Int J Environ Res Public Health. 2010 Oct;7(10):3804-15. Epub 2010 Oct 22.
Effects of Various Doses of Selenite on Stinging Nettle (Urtica dioica L.).
Krystofova O, Adam V, Babula P, Zehnalek J, Beklova M, Havel L, Kizek R.
Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; E-Mails: olga.krystofova@seznam.cz (O.K.); vojtech.adam@mendelu.cz (V.A.); zehnalek@mendelu.cz (J.Z.).
Abstract
The aim of this study was to investigate the effects of selenium (Se) on the growth, accumulation and possible mechanisms of Se transport in certain parts (roots, leaves, stamp and apex) of nettle (Urtica dioica L.) plants. Se was supplemented by one-shot and two repeated doses to the soil (2.0 and 4.0 mg Se per kg of substrate). Selenium content in roots increased linearly with dose and was significantly higher compared to other plant parts of interest. However, growth of the above-ground parts of plant as well as roots was slightly inhibited with increasing selenium concentration in comparison to the untreated plants. The content of phytochelatin2, a low molecular mass peptide containing a sulfhydryl group, correlated well with the Se content. This suggests a possible stimulation of synthesis of this plant peptide by Se.
PMID: 21139861 [PubMed - in process]
Bioorg Med Chem. 2010 Nov 12. [Epub ahead of print]
Synthesis of a-factor peptide from Saccharomyces cerevisiae and photoactive analogues via Fmoc solid phase methodology.
Mullen DG, Kyro K, Hauser M, Gustavsson M, Veglia G, Becker JM, Naider F, Distefano MD.
Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, United States.
Abstract
a-Factor from Saccharomyces cerevisiae is a farnesylated dodecapeptide involved in mating. The molecule binds to a G-protein coupled receptor and hence serves as a simple system for studying the interactions between prenylated molecules and their cognate receptors. Here, we describe the preparation of a-factor and two photoactive analogues via Fmoc solid-phase peptide synthesis using hydrazinobenzoyl AM NovaGel™ resin; the structure of the synthetic a-factor was confirmed by MS-MS analysis and NMR; the structures of the analogues were confirmed by MS-MS analysis. Using a yeast growth arrest assay, the analogues were found to have activity comparable to a-factor itself.
Copyright © 2010 Elsevier Ltd. All rights reserved.PMID: 21134758 [PubMed - as supplied by publisher]
Chemistry. 2010 Dec 3. [Epub ahead of print]
Structural Design, Solid-Phase Synthesis and Activity of Membrane-Anchored β-Secretase Inhibitors on Aβ Generation from Wild-Type and Swedish-Mutant APP.
Schieb H, Weidlich S, Schlechtingen G, Linning P, Jennings G, Gruner M, Wiltfang J, Klafki HW, Knölker HJ.
Department of Psychiatry and Psychotherapy, University of Duisburg-Essen, LVR-Klinikum, Essen (Germany).
Abstract
Covalent coupling of β-secretase inhibitors to a raftophilic lipid anchor via a suitable spacer by using solid-phase peptide synthesis leads to tripartite structures displaying substantially improved inhibition of cellular secretion of the β-amyloid peptide (Aβ). Herein, we describe a series of novel tripartite structures, their full characterization by NMR spectroscopy and mass spectrometry, and the analysis of their biological activity in cell-based assays. The tripartite structure concept is applicable to different pharmacophores, and the potency in terms of β-secretase inhibition can be optimized by adjusting the spacer length to achieve an optimal distance of the inhibitor from the lipid bilayer. A tripartite structure containing a transition-state mimic inhibitor was found to be less potent on Aβ generation from Swedish-mutant amyloid precursor protein (APP) than from the wild-type protein. Moreover, our observations suggest that specific variants of Aβ are generated from wild-type APP but not from Swedish-mutant APP and are resistant to β-secretase inhibition. Efficient inhibition of Aβ secretion by tripartite structures in the absence of appreciable neurotoxicity was confirmed in a primary neuronal cell culture, thus further supporting the concept.
PMID: 21132705 [PubMed - as supplied by publisher]
J Bacteriol. 2010 Dec 3. [Epub ahead of print]
Complete Genome Sequence of Burkholderia rhizoxinica, the Endosymbiont of Rhizopus microsporus.
Lackner G, Moebius N, Partida-Martinez L, Hertweck C.
Leibniz Institute for Natural Product Research and Infection Biology (HKI), Department of Biomolecular Chemistry, Beutenbergstr. 11a, 07745 Jena, Germany; Friedrich Schiller University, 07743 Jena, Germany.
Abstract
Burkholderia rhizoxinica is an intracellular symbiont of the phytopathogenic fungus Rhizopus microsporus. The vertically transmitted endosymbiont not only delivers the antimitotic macrolide rhizoxin to its host, but is also essential for vegetative spore formation of the fungus. To shed light on the genetic equipment of this model organism, we sequenced the whole genome of B. rhizoxinica HKI 0454, thus providing the first genomic insight into of an intracellular mutualist of a fungal species. The 3.75 Mb genome consists of a chromosome and two strain-specific plasmids. Primary metabolism appears to be specialized for the uptake of fungal metabolites. Besides the rhizoxin biosynthesis gene cluster, there are 14 loci coding for nonribosomal peptide synthetase (NRPS) assembly lines, which represent novel targets for genomic mining of cryptic natural products. Furthermore, the endosymbionts are equipped with a repertoire of virulence-related factors, which can now be studied to elucidate molecular mechanisms underlying bacterial-fungal interaction.
PMID: 21131495 [PubMed - as supplied by publisher]
J Diabetes Sci Technol. 2010 Nov 1;4(6):1322-31.
Optimization of the native glucagon sequence for medicinal purposes.
Chabenne JR, Dimarchi MA, Gelfanov VM, Dimarchi RD.
Department of Chemistry, Indiana University, Bloomington, IN.
Abstract
BACKGROUND: Glucagon is a life-saving medication used in the treatment of hypoglycemia. It possesses poor solubility in aqueous buffers at or near physiological pH values. At low and high pH, at which the peptide can be formulated to concentrations of a milligram or more per milliliter, the chemical integrity of the hormone is limited, as evidenced by the formation of multiple degradation-related peptides. Consequently, the commercial preparation is provided as a lyophilized solid with an acidic diluent and directions for rendering it soluble at the time of use. Any unused material is recommended for disposal immediately after initial use.
METHODS: A set of glucagon analogs was prepared by solid-phase peptide synthesis to explore the identification of a glucagon analog with enhanced solubility and chemical stability at physiological pH. The physical properties of the peptide analogs were studied by solubility determination, high-performance chromatography, and mass spectral analysis. The biochemical properties were determined in engineered human embryonic kidney cell line 293 (HEK293) cells that overexpressed either the human glucagon or glucagon-like peptide-1 (GLP-1) receptors linked to a luciferase reporter gene.
RESULTS: We observed the previously characterized formation of glucagon degradation products upon incubation of the peptide in dilute acid for extended periods or elevated temperature. Lowering the isoelectric point of the hormone through the substitution of asparagine-28 with aspartic acid significantly increased the solubility at physiological pH. Similarly, the C-terminal extension (Cex) of the hormone with an exendin-based, 10-residue, C-terminal sequence yielded a peptide of dramatically enhanced solubility. These two glucagon analogs, D28 and Cex, maintained high potency and selectivity for the glucagon receptor relative to GLP-1 receptor.
CONCLUSIONS: Glucagon presents unique structural challenges to the identification of an analog of high biological activity and selectivity that also possesses sufficient aqueous solubility and stability such that it might be developed as a ready-to-use medicine. The glucagon analogs D28 and Cex demonstrated all of the chemical, physical, and biochemical properties supportive of further study as potential clinical candidates for treatment of hypoglycemia.
© 2010 Diabetes Technology Society.PMID: 21129326 [PubMed - in process]
Nat Protoc. 2010 Dec;5(12):1867-87. Epub 2010 Nov 4.
Synthesis of photodegradable hydrogels as dynamically tunable cell culture platforms.
Kloxin AM, Tibbitt MW, Anseth KS.
[1] Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, Colorado, USA. [2] Howard Hughes Medical Institute, University of Colorado at Boulder, Boulder, Colorado, USA.
