Thiol-Mediated Chemoselective Strategies for in Situ Formation of Hydrogels
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Alkyldihydropyrones, New Polyketides Synthesized by a Type III Polyketide Synthase from Streptomyces Reveromyceticus
The Journal of Antibiotics (2014) 67, 819–823 & 2014 Japan Antibiotics Research Association All rights reserved 0021-8820/14 www.nature.com/ja ORIGINAL ARTICLE Alkyldihydropyrones, new polyketides synthesized by a type III polyketide synthase from Streptomyces reveromyceticus Teruki Aizawa1, Seung-Young Kim1, Shunji Takahashi2,3, Masahiko Koshita1, Mioka Tani1, Yushi Futamura3, Hiroyuki Osada2,3 and Nobutaka Funa1 Genome sequencing allows a rapid and efficient identification of novel catalysts that produce novel secondary metabolites. Here we describe the catalytic properties of dihydropyrone synthase A (DpyA), a novel type III polyketide synthase encoded in a linear plasmid of Streptomyces reveromyceticus. Heterologous expression of dpyA led to the accumulation of alkyldihydropyrones A (1), B (2), C (3) and D (4), which are novel dihydropyran compounds that exhibit weak cytotoxicity against the leukemia cell line HL-60. DpyA catalyzes the condensation of b-hydroxyl acid thioester and methylmalonyl-CoA to yield a triketide intermediate that then undergoes lactonization of a secondary alcohol and a thioester to give alkyldihydropyrone. The Journal of Antibiotics (2014) 67, 819–823; doi:10.1038/ja.2014.80; published online 2 July 2014 INTRODUCTION Very recently, Tang et al.11 discovered that presulficidin, which is Type III polyketide synthase (PKS), which is widely distributed synthesized by Cpz6, a type III PKS from the caprazamycin among higher plants, fungi and bacteria, catalyzes the assembly of biosynthetic cluster, relays sulfonate from 30-phosphoadenine-50- primary metabolites such as acyl-CoA compounds to synthesize phosphosulfate to caprazamycin. structurally complex polyketides.1 The reaction catalyzed by type III Genome sequence analyses of Streptomyces species have shown that PKS starts with the formation of a thioester bond between the the number of biosynthetic gene clusters encoded on the chromosome catalytic center cysteine and an acyl group derived from a starter is much higher than the number of secondary metabolites isolated substrate. -
The Reaction of Aminonitriles with Aminothiols: a Way to Thiol-Containing Peptides and Nitrogen Heterocycles in the Primitive Earth Ocean
life Article The Reaction of Aminonitriles with Aminothiols: A Way to Thiol-Containing Peptides and Nitrogen Heterocycles in the Primitive Earth Ocean Ibrahim Shalayel , Seydou Coulibaly, Kieu Dung Ly, Anne Milet and Yannick Vallée * Univ. Grenoble Alpes, CNRS, Département de Chimie Moléculaire, Campus, F-38058 Grenoble, France; [email protected] (I.S.); [email protected] (S.C.); [email protected] (K.D.L.); [email protected] (A.M.) * Correspondence: [email protected] Received: 28 September 2018; Accepted: 18 October 2018; Published: 19 October 2018 Abstract: The Strecker reaction of aldehydes with ammonia and hydrogen cyanide first leads to α-aminonitriles, which are then hydrolyzed to α-amino acids. However, before reacting with water, these aminonitriles can be trapped by aminothiols, such as cysteine or homocysteine, to give 5- or 6-membered ring heterocycles, which in turn are hydrolyzed to dipeptides. We propose that this two-step process enabled the formation of thiol-containing dipeptides in the primitive ocean. These small peptides are able to promote the formation of other peptide bonds and of heterocyclic molecules. Theoretical calculations support our experimental results. They predict that α-aminonitriles should be more reactive than other nitriles, and that imidazoles should be formed from transiently formed amidinonitriles. Overall, this set of reactions delineates a possible early stage of the development of organic chemistry, hence of life, on Earth dominated by nitriles and thiol-rich peptides (TRP). Keywords: origin of life; prebiotic chemistry; thiol-rich peptides; cysteine; aminonitriles; imidazoles 1. Introduction In ribosomes, peptide bonds are formed by the reaction of the amine group of an amino acid with an ester function. -
