allowed the reaction to be performed in a single vial. The method also enables versatile substitution of side chains, side-chain-to-side-chain cyclizations, and selective [(13)C] acyl labeling of modified peptides...
May 12, 2017: Organic Letters
https://www.readbyqxmd.com/read/28483279/macrocyclization-of-a-potent-pace4-inhibitor-benefits-and-limitations
#13
Teresa Łepek, Anna Kwiatkowska, Frédéric Couture, Kévin Ly, Roxane Desjardins, Yves Dory, Adam Prahl, Robert Day
PACE4, one of the seven members of the proprotein convertase family, plays an important role in the progression of prostate cancer. Therefore, its inhibition has become an attractive target to develop new therapies against this disease. Recently, we have developed a highly potent and selective PACE4 inhibitor, known as the multi-Leu peptide with the following sequence Ac-LLLLRVKR-NH2. Herein, with the aim of improving the stability profile of this inhibitor for potential in vivo application, we investigated the impact of different cyclization strategies...
April 23, 2017: European Journal of Cell Biology
https://www.readbyqxmd.com/read/28475844/a-blind-test-of-computational-technique-for-predicting-the-likelihood-of-peptide-sequences-to-cyclize
#14
Jonathan Booth, Christina-Nicoleta Alexandru-Crivac, Kirstie A Rickaby, Ada F Nneoyiegbe, Ugochukwu Umeobika, Andrew R McEwan, Laurent Trembleau, Marcel Jaspars, Wael E Houssen, Dmitrii V Shalashilin
An in silico computational technique for predicting peptide sequences that can be cyclized by cyanobactin macrocyclases, e.g., PatGmac, is reported. We demonstrate that the propensity for PatGmac-mediated cyclization correlates strongly with the free energy of the so-called pre-cyclization conformation (PCC), which is a fold where the cyclizing sequence C and N termini are in close proximity. This conclusion is driven by comparison of the predictions of boxed molecular dynamics (BXD) with experimental data, which have achieved an accuracy of 84%...
May 18, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28466571/synthesis-of-relaxin-2-and-insulin-like-peptide-5-enabled-by-novel-tethering-and-traceless-chemical-excision
#15
Kishore Thalluri, Binbin Kou, Xu Yang, Alexander N Zaykov, John P Mayer, Vasily M Gelfanov, Fa Liu, Richard D DiMarchi
This report presents an entirely chemical, general strategy for the synthesis of relaxin-2 and insulin-like peptide 5. Historically, these two peptides have represented two of the more synthetically challenging members of the insulin superfamily. The key synthetic steps involve two sequential oxime ligations to covalently link the individual A-chain and B-chain, followed by disulfide bond formation under aqueous, redox conditions. This is followed by two chemical reactions that employ diketopiperazine cyclization-mediated cleavage and ester hydrolysis to liberate the connecting peptide and the heterodimeric product...
May 3, 2017: Journal of Peptide Science: An Official Publication of the European Peptide Society
https://www.readbyqxmd.com/read/28460065/sbspksv2-structure-based-sequence-analysis-of-polyketide-synthases-and-non-ribosomal-peptide-synthetases
#16
Shradha Khater, Money Gupta, Priyesh Agrawal, Neetu Sain, Jyoti Prava, Priya Gupta, Mansi Grover, Narendra Kumar, Debasisa Mohanty
Genome guided discovery of novel natural products has been a promising approach for identification of new bioactive compounds. SBSPKS web-server has been a valuable resource for analysis of polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) gene clusters. We have developed an updated version - SBSPKSv2 which is based on comprehensive analysis of sequence, structure and secondary metabolite chemical structure data from 311 experimentally characterized PKS/NRPS gene clusters with known biosynthetic products...
April 29, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28457894/lipophilic-peptide-character-what-oral-barriers-fear-the-most
#17
REVIEW
Ožbej Zupančič, Andreas Bernkop-Schnürch
Peptide therapeutics is currently one of the fastest growing markets worldwide and consequently convenient ways of administration for these drugs are highly on demand. In particular, oral dosage forms would be preferred. A relative large molecular weight and high hydrophilicity, however, result in comparatively very low oral bioavailability being in most cases below 1%. Lipid based formulations (LBF), in particular self-emulsifying drug delivery systems (SEDDS) and solid lipid nanoparticles (SLN) as well as liposomes are among the most promising tools for oral peptide delivery...
April 28, 2017: Journal of Controlled Release: Official Journal of the Controlled Release Society
https://www.readbyqxmd.com/read/28451290/activation-and-characterization-of-a-cryptic-gene-cluster-reveals-a-cyclization-cascade-for-polycyclic-tetramate-macrolactams
#18
Subhasish Saha, Wenjun Zhang, Guangtao Zhang, Yiguang Zhu, Yuchan Chen, Wei Liu, Chengshan Yuan, Qingbo Zhang, Haibo Zhang, Liping Zhang, Weimin Zhang, Changsheng Zhang
Polycyclic tetramate macrolactams (PTMs) are a growing class of natural products and are derived from a hybrid polyketide synthase (PKS)/non-ribosomal peptide synthetase (NRPS) pathway. PTM biosynthetic gene clusters are conserved and widely distributed in bacteria, however, most of them remain silent. Herein we report the activation of a PTM gene cluster in marine-derived Streptomyces pactum SCSIO 02999 by promoter engineering and heterologous expression, leading to the discovery of six new PTMs, pactamides A-F (11-16), with potent cytotoxic activity upon several human cancer cell lines...
February 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28444893/catalytic-reductive-synthesis-and-direct-derivatization-of-unprotected-aminoindoles-aminopyrroles-and-iminoindolines
#19
Leonardus H Leijendekker, Jens Weweler, Tobias M Leuther, Jan Streuff
A titanium(III)-catalyzed radical cyclization to unprotected 3-aminoindoles, 3-aminopyrroles, or 3-iminoindolines is reported. The reaction is non-hazardous, scalable, and allows facile isolation of the free products by extraction. The method is demonstrated on a large substrate scope and it further allows the direct installation of various nitrogen protecting groups or the synthesis of building blocks for peptide chemistry in a single sequence. Fused bisindoles can be directly accessed from the cyclization products...
April 26, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28428776/mapping-and-identification-of-antifungal-peptides-in-the-putative-antifungal-protein-afpb-from-the-filamentous-fungus-penicillium-digitatum
#20
Sandra Garrigues, Mónica Gandía, Attila Borics, Florentine Marx, Paloma Manzanares, Jose F Marcos
Antifungal proteins (AFPs) from Ascomycetes are small cysteine-rich proteins that are abundantly secreted and show antifungal activity against non-producer fungi. A gene coding for a class B AFP (AfpB) was previously identified in the genome of the plant pathogen Penicillium digitatum. However, previous attempts to detect the AfpB protein were not successful despite the high expression of the corresponding afpB gene. In this work, the structure of the putative AfpB was modeled. Based on this model, four synthetic cysteine-containing peptides, PAF109, PAF112, PAF118, and PAF119, were designed and their antimicrobial activity was tested and characterized...
2017: Frontiers in Microbiology
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