Abstract
We describe a detailed procedure to create photolabile, polyethylene glycol (PEG)-based hydrogels and manipulate material properties in situ. The cytocompatible chemistry and degradation process enable dynamic, tunable changes for applications in two-dimensional (2D) or 3D cell culture. The materials are created by synthesizing an o-nitrobenzylether-based photodegradable monomer that can be coupled to primary amines. In this study, we provide coupling procedures to PEG-bis-amine to form a photodegradable cross-linker or to the fibronectin-derived peptide RGDS to form a photoreleasable tether. Hydrogels are synthesized with the photodegradable cross-linker in the presence or absence of cells, allowing direct encapsulation or seeding on surfaces. Cell-material interactions can be probed in 2D or 3D by spatiotemporally controlling the gel microenvironment, which allows unique experiments to be performed to monitor cell response to changes in their niche. Degradation is readily achieved with cytocompatible wavelengths of low-intensity flood irradiation (365-420 nm) in minutes or with high-intensity laser irradiation (405 nm) in seconds. In this protocol, synthesis and purification of photodegradable monomers take approximately 2 weeks, but the process can be substantially shortened by purchasing the o-nitrobenzylether precursor. Preparation of sterile solutions for hydrogel fabrication takes hours, whereas the reaction to form the final hydrogel is complete in minutes. Hydrogel degradation occurs on demand, in seconds to minutes, with user-directed light exposure. This comprehensive protocol is useful for controlling peptide presentation and substrate modulus during cell culture on or within an elastic matrix. These PEG-based materials are useful for probing the dynamic influence of cell-cell and cell-material interactions on cell function in 2D or 3D. Although other protocols are available for controlling peptide presentation or modulus, few allow manipulation of material properties in situ and in the presence of cells down to the micrometer scale.
PMID: 21127482 [PubMed - in process]
Proc Natl Acad Sci U S A. 2010 Dec 2. [Epub ahead of print]
Molecular recognition between ketosynthase and acyl carrier protein domains of the 6-deoxyerythronolide B synthase.
Kapur S, Chen AY, Cane DE, Khosla C.
Department of Chemistry, Department of Chemical Engineering, and Department of Biochemistry, Stanford University, Stanford, CA 94305.
Abstract
Every polyketide synthase module has an acyl carrier protein (ACP) and a ketosynthase (KS) domain that collaborate to catalyze chain elongation. The same ACP then engages the KS domain of the next module to facilitate chain transfer. Understanding the mechanism for this orderly progress of the growing polyketide chain represents a fundamental challenge in assembly line enzymology. Using both experimental and computational approaches, the molecular basis for KS-ACP interactions in the 6-deoxyerythronolide B synthase has been decoded. Surprisingly, KS-ACP recognition is controlled at different interfaces during chain elongation versus chain transfer. In fact, chain elongation is controlled at a docking site remote from the catalytic center. Not only do our findings reveal a new principle in the modular control of polyketide antibiotic biosynthesis, they also provide a rationale for the mandatory homodimeric structure of polyketide synthases, in contrast to the monomeric nonribosomal peptide synthetases.
PMID: 21127271 [PubMed - as supplied by publisher]
Chemistry. 2010 Dec 1. [Epub ahead of print]
Regioisomeric Control Induced by DABCO Coordination to Rotatable Self-Assembled Bis- and Tetraporphyrin α,γ-Cyclic Octapeptide Dimers.
Hernández-Eguía LP, Brea RJ, Castedo L, Ballester P, Granja JR.
Institute of Chemical Research of Catalonia (ICIQ), Av. Països Catalans 16, 43007 Tarragona (Spain), Fax: (+34) 977-920-221.
Abstract
The design and synthesis of two α,γ-cyclic octapeptides decorated with one and two Zn-porphyrin units in their periphery is described. In nonpolar organic solvents the α,γ-cyclic octapeptides quantitatively self-assemble into Zn-bis- or -tetraporphyrin architectures that could act as molecular tweezers. The self-assembly process, however, is not regioselective and affords a mixture of different regioisomers that are involved in chemical exchange processes. The regioisomers with the Zn-porphyrin units positioned in register with respect to each other are proposed to be the less abundant species in the solution mixture. It has been demonstrated that the coordination of 1,4-diazabicyclo[2.2.2]octane (DABCO) to the supramolecular bis- or tetraporphyrin tweezers is an effective way to achieve regioisomeric control of the self-assembled mixture of dimers. Thus, DABCO functions as an external molecular trigger and, when used under strict stoichiometric control with respect to the Zn-porphyrin units, provokes the exclusive formation of self-assembled dimers with a cofacial arrangement of Zn-porphyrin units through the formation of sandwich-type complexes. The use of excess DABCO fragments the sandwich complexes and affords open dimers of high stoichiometry with DABCO molecules axially monocoordinated to the Zn-porphyrin units, probably as a regioisomeric mixture. In the case of Zn-tetraporphyrin tweezers, the ditopic coordination of DABCO at the two binding sites shows a moderate positive cooperativity factor, αP=5. These assemblies have potential applications as light-induced energy and electron-transfer switches regulated by DABCO coordination; such applications would require the introduction of additional chromophores in the cyclic peptide scaffold.
PMID: 21125624 [PubMed - as supplied by publisher]
Methods Mol Biol. 2011;705:151-74.
Semi-synthesis of Glycoproteins from E. coliThrough Native Chemical Ligation.
Department of Chemistry, Christopher Ingold Laboratories, University College London, London, WC1H 0AJ, UK, jrichard@sgul.ac.uk.
Abstract
Sufficient quantities of homogeneous samples of post-translationally modified proteins are often not readily available from biological sources to facilitate structure-function investigations. Native chemical ligation (NCL) is a convenient method for the production of biologically active proteins from smaller fragments. Such an approach allows protein modifications to be introduced in a controlled fashion into smaller peptide fragments which are amenable to total chemical synthesis. These fragments of defined sequence and structure can be elaborated to full-length proteins through NCL reactions with suitable components derived from bacterial origin. This report describes methods for the bacterial production of components for NCL and their use in typical reactions.
PMID: 21125385 [PubMed - in process]
Nat Chem. 2010 Apr;2(4):252-4.
Marine natural products: Totally tubular peptide synthesis.
Craig Forsyth is in the Department of Chemistry at The Ohio State University, Newman & Wolfrom Lab, 100 W. 18th Avenue, Columbus, Ohio 43210, USA. forsyth@chemistry.ohio-state.edu.
PMID: 21124502 [PubMed - in process]
J Biomater Appl. 2010 Dec 1. [Epub ahead of print]
Synthesis and Inhibition Study on Tripeptide Inhibitor Modified Poly(L-lysine) Dendrimers.
Zhang X, Luo K, Wang G, Nie Y, He B, Wu Y, Gu Z.
Department of Chemistry, Sichuan University, Chengdu 610064, China.
Abstract
Peptide dendrimers are attractive nonviral gene vectors. But a biological barrier for their application in gene delivery is the fast degradation catalyzed by proteasomes. Proteasome inhibitors are efficient at prohibiting the degradation of peptide nonviral vectors, thus enhancing gene transfection efficiency. In this study, N(α)-Boc-protected leucine vinyl ester proteasome inhibitor Boc-Leu-Leu-Leu-ve was synthesized by the liquid-phase method and was then immobilized onto poly(L-lysine) dendrimers. Suc-Leu-Leu-Val-Tyr-AMC was used as fluorimetric substrate and the inhibition capacity of Boc-Leu-Leu-Leu-ve immobilized onto G(3) and G(6) poly(L-lysine) dendrimers for the chymotrypsin-like activity of ACHN cell proteasome was tested. The results indicated that both Boc-Leu-Leu-Leu-ve peptide and the peptide immobilized on G(3) dendrimer showed low inhibition capacity when the concentration was below 0.2 μM. When the inhibitor concentrations were increased to 5.0 μM, however, the percentage inhibition of Boc-Leu-Leu-Leu-ve peptide and the peptide immobilized on G(3) dendrimer became about 50% and 25%, and that of peptide immobilized on the G(6) dendrimer was 7.5% only. These results indicated that dendritic structure and linker length could be the main factors affecting proteasome inhibition capacity. The cytotoxicity of the dendritic inhibitors was found to be low. Thus, whilst the synthetic production of poly(L-lysine) dendrimers immobilized with peptide inhibitors was successful and these modified dendrimers could work to inhibit proteasome activity, further studies will need to be carried out to improve inhibition capacity.
PMID: 21123282 [PubMed - as supplied by publisher]
J Pept Sci. 2010 Nov 30. [Epub ahead of print]
Influenza virus H5N1 hemagglutinin (HA) T-cell epitope conjugates: design, synthesis and immunogenicity.
Skarlas T, Zevgiti S, Droebner K, Panou-Pomonis E, Planz O, Sakarellos-Daitsiotis M.
Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece.
Abstract
The influenza virus, major surface glycoprotein hemagglutinin (HA) is one of the principal targets for the development of protective immunity. Aiming at contributing to the development of a vaccine that remains the first choice for prophylactic intervention, a reconstituted model of HA, mimicking its antigenic properties was designed, synthesized and tested in mice for the induction of protective immunity. Four helper T lymphocyte [HTL (T(1), T(3), T(7) and T(8))] and four cytotoxic lymphocyte [CTL (T(2), T(4), T(5) and T(6))] epitopes were coupled in two copies each to an artificial carrier, SOC(4), which was formed by the repeating tripeptide Lys-Aib-Gly. The helical conformation of the SOC(4)-conjugates preserves the initial topology of the attached epitopes, which is critical for their immunogenic properties. Survival of immunized animals, ranged from 30 to 50%, points out the induction of protective immunity by using the SOC(4)-conjugates. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd.
PMID: 21120842 [PubMed - as supplied by publisher]
J Pept Sci. 2010 Dec;16(12):716-22. doi: 10.1002/psc.1325.
Synthesis and analysis of the membrane proximal external region epitopes of HIV-1.
