Advances in Chemical Biology: Bioactive Peptides and Protein Delivery, Study notes of Chemistry

Download Advances in Chemical Biology: Bioactive Peptides and Protein Delivery and more Study notes Chemistry in PDF only on Docsity! 1 Chmielewski Group Literature Abstracts February 2007 Contributing Editors: Stefan Hershberger (Science) Marcos Pires (Nature and Nature subdivisions) Brandon Gaddis/Iris Geisler (JACS) Jee Yeon Lee (PNAS) Dawn Ernenwein (Chem & Bio/Chem Biol & Drug Design) Dave Przybyla (Angewandte Chemie) Hilda Namanja (ACS Chemical Biology) Nicole O’Neil (Org Lett) 2 Nature Enantioselective halocyclization of polyprenoids induced by nucleophilic phosphoramidites Nature 445, 900-903 (22 February 2007) Akira Sakakura1, Atsushi Ukai1 and Kazuaki Ishihara1 Polycyclic bio-active natural products that contain halogen atoms have been isolated from a number of different marine organisms1. The biosynthesis of these natural products appears to be initiated by an electrophilic halogenation reaction at a carbon– carbon double bond2, 3, 4 via a mechanism that is similar to a proton-induced olefin polycyclization5, 6, 7, 8. Enzymes such as haloperoxidases generate an electrophilic halonium ion (or its equivalent), which reacts with the terminal carbon–carbon double bond of the polyprenoid, enantioselectively inducing a cyclization reaction that produces a halogenated polycyclic terpenoid. Use of an enantioselective halocyclization reaction is one possible way to chemically synthesize these halogenated cyclic terpenoids; although several brominated cyclic terpenoids have been synthesized via a diastereoselective halocyclization reaction that uses stoichiometric quantities of a brominating reagent9, 10, 11, 12, the enantioselective halocyclization of isoprenoids induced by a chiral promoter has not yet been reported. Here we report the enantioselective halocyclization of simple polyprenoids using a nucleophilic promoter. Achiral nucleophilic phosphorus compounds are able to promote the diastereoselective halocyclization reaction to give a halogenated cyclic product in excellent yields. Moreover, chiral phosphoramidites promote the enantioselective halocyclization of simple polyprenoids with N- iodosuccinimide to give iodinated cyclic products in up to 99% enantiomeric excess and diastereomeric excess. To the best of our knowledge, this is the first successful example of the enantioselective halopolycyclization of polyprenoids. Nature Chemical Biology Bioinformatic discovery of novel bioactive peptides Nature Chemical Biology 3, 108-112 (2007) Richard J Edwards1,2,4, Niamh Moran1,4, Marc Devocelle3, Aoife Kiernan1, Gerardene Meade1, William Signac1, Martina Foy1, Stephen D E Park1, Eimear Dunne1, Dermot Kenny1 and Denis C Shields 5 Due to their small size, nanoparticles have distinct properties compared with the bulk form of the same materials. These properties are rapidly revolutionizing many areas of medicine and technology. Despite the remarkable speed of development of nanoscience, relatively little is known about the interaction of nanoscale objects with living systems. In a biological fluid, proteins associate with nanoparticles, and the amount and presentation of the proteins on the surface of the particles leads to an in vivo response. Proteins compete for the nanoparticle "surface," leading to a protein "corona" that largely defines the biological identity of the particle. Thus, knowledge of rates, affinities, and stoichiometries of protein association with, and dissociation from, nanoparticles is important for understanding the nature of the particle surface seen by the functional machinery of cells. Here we develop approaches to study these parameters and apply them to plasma and simple model systems, albumin and fibrinogen. A series of copolymer nanoparticles are used with variation of size and composition (hydrophobicity). We show that isothermal titration calorimetry is suitable for studying the affinity and stoichiometry of protein binding to nanoparticles. We determine the rates of protein association and dissociation using surface plasmon resonance technology with nanoparticles that are thiol-linked to gold, and through size exclusion chromatography of protein–nanoparticle mixtures. This method is less perturbing than centrifugation, and is developed into a systematic methodology to isolate nanoparticle- associated proteins. The kinetic and equilibrium binding properties depend on protein identity as well as particle surface characteristics and size. Journal of the American Chemical Society Ambient Temperature Synthesis of High Enantiopurity N- Protected Peptidyl Ketones by Peptidyl Thiol Ester-Boronic Acid Cross-Coupling J. Am. Chem. Soc., 2007, 129 (5), 1132 -1140 Hao Yang, Hao Li, Rüdiger Wittenberg, Masahiro Egi, Wenwei Huang, and Lanny S. Liebeskind -Amino acid thiol esters derived from N-protected mono-, di-, and tripeptides couple with aryl, -electron-rich heteroaryl, or alkenyl boronic acids in the presence of stoichiometric Cu(I) thiophene-2-carboxylate and catalytic Pd2(dba)3/triethylphosphite to generate the corresponding N-protected peptidyl ketones in good-to-excellent yields and in high enantiopurity. Triethylphosphite plays a key role as a supporting ligand by mitigating an undesired palladium-catalyzed decarbonylation- -elimination of the - amino thiol esters. The peptidyl ketone synthesis proceeds at room temperature under nonbasic conditions and demonstrates a high tolerance to functionality. Discovery of Chemical Reactions through Multidimensional Screening 6 J. Am. Chem. Soc., 2007, 129 (5), 1413 -1419 Aaron B. Beeler,* Shun Su, Chris A. Singleton, and John A. Porco, Jr Multidimensional reaction screening of ortho-alkynyl benzaldehydes with a variety of catalysts and reaction partners was conducted in an effort to identify new chemical reactions. Reactions affording unique products were selected for investigation of preliminary scope and limitations. Quantitative Evaluation of the Relative Cell Permeability of Peptoids and Peptides J. Am. Chem. Soc., 2007, 129 (6), 1508 -1509 Yong-Uk Kwon and Thomas Kodadek We evaluated quantitatively the relative cell permeability of peptoids and peptides using a cell-based reporter gene-based assay. Generally, peptoids were much more cell permeable than the corresponding peptides, though the difference decreased with increasing length. These results suggest that peptoids may be useful reagents for manipulating the activities of intracellular proteins. Controlling Multiple Fluorescent Signal Output in Cyclic Peptide- Based Supramolecular Systems J. Am. Chem. Soc., 2007, 129 (6), 1653 -1657 Roberto J. Brea, M. Eugenio V zquez, Manuel Mosquera, Luis Castedo, and Juan R. Granja A multicomponent equilibrium network based on self-assembling , -cyclic peptides with controlled fluorescence output is described. The network takes advantage of the large association constant of , -cyclic peptides and the controlled formation homo- and heterodimers, making use for the first time of excimer/FRET effects in conjunction for 7 studying complex interaction networks. In addition, we study the Dapoxyl/pyrene FRET pair for the first time. DNA-Encoded Antibody Libraries: A Unified Platform for Multiplexed Cell Sorting and Detection of Genes and Proteins J. Am. Chem. Soc., 129 (7), 1959 -1967, 2007 Whether for pathological examination or for fundamental biology studies, different classes of biomaterials and biomolecules are each measured from a different region of a typically heterogeneous tissue sample, thus introducing unavoidable sources of noise that are hard to quantitate. We describe the method of DNA-encoded antibody libraries (DEAL) for spatially multiplexed detection of ssDNAs and proteins as well as for cell sorting, all on the same diagnostic platform. DEAL is based upon the coupling of ssDNA oligomers onto antibodies which are then combined with the biological sample of interest. Spotted DNA arrays, which are found to inhibit biofouling, are utilized to spatially stratify the biomolecules or cells of interest. We demonstrate the DEAL technique for (1) the rapid detection of multiple proteins within a single microfluidic channel, and, with the additional step of electroless amplification of gold-nanoparticle labeled secondary antibodies, we establish a detection limit of 10 fM for the protein IL- 2, 150 times more sensitive than the analogue ELISA; (2) the multiplexed, on-chip sorting of both immortalized cell lines and primary immune cells with an efficiency that exceeds surface-confined panning approaches; and (3) the co-detection of ssDNAs, proteins, and cell populations on the same platform. Collagen-Related Peptides: Self-Assembly of Short, Single Strands into a Functional Biomaterial of Micrometer Scale J. Am. Chem. Soc., 129 (8), 2202 -2203, 2007. Mabel A. Cejas, William A. Kinney,* Cailin Chen, Gregory C. Leo, Brett A. Tounge, Jeremy G. Vinter, Pratik P. Joshi, and Bruce E. Maryanoff We have designed, synthesized, and characterized a short (32-mer; 8-nm), single- stranded, collagen-related peptide (CRP), 1a, which forms triple-helical building blocks that self-assemble into large, composite fibrils by strictly noncovalent means. Computational analysis suggested that the installation of complementary, aromatic - 10 ACS Chemical Biology The 3D Structure of Protein Phosphatase 2A: New Insights into a Ubiquitous Regulator of Cell Signaling ACS Chem. Biol. 2 (2), 99–103 Marc Mumby Protein phosphatase 2A (PP2A) is a serine/threonine phosphatase implicated in cancer. Three new crystal structures of PP2A show how it interacts with inhibitory toxins and with one of its regulatory subunits. The structures also explain how specific site mutations may lead to cancer and suggest a novel role for PP2A methylation in the formation of PP2A holoenzymes. Selective Tumor Cell Targeting Using Low-Affinity, Multivalent Interactions ACS Chem. Biol. 2 (2), 119–127 Coby B. Carlson†,‡, Patricia Mowery‡, Robert M. Owen†, Emily C. Dykhuizen†, and Laura L. Kiessling This report highlights the advantages of low-affinity, multivalent interactions to recognize one cell type over another. Our goal was to devise a strategy to mediate selective killing of tumor cells, which are often distinguished from normal cells by their higher levels of particular cell surface receptors. To test whether multivalent interactions could lead to highly specific cell targeting, we used a chemically synthesized small-molecule ligand composed of two distinct motifs: (1) an Arg-Gly-Asp (RGD) peptidomimetic that binds tightly (Kd ≈ 10–9 M) to αvβ3 integrins and (2) the galactosyl-α(1–3)galactose (α-Gal epitope), which is