Ingale S, Gach JS, Zwick MB, Dawson PE.
Department of Chemistry and Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Abstract
The membrane proximal external region (MPER) of gp41 abuts the viral membrane at the base of HIV-1 envelope glycoprotein spikes. The MPER is highly conserved and is rich in Trp and other lipophilic residues. The MPER is also required for the infection of host cells by HIV-1 and is the target of the broadly neutralizing antibodies, 4E10, 2F5, and Z13e1. These neutralizing antibodies are valuable tools for understanding relevant conformations of the MPER and for studying HIV-1 neutralization, but multiple approaches used to elicit MPER binding antibodies with similar neutralization properties have failed. Here we report our efforts to mimic the MPER using linear as well as constrained peptides. Unnatural amino acids were also introduced into the core epitope of 4E10 to probe requirements of antibody binding. Peptide analogs with C-terminal Api or Aib residues designed to be helical transmembrane (TM) domain surrogates exhibit enhanced binding to the 4E10 and Z13e1 antibodies. However, we find that placement of constrained amino acids at nonbinding sites within the core epitope significantly reduce binding. These results are relevant to an understanding of native MPER structure on HIV-1, and form a basis for a chemical synthesis approach to mimic MPER stricture and to construct an MPER-based vaccine.
Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd.PMID: 21104968 [PubMed - in process]
Chem Commun (Camb). 2010 Nov 22. [Epub ahead of print]
Fmoc-chemistry of a stable phosphohistidine analogue.
McAllister TE, Nix MG, Webb ME.
School of Chemistry, University of Leeds, Leeds, UK.
Abstract
We report the synthesis of the phosphohistidine analogue, Fmoc-4-diethylphosphonotriazolylalanine 5 and its incorporation into peptides. Our synthesis of 5 has enabled us to demonstrate that the analogue is compatible with Fmoc-solid phase peptide synthesis (SPPS) conditions. Standard cleavage conditions yield the diethyl phosphonate-protected peptide, however this can be subsequently deprotected using trimethylsilyl bromide to yield the free phosphonic acid-containing peptides.
PMID: 21103476 [PubMed - as supplied by publisher]
J Antibiot (Tokyo). 2010 Nov 24. [Epub ahead of print]
Involvement of common intermediate 3-hydroxy-L-kynurenine in chromophore biosynthesis of quinomycin family antibiotics.
Hirose Y, Watanabe K, Minami A, Nakamura T, Oguri H, Oikawa H.
Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo, Japan.
Abstract
Quinomycin antibiotics, represented by echinomycin, are an important class of antitumor antibiotics. We have recently succeeded in identification of biosynthetic gene clusters of echinomycin and SW-163D, and have achieved heterologous production of echinomycin in Escherichia coli. In addition, we have engineered echinomycin non-ribosomal peptide synthetase to generate echinomycin derivatives. However, the biosynthetic pathways of intercalative chromophores quinoxaline-2-carboxylic acid (QXC) and 3-hydroxyquinaldic acid (HQA), which are important for biological activity, were not fully elucidated. Here, we report experiments involving incorporation of a putative advanced precursor, (2S, 3R)-[6'-(2)H]-3-hydroxy-L-kynurenine, and functional analysis of the enzymes Swb1 and Swb2 responsible for late-stage biosynthesis of HQA. On the basis of these experimental results, we propose biosynthetic pathways for both QXC and HQA through the common intermediate 3-hydroxy-L-kynurenine.The Journal of Antibiotics advance online publication, 24 November 2010; doi:10.1038/ja.2010.142.
PMID: 21102595 [PubMed - as supplied by publisher]
Vitam Horm. 2010;84:251-78.
Structural basis for ligand recognition of incretin receptors.
Underwood CR, Parthier C, Reedtz-Runge S.
Department of Chemistry, MEMPHYS Center for Biomembrane Physics, Technical University of Denmark, Kgs. Lyngby, Denmark, GLP-1 and Obesity Biology, Novo Nordisk, Måløv, Denmark.
Abstract
The glucose-dependent insulinotropic polypeptide (GIP) receptor and the glucagon-like peptide-1 (GLP-1) receptor are homologous G-protein-coupled receptors (GPCRs). Incretin receptor agonists stimulate the synthesis and secretion of insulin from pancreatic β-cells and are therefore promising agents for the treatment of type 2 diabetes. It is well established that the N-terminal extracellular domain (ECD) of incretin receptors is important for ligand binding and ligand specificity, whereas the transmembrane domain is involved in receptor activation. Structures of the ligand-bound ECD of incretin receptors have been solved recently by X-ray crystallography. The crystal structures reveal a similar fold of the ECD and a similar mechanism of ligand binding, where the ligand adopts an α-helical conformation. Residues in the C-terminal part of the ligand interact directly with the ECD and hydrophobic interactions appear to be the main driving force for ligand binding to the ECD of incretin receptors. Obviously, the-still missing-structures of full-length incretin receptors are required to construct a complete picture of receptor function at the molecular level. However, the progress made recently in structural analysis of the ECDs of incretin receptors and related GPCRs has shed new light on the process of ligand recognition and binding and provided a basis to disclose some of the mechanisms underlying receptor activation at high resolution.
Copyright © 2010 Elsevier Inc. All rights reserved.PMID: 21094903 [PubMed - in process]
Curr Opin Chem Biol. 2010 Nov 17. [Epub ahead of print]
Proteomic analysis of polyketide and nonribosomal peptide biosynthesis.
Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, United States.
Abstract
Polyketides and non-ribosomal peptides are in a class of natural products important both as drug sources and as dangerous toxins and virulence factors. While studies over the last two decades have provided substantial characterization of the modular synthases that produce these compounds at the genetic level, their understanding at the protein level is much less understood. New proteomic platforms called an orthogonal active site identification system (OASIS) and proteomic interrogation of secondary metabolism (PrISM) have been developed to identify and quantify natural product synthase enzymes. Reviewed here, these tools offer the means to discover and analyze modular synthetic pathways that are limited by genetic techniques, opening the tools of contemporary proteomics to natural product sciences.
Copyright © 2010 Elsevier Ltd. All rights reserved.PMID: 21087894 [PubMed - as supplied by publisher]
Beilstein J Org Chem. 2010 Oct 4;6:945-59.
Oxalyl retro-peptide gelators. Synthesis, gelation properties and stereochemical effects.
Makarević J, Jokić M, Frkanec L, Caplar V, Sijaković Vujičić N, Zinić M.
Laboratory for Supramolecular and Nucleoside Chemistry, Ruđer Bošković Institute, P.O.B. 180, HR-10002 Zagreb, Croatia.
Abstract
In this work we report on gelation properties, self-assembly motifs, chirality effects and morphological characteristics of gels formed by chiral retro-dipeptidic gelators in the form of terminal diacids (1a-5a) and their dimethyl ester (1b-5b) and dicarboxamide (1c-5c) derivatives. Terminal free acid retro-dipeptides (S,S)-bis(LeuLeu) 1a, (S,S)-bis(PhgPhg) 3a and (S,S)-bis(PhePhe) 5a showed moderate to excellent gelation of highly polar water/DMSO and water/DMF solvent mixtures. Retro-peptides incorporating different amino acids (S,S)-(LeuPhg) 2a and (S,S)-(PhgLeu) 4a showed no or very weak gelation. Different gelation effectiveness was found for racemic and single enantiomer gelators. The heterochiral (S,R)-1c diastereoisomer is capable of immobilizing up to 10 and 4 times larger volumes of dichloromethane/DMSO and toluene/DMSO solvent mixtures compared to homochiral (S,S)-1c. Based on the results of (1)H NMR, FTIR, CD investigations, molecular modeling and XRPD studies of diasteroisomeric diesters (S,S)-1b/(S,R)-1b and diacids (S,S)-1b/(S,R)-1a, a basic packing model in their gel aggregates is proposed. The intermolecular hydrogen bonding between extended gelator molecules utilizing both, the oxalamide and peptidic units and layered organization were identified as the most likely motifs appearing in the gel aggregates. Molecular modeling studies of (S,S)-1a/(S,R)-1a and (S,S)-1b/(S,R)-1b diasteroisomeric pairs revealed a decisive stereochemical influence yielding distinctly different low energy conformations: those of (S,R)-diastereoisomers with lipophilic i-Bu groups and polar carboxylic acid or ester groups located on the opposite sides of the oxalamide plane resembling bola amphiphilic structures and those of (S,S)-diasteroisomers possessing the same groups located at both sides of the oxalamide plane. Such conformational characteristics were found to strongly influence both, gelator effectiveness and morphological characteristics of gel aggregates.
PMID: 21085503 [PubMed - in process]PMCID: PMC2981816Free PMC Article
Bioconjug Chem. 2010 Nov 17. [Epub ahead of print]
One-Step (18)F-Labeling of Carbohydrate-Conjugated Octreotate-Derivatives Containing a Silicon-Fluoride-Acceptor (SiFA): In Vitro and in Vivo Evaluation as Tumor Imaging Agents for Positron Emission Tomography (PET).
Wängler C, Waser B, Alke A, Iovkova L, Buchholz HG, Niedermoser S, Jurkschat K, Fottner C, Bartenstein P, Schirrmacher R, Reubi JC, Wester HJ, Wängler B.
Department of Nuclear Medicine, Hospital of the Ludwig-Maximilians-University, Munich, Germany, Institute of Pathology, University of Berne, Berne, Switzerland, Department of Nuclear Medicine, Technical University Munich, Munich, Germany, Department of Inorganic Chemistry II, University of Dortmund, Dortmund, Germany, Department of Nuclear Medicine and I. Medical Clinic, University of Mainz, Germany, and McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Canada.
Abstract
The synthesis, radiolabeling, and initial evaluation of new silicon-fluoride acceptor (SiFA) derivatized octreotate derivatives is reported. So far, the main drawback of the SiFA technology for the synthesis of PET-radiotracers is the high lipophilicity of the resulting radiopharmaceutical. Consequently, we synthesized new SiFA-octreotate analogues derivatized with Fmoc-NH-PEG-COOH, Fmoc-Asn(Ac(3)AcNH-β-Glc)-OH, and SiFA-aldehyde (SIFA-A). The substances could be labeled in high yields (38 ± 4%) and specific activities between 29 and 56 GBq/μmol in short synthesis times of less than 30 min (e.o.b.). The in vitro evaluation of the synthesized conjugates displayed a sst2 receptor affinity (IC(50) = 3.3 ± 0.3 nM) comparable to that of somatostatin-28. As a measure of lipophilicity of the conjugates, the log P(ow) was determined and found to be 0.96 for SiFA-Asn(AcNH-β-Glc)-PEG-Tyr(3)-octreotate and 1.23 for SiFA-Asn(AcNH-β-Glc)-Tyr(3)-octreotate, which is considerably lower than for SiFA-Tyr(3)-octreotate (log P(ow) = 1.59). The initial in vivo evaluation of [(18)F]SiFA-Asn(AcNH-β-Glc)-PEG-Tyr(3)-octreotate revealed a significant uptake of radiotracer in the tumor tissue of AR42J tumor-bearing nude mice of 7.7% ID/g tissue weight. These results show that the high lipophilicity of the SiFA moiety can be compensated by applying hydrophilic moieties. Using this approach, a tumor-affine SiFA-containing peptide could successfully be used for receptor imaging for the first time in this proof of concept study.
PMID: 21082773 [PubMed - as supplied by publisher]
Amino Acids. 2010 Nov 17. [Epub ahead of print]
A practical synthesis of N ( α )-Fmoc protected L: -threo-β-hydroxyaspartic acid derivatives for coupling via α- or β-carboxylic group.
Bionda N, Cudic M, Barisic L, Stawikowski M, Stawikowska R, Binetti D, Cudic P.
Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL, 33431, USA.
Abstract
A simple and practical general synthetic protocol towards orthogonally protected tHyAsp derivatives fully compatible with Fmoc solid-phase peptide synthetic methodology is reported. Our approach includes enantioresolution of commercially available D: ,L: -tHyAsp racemic mixture by co-crystallization with L: -Lys, followed by ion exchange chromatography yielding enantiomerically pure L: -tHyAsp and D: -tHyAsp, and their selective orthogonal protection. In this way N ( α )-Fmoc protected tHyAsp derivatives were prepared ready for couplings via either α- or β-carboxylic group onto the resins or the growing peptide chain. In addition, coupling of tHyAsp via β-carboxylic group onto amino resins allows preparation of peptides containing tHyAsn sequences, further increasing the synthetic utility of prepared tHyAsp derivatives.
PMID: 21082204 [PubMed - as supplied by publisher]
J Am Chem Soc. 2010 Nov 16. [Epub ahead of print]
Synthesis of a Single-Molecule l-Rhamnose-Containing Three-Component Vaccine and Evaluation of Antigenicity in the Presence of Anti-l-Rhamnose Antibodies.
Sarkar S, Lombardo SA, Herner DN, Talan RS, Wall KA, Sucheck SJ.
Department of Chemistry and Department of Medicinal and Biological Chemistry, The University of Toledo, 2801 West Bancroft Street, Toledo, Ohio 43606, United States.
Abstract
Carbohydrates are generally considered to be poorly immunogenic. Therefore, new approaches for enhancing their immunogenicity are important for the development of carbohydrates as vaccine components. We hypothesized that conjugation of an l-rhamnose (Rha) moiety to a carbohydrate antigen would enhance the antigenicity of the antigen in mice possessing anti-Rha antibodies via an antibody-dependent antigen uptake mechanism. To explore this hypothesis, we synthesized a single-molecule three-component vaccine containing the GalNAc-O-Thr (Tn) tumor-specific antigen, a 20 amino acid helper T-cell epitope (YAF) derived from an outer-membrane protein of Neisseria meningitides, and a Rha moiety. The vaccine was synthesized by automated Fmoc-based solid-phase peptide synthesis and deacetylated by brief treatment with NaOMe. Groups of female BALB/c mice were immunized and boosted with Rha-ovalbumin (Rha-OVA) formulated with either TiterMax Gold or Sigma Adjuvant System for a period of 35 days in order to determine optimal conditions for generating anti-Rha titers in mice. Anti-Rha antibody titers were >100 fold higher in groups of mice immunized with Rha-OVA than in the control groups. Mice producing anti-Rha were challenged with Rha-YAF-Tn or YAF-Tn. Sera collected from the groups initially immunized with Rha-OVA and later challenged with Rha-YAF-Tn showed a 2-fold increase in anti-Tn titer at 1/100 serum dilution relative to mice not immunized with Rha-OVA. An in vitro T-cell proliferation study using cells primed with either Rha-YAF-Tn or YAF-Tn was done to examine possible differences in antigen uptake and presentation due to anti-Rha antibody and chemical modification. Proliferation of T cells was stimulated by a 10-fold lower antigen concentration in the presence of Rha antibodies. The results strongly suggest that T cells present in the spleen were presented with higher concentrations of Rha-YAF-Tn as a result of the presence of the anti-Rha antibodies.
PMID: 21080675 [PubMed - as supplied by publisher]
Bioconjug Chem. 2010 Nov 12. [Epub ahead of print]
Radiofluorinated Rhenium Cyclized α-MSH Analogues for PET Imaging of Melanocortin Receptor 1.
Ren G, Liu S, Liu H, Miao Z, Cheng Z.
Molecular Imaging Program at Stanford (MIPS), Department of Radiology and Bio-X Program, Canary Center at Stanford for Cancer Early Detection, Stanford University, Stanford, California, 94305-5344, United States.
Abstract
In order to accomplish in vivo molecular imaging of melanoma biomarker melanocortin 1 receptor (MC1R), several α-melanocyte-stimulating hormone (α-MSH) analogues have been labeled with N-succinimidyl-4-(18)F-fluorobenzoate ((18)F-SFB) and studied as positron emission tomography (PET) probes in our recent studies. To further pursue a radiofluorinated α-MSH peptide with high clinical translation potential, we utilized 4-nitrophenyl 2-(18)F-fluoropropionate ((18)F-NFP) to radiofluorinate the transition metal rhenium cyclized α-MSH metallopeptides for PET imaging of MC1R positive malignant melanoma. Metallopeptides Ac-d,Lys-ReCCMSH(Arg(11)) (two isomers, namely RMSH-1 and RMSH-2) were synthesized using conventional solid phase peptide synthesis chemistry and rhenium cyclization reaction. The two isomers were then conjugated with (19)F-NFP or (18)F-NFP. The resulting cold or radiofluorinated metallopeptides, (18/19)F-FP-RMSH-1 and (18/19)F-FP-RMSH-2, were further evaluated for their in vitro receptor binding affinities, in vivo biodistribution, and small-animal PET imaging properties. The binding affinities of (19)F-FP-RMSH-1 and (19)F-FP-RMSH-2 were determined to be within low nanomolar range. In vivo studies revealed that both (18)F-labeled metallopeptides possessed good tumor uptake in the B16F10 murine model with high MC1R expression, while possessing much lower uptake in A375M human melanoma xenografts. Moreover, (18)F-FP-RMSH-1 displayed more favorable in vivo performance in terms of higher tumor uptake and much lower accumulation in the kidney and liver, when compared to that of (18)F-FP-RMSH-2 at 2 h postinjection (p.i.). (18)F-FP-RMSH-1 also displayed lower liver and lung uptake when compared with that of the same peptide labeled with (18)F-SFB (named as (18)F-FB-RMSH-1). Small animal PET imaging of (18)F-FP-RMSH-1 in mice bearing B16F10 tumors at 1 and 2 h showed good tumor imaging quality. As expected, much lower tumor uptake and poorer tumor/normal organ contrast were observed for A375M model compared to those of the B16F10 model. (18)F-FP-RMSH-1 also exhibited higher tumor uptake and better tumor retention when compared with (18)F-FB-RMSH-1. (18)F-FP-RMSH-1 demonstrates significant advantages over (18)F-FB-RMSH-1 and (18)F-FP-RMSH-2. It is a promising PET probe for imaging MC1R positive melanoma and MC1R expression in vivo.