recognized by human anti-α- galactosyl antibodies (anti-Gal). Importantly, anti-Gal binding requires a multivalent presentation of carbohydrate residues; anti-Gal antibodies interact weakly with the monovalent oligosaccharide (Kd ≈ 10–5 M) but bind tightly (Kd ≈ 10–11 M) to multivalent displays of α-Gal epitopes. Such a display is generated when the bifunctional conjugate decorates a cell possessing a high level of αvβ3 integrin; the resulting cell surface, which presents many α-Gal epitopes, can recruit anti-Gal, thereby 11 triggering complement-mediated lysis. Only those cells with high levels of the integrin receptor are killed. In contrast, doxorubicin tethered to the RGD-based ligand affords indiscriminate cell death. These results highlight the advantages of exploiting the type of the multivalent recognition processes used by physiological systems to discriminate between cells. The selectivity of this strategy is superior to traditional, abiotic, high- affinity targeting methods. Our results have implications for the treatment of cancer and other diseases characterized by the presence of deleterious cells. Chemistry and Biology Hydrophobic Amino Acid and Single-Atom Substitutions Increase DNA Polymerase Selectivity Volume 14, Issue 2, February 2007, Pages 185-194 Nicolas Z. Rudinger, Ramon Kranaster and Andreas Marx DNA polymerase fidelity is of immense biological importance due to the fundamental requirement for accurate DNA synthesis in both replicative and repair processes. Subtle hydrogen-bonding networks between DNA polymerases and their primer/template substrates are believed to have impact on DNA polymerase selectivity. We show that deleting defined interactions of that kind by rationally designed hydrophobic substitution mutations can result in a more selective enzyme. Furthermore, a single- atom replacement within the DNA substrate through chemical modification, which leads to an altered acceptor potential and steric demand of the DNA substrate, further increased the selectivity of the developed systems. Accordingly, this study about the impact of hydrophobic alterations on DNA polymerase selectivity—enzyme and substrate wise—further highlights the relevance of shape complementary and polar interactions on DNA polymerase selectivity. A High-Throughput Screen for Synthetic Riboswitches Reveals Mechanistic Insights into Their Function Volume 14, Issue 2, February 2007, Pages 173-184 Sean A. Lynch, Shawn K. Desai, Hari Krishna Sajja and Justin P. Gallivan Riboswitches are RNA-based genetic control elements that regulate gene expression in a ligand-dependent fashion without the need for proteins. The ability to create synthetic riboswitches that control gene expression in response to any desired small-molecule ligand will enable the development of sensitive genetic screens that can detect the presence of small molecules, as well as designer genetic control elements to conditionally modulate cellular behavior. Herein, we present an automated high- throughput screening method that identifies synthetic riboswitches that display extremely low background levels of gene expression in the absence of the desired ligand and robust increases in expression in its presence. Mechanistic studies reveal how these riboswitches function and suggest design principles for creating new synthetic 12 riboswitches. We anticipate that the screening method and design principles will be generally useful for creating functional synthetic riboswitches. Chemical Biology and Drug Design Improved Acylation Method Enables Efficient Delivery of Functional Palmitoylated Cystatin into Epithelial Cells Chem Biol Drug Des 2007; 69: 124–131 Nina Kocˇevar*, Natasˇa Obermajer, Borut Strukelj, Janko Kos and Samo Kreft The effective delivery of therapeutic proteins to the site of action is of great importance in achieving an effective therapy. Due to hydrophilicity, proteins are generally poorly transported across biological membranes. Chemical acylation represents one of the basic methods for improving their membrane permeability. A novel method for acylation is presented, based on the formation of palmitoylchloride dispersion in aqueous acetonitrile solution, using chicken cystatin as a model protein. We examined the effects of palmitoylchloride/cystatin molar ratio, reaction pH and introduction of successive palmitoylation cycles on the protein modification degree. The reaction products were analysed by capillary electrophoresis and SDS-PAGE, and the in vitro inhibitory activity was determined by N-benzoyl-d,l-arginine-β-naphthylamide assay. Using cell culture-based assays, we examined the transport properties of unmodified and palmitoylated cystatin, its efficiency to inhibit intracellular enzymes, and its cytotoxicity. We demonstrated that palmitoylated cystatin rapidly internalized into the cell and caused a complete loss of cathepsin B activity. In contrast, the unmodified control cystatin was unable to inhibit the intracellular enzymes. These results strongly suggest protein palmitoylation to be a very effective strategy for improving cell internalization. Organic Letters Selective Recognition of Tryptophan through Inhibition of Intramolecular Charge-Transfer Interactions in an Aqueous Medium Org. Lett., 9 (3), 417 -420, 2007. Mahesh Hariharan, Suneesh C. Karunakaran, and Danaboyina Ramaiah