PMID: 21073170 [PubMed - as supplied by publisher]
Mol Divers. 2010 Nov 12. [Epub ahead of print]
Novel and efficient one-pot five- and six-component reactions for the stereoselective synthesis of highly functionalized enaminones and dithiocarbamates.
Bararjanian M, Balalaie S, Rominger F, Movassagh B, Bijanzadeh HR.
Peptide Chemistry Research Group, K. N. Toosi University of Technology, P.O. Box 15875-4416, Tehran, Iran.
Abstract
Efficient methods for stereoselective synthesis of polyfunctional (E)-enaminones and (Z)-dithiocarbamates via one-pot five- and six-component sequential Ugi/Nucleophilic addition reactions are described. High yields and high bond forming efficiency, and simple operations are the advantages of this method.
PMID: 21072590 [PubMed - as supplied by publisher]
J Biomed Mater Res B Appl Biomater. 2011 Jan;96(1):152-91.
Nanosized hydroxyapatite and other calcium phosphates: Chemistry of formation and application as drug and gene delivery agents.
Division of Biomaterials and Bioengineering, Department of Preventive and Restorative Dental Sciences, University of California, San Francisco, California 94143.
Abstract
The first part of this review looks at the fundamental properties of hydroxyapatite (HAP), the basic mineral constituent of mammalian hard tissues, including the physicochemical features that govern its formation by precipitation. A special emphasis is placed on the analysis of qualities of different methods of synthesis and of the phase transformations intrinsic to the formation of HAP following precipitation from aqueous solutions. This serves as an introduction to the second part and the main subject of this review, which relates to the discourse regarding the prospects of fabrication of ultrafine, nanosized particles based on calcium phosphate carriers with various therapeutic and/or diagnostic agents coated on and/or encapsulated within the particles. It is said that the particles could be either surface-functionalized with amphiphiles, peptides, proteins, or nucleic acids or injected with therapeutic agents, magnetic ions, or fluorescent molecules. Depending on the additive, they could be subsequently used for a variety of applications, including the controlled delivery and release of therapeutic agents (extracellularly or intracellularly), magnetic resonance imaging and hyperthermia therapy, cell separation, blood detoxification, peptide or oligonucleotide chromatography and ultrasensitive detection of biomolecules, and in vivo and in vitro gene transfection. Calcium phosphate nanoparticles as carriers of therapeutic agents that would enable a controlled drug release to treat a given bone infection and at the same be resorbed in the body so as to regenerate hard tissue lost to disease are emphasized hereby as one of the potentially attractive smart materials for the modern medicine. © 2010 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2011.
PMID: 21061364 [PubMed - in process]
Amino Acids. 2010 Aug 3. [Epub ahead of print]
Peptide and glycopeptide dendrimers and analogous dendrimeric structures and their biomedical applications.
Sebestik J, Niederhafner P, Jezek J.
Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10, Prague 6, Czech Republic, sebestik@uochb.cas.cz.
Abstract
The size of information that can be stored in nucleic acids, proteins, and carbohydrates was calculated. The number of hexamers for peptides is 64,000,000 (20(6)) and seems to be impressive in comparison with 4,096 (4(6)) hexanucleotides, but the number of isomers of hexasaccharides is 1.44 × 10(15). Carbohydrates are therefore the best high-density coding system. This language has been named glycocode resp. sugar code. In comparison with peptide dendrimers, the amount of information carried by glycopeptide dendrimers or glycodendrimers is therefore much higher. This is reflected by the variability of structures and functions (activities). This review is about the broad area of peptide and glycopeptide dendrimers. The dendrimeric state and physicochemical properties and general consequences are described, together with a cluster effect. The impact of cluster effect to biological, chemical, and physical properties is discussed. Synthesis of dendrimers by convergent and divergent approaches, "Lego" chemistry, ligation strategies, and click chemistry is given with many examples. Purification and characterization of dendrimers by chromatographic methods, electromigration methods, and mass spectrometry are briefly mentioned. Different types of dendrimers with cyclic core, i.e. RAFTs, TASPs and analogous cyclic structures, carbopeptides, carboproteins, octopus glycosides, inositol-based dendrimers, cyclodextrins, calix[4]arenes, resorcarenes, cavitands, and porphyrins are given. Dendrimers can be used for creation of libraries, catalysts, and solubilizing agents. Biocompatibility and toxicity of dendrimers is discussed, as well as their applications in nanoscience, nanotechnology, drug delivery, and gene delivery. Carbohydrate interactions of glycopeptide dendrimers (bacteria, viruses, and cancer) are described. Examples of dendrimers as anti-prion agents are given. Dendrimers represent a fast developing area which partly overlaps with nanoparticles and nanotechnologies.
PMID: 21058024 [PubMed - as supplied by publisher]
Bioorg Med Chem. 2010 Dec 15;18(24):8679-86. Epub 2010 Sep 29.
A protected l-bromophosphonomethylphenylalanine amino acid derivative (BrPmp) for synthesis of irreversible protein tyrosine phosphatase inhibitors.
Tulsi NS, Downey AM, Cairo CW.
Alberta Ingenuity Centre for Carbohydrate Science, Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2.
Abstract
Protein tyrosine phosphatases (PTPs) are important therapeutic targets for medicinal chemists and biochemists. General strategies for the development of inhibitors of these enzymes are needed. Several modular strategies which rely on phosphotyrosine mimics are known for PTP inhibitors. Previous strategies include phosphonomethylphenylalanine (Pmp) derivatives which act as competitive inhibitors. Pmp amino acid derivatives have been used to develop specific inhibitors by incorporation into sequences recognized by the PTP of interest. We report the synthesis of a new phosphonotyrosine analog, l-phosphonobromomethylphenylalanine (BrPmp), which acts as an inhibitor of PTPs. The BrPmp derivative was prepared as an Fmoc-protected amino acid which can be used in standard solid phase peptide synthesis (SPPS) methods. The synthesis of the protected amino acid derivative requires 11 steps from tyrosine with a 30% overall yield. Enzyme inhibition studies with the PTP CD45 demonstrate that BrPmp derivatives are irreversible inhibitors of the enzyme. A tripeptide which incorporated BrPmp had increased inhibitory potency against PTP relative to BrPmp alone, confirming that the incorporation of BrPmp into peptide sequences provides additional context to improve enzyme binding.
Copyright © 2010 Elsevier Ltd. All rights reserved.PMID: 21055952 [PubMed - in process]
Bioorg Med Chem. 2010 Dec 1;18(23):8365-73. Epub 2010 Oct 7.
Design, synthesis and inhibition activity of novel cyclic peptides against protein tyrosine phosphatase A from Mycobacterium tuberculosis.
Chandra K, Dutta D, Das AK, Basak A.
Department of Chemistry, Department of Biotechnology, Indian Institute of Technology, Kharagpur, India.
Abstract
Mycobacterium tuberculosis, the causative agent for tuberculosis has employed several signalling molecules to sense the host cellular environment and act accordingly. For example, protein tyrosine phosphatase A (MPtpA) of M. tuberculosis, a signalling protein belonging to the tyrosine phosphatase superfamily, is involved in phagocytosis and is active in virulent mycobacterial form. Starting from a β-lactam framework a new class of structure based cyclic peptide (CP) inhibitors was designed. The synthesis involves a crucial intramolecular transamidation via a ring opening reaction. All the compounds show moderate to good inhibitory activities against MPtpA in micromolar concentrations. The results of inhibition kinetics suggest mixed mode of inhibition. The binding constant determined from circular dichroism (CD) and fluorescence quenching studies shows strong binding of the hydrophilic side chain of CPs with the enzyme active site residues. All these are well supported by docking studies.
Copyright © 2010 Elsevier Ltd. All rights reserved.PMID: 21050767 [PubMed - in process]
Bioorg Med Chem Lett. 2010 Dec 15;20(24):7337-40. Epub 2010 Oct 21.
Synthesis of novel cyclic NGR/RGD peptide analogs via on resin click chemistry.
Metaferia BB, Rittler M, Gheeya JS, Lee A, Hempel H, Plaza A, Stetler-Stevenson WG, Bewley CA, Khan J.
Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Abstract
Targeted drug deliveries as well as high resolution imaging of cancerous tissues and organs via specific cancer cell markers have become important in chemotherapeutic interventions of cancer treatment. Short peptides such as RGD and NGR are showing promising results for targeted drug delivery and in vivo imaging. We have applied on resin Huisgen's 1,3-dipolar cycloaddition to synthesize new cyclic RGD and NGR peptide analogs. Preliminary binding assays of these new analogs by fluorescence polarization indicates specific binding to purified CD13 (Aminopeptidase N) and cell lysates from MCF-7 and SKOV-3 cancer cell lines.
Published by Elsevier Ltd.PMID: 21050757 [PubMed - in process]
Org Lett. 2010 Dec 3;12(23):5414-7. Epub 2010 Nov 4.
Traceless Azido Linker for the Solid-Phase Synthesis of NH-1,2,3-Triazoles via Cu-Catalyzed Azide-Alkyne Cycloaddition Reactions.
Cohrt AE, Jensen JF, Nielsen TE.
Department of Chemistry, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
Abstract
A broadly useful acid-labile traceless azido linker for the solid-phase synthesis of NH-1,2,3-triazoles is presented. A variety of alkynes were efficiently immobilized on a range of polymeric supports by Cu(I)-mediated azide-alkyne cycloadditions. Supported triazoles showed excellent compatibility with subsequent peptide chemistry. Release of pure material (typically >95%) from the solid support was readily achieved by treatment with aqueous TFA.
PMID: 21049916 [PubMed - in process]
Org Lett. 2010 Dec 3;12(23):5486-9. Epub 2010 Nov 4.
Synthesis of oligoribonucleic Acid conjugates using a cyclooctyne phosphoramidite.
van Delft P, Meeuwenoord NJ, Hoogendoorn S, Dinkelaar J, Overkleeft HS, van der Marel GA, Filippov DV.
Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands.
Abstract
The conjugation of a ribonucleic acid 16-mer with the cationic amphiphilic peptide penetratin and an anionic hyaluronan tetrasaccharide by means of Cu-free "click" chemistry is reported. The alkyne-functionalized 16-mer was prepared by automated solid-phase synthesis, using a newly developed strained cyclooctyne phosphoramidite in the final coupling. Cycloaddition of the alkyne functionalized RNA to the azide containing biomolecules led to a clean conversion into the corresponding nucleic acid conjugates.
PMID: 21049910 [PubMed - in process]
Yakugaku Zasshi. 2010 Nov;130(11):1463-9.
[Novel L-amino acid ligases catalyzing oligopeptide synthesis].
[Article in Japanese]
Department of Applied Chemistry, School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Japan. kkino.@waseda,jp
Abstract
L-Amino acid ligase (EC 6.3.2.28) is a microbial enzyme catalyzing formation of an alpha-peptide bond from unprotected L-amino acids in an ATP-dependent manner. The YwfE protein from Bacillus subtilis 168 was the first reported L-amino acid ligase, and it synthesizes various dipeptides. Thereafter, several L-amino acid ligases were newly obtained by in silico analysis using the ATP-grasp motif. But these L-amino acid ligases synthesize only dipeptide and no longer peptide. A novel L-amino acid ligase capable of catalyzing oligopeptide synthesis is required to increase the variety of peptides. We have previously found a new member of L-amino acid ligase, RizA, from B. subtilis NBRC3134, a microorganism that produces the peptide-antibiotic rhizocticin. We newly found that a gene at approximately 9 kbp upstream of rizA encoded a novel L-amino acid ligase RizB. Recombinant RizB synthesized homo-oligomers of branched-chain amino acids consisting of 2 to 5 amino acids, and also synthesized various heteropeptides. RizB is the first reported L-amino acid ligase that catalyzes oligopeptide synthesis. In addition, we obtained L-amino acid ligases showing oligopeptide synthesis activities by in silico analysis using BLAST, which is a set of similarity search programs. These L-amino acid ligases showed low similarity in amino acid sequence, but commonly used branched-chain amino acids, such as RizB, as substrates. Furthermore, the spr0969 protein of Streptococcus pneumoniae synthesized longer peptides than those synthesized by RizB, and the BAD_1200 protein of Bifidobacteria adolescentis showed higher activity toward aromatic amino acids than toward branched-chain ones.
PMID: 21048404 [PubMed - in process]Free Article
J Am Chem Soc. 2010 Nov 24;132(46):16324-6. Epub 2010 Nov 3.
NosA catalyzing carboxyl-terminal amide formation in nosiheptide maturation via an enamine dealkylation on the serine-extended precursor peptide.
Yu Y, Guo H, Zhang Q, Duan L, Ding Y, Liao R, Lei C, Shen B, Liu W.
State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
Abstract
The carboxyl-terminal amide group has been often found in many bioactive peptide natural products, including nosiheptide belonging to the over 80 entity-containing thiopeptide family. Upon functional characterization of a novel protein NosA in nosiheptide biosynthesis, herein we report an unusual C-terminal amide forming strategy in general for maturating certain amide-terminated thiopeptides by processing their precursor peptides featuring a serine extension. NosA acts on an intermediate bearing a bis-dehydroalanine tail and catalyzes an enamide dealkylation to remove the acrylate unit originating from the extended serine residue.
PMID: 21047073 [PubMed - in process]PMCID: PMC2990472 [Available on 2011/11/1]
Chem Commun (Camb). 2010 Dec 21;46(47):8935-7. Epub 2010 Nov 2.
Photochemical cleavage of leader peptides.
Bindman N, Merkx R, Koehler R, Herrman N, van der Donk WA.
Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 S Mathews Ave, Urbana, IL 61801, USA.
Abstract
We report a photolabile linker compatible with Fmoc solid phase peptide synthesis and Cu(I)-catalyzed alkyne-azide cycloaddition that allows photochemical cleavage to afford a C-terminal peptide fragment with a native amino terminus.
PMID: 21046030 [PubMed - in process]
Proc Natl Acad Sci U S A. 2010 Nov 16;107(46):19731-5. Epub 2010 Nov 1.
Identification of the gene cluster for the dithiolopyrrolone antibiotic holomycin in Streptomyces clavuligerus.
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
Abstract
Streptomyces clavuligerus, an industrially important producer of clavulanate as well as cephem antibiotics, also produces the N-acylated dithiolopyrrolone antibiotic holomycin, a reported inhibitor of RNA synthesis. The genome sequence of S. clavuligerus ATCC 27064 was examined for a potential biosynthetic gene cluster, assuming that holomycin arises from some derivative of an L-Cys-L-Cys dipeptide that has undergone eight-electron oxidation, fused five-five ring formation, and decarboxylation. ORFs 3483-3492 comprise a candidate cluster, with a predicted acyltransferase, a stand-alone nonribosomal peptide synthetase (NRPS) module, and four flavin-dependent oxidoreductases. Deletions of ORF3488, the NRPS module, and ORF3489, a phosphopantothenoylcysteine decarboxylase homolog, abolished holomycin production both in wild type and in a holomycin-overproducing mutant. Heterologous expression and purification of ORF3488 allowed demonstration of L-Cys-AMP formation and subsequent covalent tethering of Cys to the phosphopantetheinyl arm of the thiolation domain of this NRPS protein. Purified ORF3483 shows acyltransferase activity, converting holothin to holomycin and longer acylated homologs as the last step in antibiotic assembly.
PMID: 21041678 [PubMed - in process]PMCID: PMC2993409 [Available on 2011/5/16]
Chirality. 2010;22 Suppl 1:E30-9.
Electronic and vibrational signatures of peptide helical structures: A tribute to Anton Mario Tamburro.
Department of Chemistry, University of Padova, 35131 Padova, Italy.
Abstract
Our efforts on the synthesis of peptides with well-characterized secondary structures, combined with detailed spectroscopic investigations, most of them performed in collaboration with internationally recognized experts, have allowed us to publish the electronic (electronic circular dichroism) and vibrational (FTIR absorption, vibrational circular dichroism, Raman, and Raman optical activity) signatures of the poorly studied peptide 3(10)-helix (and the related β-bend ribbon spiral conformation as well) in comparison with those already known for the classical α-helix.
© 2010 Wiley-Liss, Inc.PMID: 21038394 [PubMed - in process]
Appl Microbiol Biotechnol. 2010 Oct 31. [Epub ahead of print]
The unconventional antimicrobial peptides of the classical propionibacteria.
Faye T, Holo H, Langsrud T, Nes IF, Brede DA.
Dairy Technology and Food Quality, Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, P.O. Box 5003, 1432, Ås, Norway.
Abstract
The classical propionibacteria produce genetically unique antimicrobial peptides, whose biological activities are without equivalents, and to which there are no homologous sequences in public databases. In this review, we summarize the genetics, biochemistry, biosynthesis, and biological activities of three extensively studied antimicrobial peptides from propionibacteria. The propionicin T1 peptide constitutes a bona fide example of an unmodified general secretory pathway (sec)-dependent bacteriocin, which is bactericidal towards all tested species of propionibacteria except Propionibacterium freudenreichii. The PAMP antimicrobial peptide represents a novel concept within bacterial antagonism, where an inactive precursor protein is secreted in large amounts, and which activation appears to rely on subsequent processing by proteases in its resident milieu. Propionicin F is a negatively charged bacteriocin that displays an intraspecies bactericidal inhibition spectrum. The biosynthesis of propionicin F appears to proceed through a series of unusual events requiring both N- and C-terminal processing of a precursor protein, which probably requires the radical SAM superfamily enzyme PcfB.
PMID: 21038096 [PubMed - as supplied by publisher]
Colloids Surf B Biointerfaces. 2010 Oct 8. [Epub ahead of print]
Gradient immobilization of a cell adhesion RGD peptide on thermal responsive surface for regulating cell adhesion and detachment.
MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China.
Abstract
Using surface initiated atomic transfer radical polymerization (ATRP) and an injection method, a poly(N-isopropylacrylamide)-b-poly(acrylic acid)-g-RGD (PNIPAAm-b-PAA-g-RGD) gradient surface was prepared. First, a thermoresponsive surface with a constant thickness of PNIPAAm was fabricated, onto which the AA monomers were block copolymerized using the PNIPAAm macromolecules as initiators. During this process, a continuous injection method was employed to yield a molecular weight gradient of PAA on the underlying uniform PNIPAAm layer. RGD peptide was finally covalently immobilized onto the PAA gradient by carbodiimide chemistry. In vitro culture of HepG2 cells showed that immobilization of the RGD peptide could accelerate cell attachment, while the thermoresponsive layer beneath could effectively release the cells by simply lowering temperature. Thus, the PNIPAAm-b-PAA-g-RGD gradient surface, combining the thermal response with cell affinity properties, can well regulate the cell adhesion and detachment, which may thus be useful for investigation of cell-substrate interactions with a smaller number of samples.
Copyright © 2010 Elsevier B.V. All rights reserved.PMID: 21036559 [PubMed - as supplied by publisher]
Chem Biol. 2010 Oct 29;17(10):1077-83.
N-acylation during glidobactin biosynthesis by the tridomain nonribosomal peptide synthetase module GlbF.
Imker HJ, Krahn D, Clerc J, Kaiser M, Walsh CT.
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
Abstract
Glidobactins are hybrid NRPS-PKS natural products that function as irreversible proteasome inhibitors. A variety of medium chain 2(E),4(E)-diene fatty acids N-acylate the peptidolactam core and contribute significantly to the potency of proteasome inhibition. We have expressed the initiation NRPS module GlbF (C-A-T) in Escherichia coli and observe soluble active protein only on coexpression with the 8 kDa MbtH-like protein, GlbE. Following adenylation and installation of Thr as a T-domain thioester, the starter condensation domain utilizes fatty acyl-CoA donors to acylate the Thr(1) amino group and generate the fatty acyl-Thr(1)-S-pantetheinyl-GlbF intermediate to be used in subsequent chain elongation. Previously proposed to be mediated via acyl carrier protein fatty acid donors, direct utilization of fatty acyl-CoA donors for N-acylation of T-domain tethered amino acids is likely a common strategy for chain initiation in NRPS-mediated lipopeptide biosynthesis.
Copyright © 2010 Elsevier Ltd. All rights reserved.PMID: 21035730 [PubMed - in process]
Nat Protoc. 2010;5(11):1857-65. Epub 2010 Oct 28.
Solid-phase synthesis of short α-helices stabilized by the hydrogen bond surrogate approach.
Patgiri A, Menzenski MZ, Mahon AB, Arora PS.
Department of Chemistry, New York University, New York, USA.
Abstract
Stabilized α-helices and nonpeptidic helix mimetics have emerged as powerful molecular scaffolds for the discovery of protein-protein interaction inhibitors. Protein-protein interactions often involve large contact areas, which are often difficult for small molecules to target with high specificity. The hypothesis behind the design of stabilized helices and helix mimetics is that these medium-sized molecules may pursue their targets with higher specificity because of a larger number of contacts. This protocol describes an optimized synthetic strategy for the preparation of stabilized α-helices that feature a carbon-carbon linkage in place of the characteristic N-terminal main-chain hydrogen bond of canonical helices. Formation of the carbon-carbon bond is enabled by a microwave-assisted ring-closing metathesis reaction between two terminal olefins on the peptide chain. The outlined strategy allows the synthesis and purification of a hydrogen bond surrogate (HBS) α-helix in ∼ 1 week.
PMID: 21030960 [PubMed - in process]
Nat Protoc. 2010;5(11):1813-22. Epub 2010 Oct 21.
Synthesis of peptide macrocycles using unprotected amino aldehydes.
Rotstein BH, Rai V, Hili R, Yudin AK.
Davenport Research Laboratories, Department of Chemistry, University of Toronto, Toronto, Ontario, Canada.
Abstract
This protocol describes a method for synthesizing peptide macrocycles from linear peptide precursors, isocyanides and aziridine aldehydes. The effects of the reaction components on the efficiency of the process are discussed. Macrocyclization is exemplified by the preparation of a nine-membered ring peptide macrocycle. The product is further functionalized by nucleophilic opening of the aziridine ring with a fluorescent thiol. This transformation constitutes a useful late-stage functionalization of a macrocyclic peptide molecule. The experimental section describes the selection of the required starting materials, and the preparation of a representative aziridine-2-carboxaldehyde dimer. The synthesis and isolation of the peptide macrocycle can be accomplished in 6 h, and the ring-opening requires approximately 6-8 h. The aziridine-2-carboxaldehyde reagent is commercially available or can be synthesized from readily available starting materials in approximately 4 d. The strategy described is not limited to the specific peptide, isocyanide, aziridine aldehyde or nucleophile used in the representative synthesis.
PMID: 21030956 [PubMed - in process]
Science. 2010 Oct 29;330(6004):612-6.
Molecular signals of epigenetic states.
Howard Hughes Medical Institute and Department of Biochemistry, School of Medicine, New York University, New York, NY 10016, USA.
Abstract
Epigenetic signals are responsible for the establishment, maintenance, and reversal of metastable transcriptional states that are fundamental for the cell's ability to "remember" past events, such as changes in the external environment or developmental cues. Complex epigenetic states are orchestrated by several converging and reinforcing signals, including transcription factors, noncoding RNAs, DNA methylation, and histone modifications. Although all of these pathways modulate transcription from chromatin in vivo, the mechanisms by which epigenetic information is transmitted through cell division remain unclear. Because epigenetic states are metastable and change in response to the appropriate signals, a deeper understanding of their molecular framework will allow us to tackle the dysregulation of epigenetics in disease.
PMID: 21030644 [PubMed - indexed for MEDLINE]
J Med Chem. 2010 Nov 25;53(22):8072-9. Epub 2010 Oct 28.
Side chain cyclization based on serine residues: synthesis, structure, and activity of a novel cyclic analogue of the parathyroid hormone fragment 1-11.
Caporale A, Sturlese M, Gesiot L, Zanta F, Wittelsberger A, Cabrele C.
Department of Chemical Sciences, University of Padova, Institute of Biomolecular Chemistry, CNR, via Marzolo 1, 35131 Padova, Italy. caporaleandrea74@gmail.com
Abstract
The N-terminal region of the parathyroid hormone (PTH) is sufficient to activate the G-protein-coupled PTH receptor 1 (PTHR1). The shortest PTH analogue displaying nanomolar potency is the undecapeptide H-Aib-Val-Aib-Glu-Ile-Gln-Leu-Nle-His-Gln-Har-NH(2) that contains two helix-stabilizing residues (Aib(1,3)). To increase the helical character and proteolytic stability of this linear peptide, we replaced Gln(6,10) with (a) Lys(6) and Glu(10) to introduce a lactam bridge and (b) Ser(6,10) to form a diester bridge upon cross-linking with adipic acid. These cyclopeptides were, respectively, 468-fold less and 12-fold more potent agonists than the linear analogue. Despite their different potencies, all three analogues adopted similar α-helix structures, as shown by NMR and molecular dynamics studies. However, the diester bridge could better mimic the orientation and chemical properties of the side chains of Gln(6) and Gln(10) in the linear PTH analogue than the lactam moiety. This is apparently important for efficient receptor activation and provides further insights into the receptor-bound ligand conformation.
PMID: 21028829 [PubMed - in process]
J Pept Sci. 2010 Oct 25. [Epub ahead of print]
Synthesis, biological activity and solution structure of new analogues of the antimicrobial Gramicidin S.
Kamysz E, Mickiewicz B, Kamysz W, Bielińska S, Rodziewicz-Motowidło S, Ciarkowski J.
University of Gdańsk, Faculty of Chemistry, Sobieskiego 18, Gdańsk, 80-952, Poland.
Abstract
Gramicidin S (GS) is a cyclo-decapeptide antibiotic isolated from Bacillus brevis. The structural studies have shown that GS forms a two-stranded antiparallel β-sheet imposed by two II' β-turns. Despite its wide Gram+ and Gram- antimicrobial spectrum, GS is useless in therapy because of its high hemotoxicity in humans. It was found, however, that the analogues of GS-14 (GS with 14 amino acid residues) attained a better antimicrobial selectivity when their amphipatic moments were perturbed. In this study, we report effects of similar perturbations imposed on GS cyclo-decapeptide analogues. Having solved their structures by NMR/molecular dynamics and having tested their activities/selectivities, we have concluded that the idea of perturbation of the amphipatic moment does not work for GS-10_0 analogues. An innovative approach to the synthesis of head-to-tail cyclopeptides was used. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd.
PMID: 20976832 [PubMed - as supplied by publisher]
Bioconjug Chem. 2010 Nov 17;21(11):1943-7. Epub 2010 Oct 25.
Synthesis of N-terminally linked protein and peptide dimers by native chemical ligation.
Xiao J, Hamilton BS, Tolbert TJ.
Department of Chemistry, Indiana University, Bloomington, 47405, United States.
Abstract
Dimerization can be utilized to double the molecular weight of proteins and peptides and potentially increase their avidity of binding to target receptors. These dimerization effects may be utilized to increase in vivo half-lives in a manner similar to PEGylation and may also improve biological activity. In this paper, we report a new strategy for the synthesis of N-terminally linked protein and peptide homodimers utilizing native chemical ligation to conjugate a short dithioester linker to the N-terminal cysteines of protein and peptide monomers to form dimers in a single step. This strategy is general and has been applied to the production of dimers from three recombinantly expressed polypeptides, the IgG binding domain Protein G, an HIV entry inhibitor peptide C37H6, and human interleukin-1 receptor antagonist (IL-1ra). The biological activities of the C37H6 and IL-1ra dimers produced by these methods were retained or even slightly increased when compared to their corresponding monomers.
PMID: 20973495 [PubMed - in process]
J Orthop Res. 2010 Dec;28(12):1614-20.
Inhibiting nerve growth factor or its receptors downregulates calcitonin gene-related peptide expression in rat lumbar dorsal root ganglia innervating injured intervertebral discs.
Orita S, Ohtori S, Nagata M, Horii M, Yamashita M, Yamauchi K, Inoue G, Suzuki M, Eguchi Y, Kamoda H, Arai G, Ishikawa T, Miyagi M, Ochiai N, Kishida S, Takaso M, Aoki Y, Takahashi K.
Department of Orthopaedic Surgery, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan. sumihisa@silver.email.ne.jp
Abstract
Nerve growth factor (NGF) and its dual structurally unrelated receptors, tropomyosin-related kinase A (TrkA) or p75 neurotrophin receptor (p75(NTR)), cause the pathogenesis of discogenic pain. To investigate the sensory innervation of injured rat lumbar intervertebral disc (IVD), we examined the expression of neuropeptides such as calcitonin gene-related peptide (CGRP) at dorsal root ganglia (DRG) by inhibiting NGF or its dual receptors. Sprague-Dawley rats with multiply punctured L5-L6 IVD were used. Six experimental groups were prepared: naïve, sham control, and four agent-treated groups with punctured IVD (vehicle, anti-NGF antibody, anti-TrkA antibody, and anti-p75(NTR) antibody). Retrograde neurotracer Fluoro-Gold (FG) was applied together except for the naïve group. Their lumbar DRG were harvested and immunolabeled for CGRP. FG-labeled DRG neurons were most prevalent at L1 and L2 DRG, and the proportion of FG-labeled CGRP-immunoreactive DRG neurons in the vehicle group was significantly elevated (p <>© 2010 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.
PMID: 20973063 [PubMed - indexed for MEDLINE]
Biomed Mater. 2010 Oct 22;5(6):065007. [Epub ahead of print]
Molecularly imprinted nanoparticles with recognition properties towards a laminin H-Tyr-Ile-Gly-Ser-Arg-OH sequence for tissue engineering applications.
Rosellini E, Barbani N, Giusti P, Ciardelli G, Cristallini C.
Department of Chemical Engineering, Industrial Chemistry and Materials Science, University of Pisa, Largo Lucio Lazzarino, 56126 Pisa, Italy.
Abstract
Nanotechnology is an emerging field that promises to revolutionize medicine and is increasingly used in tissue engineering applications. Our research group proposed for the first time molecular imprinting as a new nanotechnology for the creation of advanced synthetic support structures for cell adhesion and proliferation. The aim of this work was the synthesis and characterization of molecularly imprinted polymers with recognition properties towards a laminin peptide sequence and their application as functionalization structures in the development of bioactive materials. Nanoparticles with an average diameter of 200 nm were synthesized by precipitation polymerization of methacrylic acid in the presence of the template molecule and trimethylpropane trimethacrylate as the cross-linking agent. The imprinted nanoparticles showed good performance in terms of recognition capacity and selectivity. The cytotoxicity tests showed normal vitality of C2C12 myoblasts cultured in the medium that was put in contact with the imprinted polymers. After the deposition on the polymeric film surface, the imprinted particles maintained their specific recognition and rebinding behaviour, showing an even higher quantitative binding than free nanoparticles. Preliminary in vitro cell culture tests demonstrated the ability of functionalized materials to promote cell adhesion, proliferation and differentiation, suggesting that molecular imprinting can be used as an innovative functionalization technique.
PMID: 20966532 [PubMed - as supplied by publisher]
Biochemistry. 2010 Nov 23;49(46):9946-7. Epub 2010 Nov 1.
Activation of the pacidamycin PacL adenylation domain by MbtH-like proteins.
Zhang W, Heemstra JR Jr, Walsh CT, Imker HJ.
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, United States.
Abstract
Nonribosomal peptide synthetase (NRPS) assembly lines are major avenues for the biosynthesis of a vast array of peptidyl natural products. Several hundred bacterial NRPS gene clusters contain a small (∼70-residue) protein belonging to the MbtH family for which no function has been defined. Here we show that two strictly conserved Trp residues in MbtH-like proteins contribute to stimulation of amino acid adenylation in some NRPS modules. We also demonstrate that adenylation can be stimulated not only by cognate MbtH-like proteins but also by homologues from disparate natural product pathways.
PMID: 20964365 [PubMed - in process]PMCID: PMC2982891 [Available on 2011/11/1]
Bioconjug Chem. 2010 Nov 17;21(11):2055-64. Epub 2010 Oct 21.
Synthesis, characterization, and thermodynamic study of a polyvalent lytic peptide-polymer conjugate as novel anticancer agent.
Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology, China.
Abstract
We designed and synthesized a new polyvalent lytic peptide-polymer conjugate as a novel chemotherapeutic agent capable of overcoming multidrug resistance. A hexapeptide (KWKWKW or (KW)₃) was designed and conjugated to dextran in multiple copies to afford a polyvalent conjugate. A robust synthesis procedure involving click chemistry and the detailed characterization of the conjugate were reported here. The conjugate Dex-(KW)₃ exhibited significantly enhanced anticancer potency in vitro by up to 500-fold compared to monomeric (KW)₃. The LC₅₀ value was comparable to that of conventional lytic peptides which have more than 20 residues. No hemolytic activity was shown by the conjugates up to 300 μM. Thermodynamic study indicated that the binding of conjugates was predominantly entropy-driven while the binding of free peptides was mainly enthalpy-driven, implying a deeper penetration of conjugate into the core of lipid bilayer. The binding affinity of conjugate to neutral membrane is much higher than that to free peptide (K(conj) ≈ 8822.9 M⁻¹, K(pep) ≈ 1884.7 M⁻¹). In binding to negatively charged membrane, the conjugate surpassed free peptides at high concentrations when the binding of free peptides became saturated. The higher binding capability, attributed to the high local concentration of peptides mounted on a polymer backbone, explains the superior anticancer activity of polyvalent Dex-(KW)₃.
PMID: 20964334 [PubMed - in process]
J Neurosci. 2010 Oct 20;30(42):14182-93.
Distinct levels of dopamine denervation differentially alter striatal synaptic plasticity and NMDA receptor subunit composition.
Paillé V, Picconi B, Bagetta V, Ghiglieri V, Sgobio C, Di Filippo M, Viscomi MT, Giampà C, Fusco FR, Gardoni F, Bernardi G, Greengard P, Di Luca M, Calabresi P.
Fondazione Santa Lucia, Instituto di Ricovero e Cura a Carattere Scientifico, 00179 Rome, Italy.
Abstract
A correct interplay between dopamine (DA) and glutamate is essential for corticostriatal synaptic plasticity and motor activity. In an experimental model of Parkinson's disease (PD) obtained in rats, the complete depletion of striatal DA, mimicking advanced stages of the disease, results in the loss of both forms of striatal plasticity: long-term potentiation (LTP) and long-term depression (LTD). However, early PD stages are characterized by an incomplete reduction in striatal DA levels. The mechanism by which this incomplete reduction in DA level affects striatal synaptic plasticity and glutamatergic synapses is unknown. Here we present a model of early PD in which a partial denervation, causing mild motor deficits, selectively affects NMDA-dependent LTP but not LTD and dramatically alters NMDA receptor composition in the postsynaptic density. Our findings show that DA decrease influences corticostriatal synaptic plasticity depending on the level of depletion. The use of the TAT2A cell-permeable peptide, as an innovative therapeutic strategy in early PD, rescues physiological NMDA receptor composition, synaptic plasticity, and motor behavior.
PMID: 20962239 [PubMed - indexed for MEDLINE]
J Am Chem Soc. 2010 Nov 10;132(44):15499-501.
Circular logic: nonribosomal peptide-like macrocyclization with a ribosomal peptide catalyst.
McIntosh JA, Robertson CR, Agarwal V, Nair SK, Bulaj GW, Schmidt EW.
Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, USA.
Abstract
A protease from ribosomal peptide biosynthesis macrocyclizes diverse substrates, including those resembling nonribosomal peptide and hybrid polyketide-peptide products. The proposed mechanism is analogous to thioesterase-catalyzed chemistry, but the substrates are amide bonds rather than thioesters.
PMID: 20961047 [PubMed - in process]PMCID: PMC2975588 [Available on 2011/11/1]