The Relative Rates of Thiol–Thioester Exchange and Hydrolysis for Alkyl and Aryl Thioalkanoates in Water
Orig Life Evol Biosph (2011) 41:399–412 DOI 10.1007/s11084-011-9243-4 PREBIOTIC CHEMISTRY The Relative Rates of Thiol–Thioester Exchange and Hydrolysis for Alkyl and Aryl Thioalkanoates in Water Paul J. Bracher & Phillip W. Snyder & Brooks R. Bohall & George M. Whitesides Received: 14 April 2011 /Accepted: 16 June 2011 / Published online: 5 July 2011 # Springer Science+Business Media B.V. 2011 Abstract This article reports rate constants for thiol–thioester exchange (kex), and for acid- mediated (ka), base-mediated (kb), and pH-independent (kw) hydrolysis of S-methyl thioacetate and S-phenyl 5-dimethylamino-5-oxo-thiopentanoate—model alkyl and aryl thioalkanoates, respectively—in water. Reactions such as thiol–thioester exchange or aminolysis could have generated molecular complexity on early Earth, but for thioesters to have played important roles in the origin of life, constructive reactions would have needed to compete effectively with hydrolysis under prebiotic conditions. Knowledge of the kinetics of competition between exchange and hydrolysis is also useful in the optimization of systems where exchange is used in applications such as self-assembly or reversible binding. For the alkyl thioester S-methyl thioacetate, which has been synthesized in −5 −1 −1 −1 −1 −1 simulated prebiotic hydrothermal vents, ka = 1.5×10 M s , kb = 1.6×10 M s , and −8 −1 kw = 3.6×10 s . At pH 7 and 23°C, the half-life for hydrolysis is 155 days. The second- order rate constant for thiol–thioester exchange between S-methyl thioacetate and 2- −1 −1 sulfonatoethanethiolate is kex = 1.7 M s . -
8.6 Acidity of Alcohols and Thiols 355
08_BRCLoudon_pgs5-1.qxd 12/8/08 11:05 AM Page 355 8.6 ACIDITY OF ALCOHOLS AND THIOLS 355 ural barrier to the passage of ions. However, the hydrocarbon surface of nonactin allows it to enter readily into, and pass through, membranes. Because nonactin binds and thus transports ions, the ion balance crucial to proper cell function is upset, and the cell dies. Ion Channels Ion channels, or “ion gates,” provide passageways for ions into and out of cells. (Recall that ions are not soluble in membrane phospholipids.) The flow of ions is essen- tial for the transmission of nerve impulses and for other biological processes. A typical chan- nel is a large protein molecule imbedded in a cell membrane. Through various mechanisms, ion channels can be opened or closed to regulate the concentration of ions in the interior of the cell. Ions do not diffuse passively through an open channel; rather, an open channel contains regions that bind a specific ion. Such an ion is bound specifically within the channel at one side of the membrane and is somehow expelled from the channel on the other side. Remark- ably, the structures of the ion-binding regions of these channels have much in common with the structures of ionophores such as nonactin. The first X-ray crystal structure of a potassium- ion channel was determined in 1998 by a team of scientists at Rockefeller University led by Prof. Roderick MacKinnon (b. 1956), who shared the 2003 Nobel Prize in Chemistry for this work. The interior of the channel contains binding sites for two potassium ions; these sites are oxygen-rich, much like the interior of nonactin. -
Identification of a Thioesterase Bottleneck in the Pikromycin Pathway Through Full-Module Processing of Unnatural Pentaketides
Article pubs.acs.org/JACS Identification of a Thioesterase Bottleneck in the Pikromycin Pathway through Full-Module Processing of Unnatural Pentaketides † ‡ † § † ‡ ⊥ ∥ Douglas A. Hansen, , Aaron A. Koch, , and David H. Sherman*, , , , † ‡ § ⊥ Life Sciences Institute, Department of Medicinal Chemistry, Cancer Biology Graduate Program, Department of Chemistry, and ∥ Department of Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan 48109, United States *S Supporting Information ABSTRACT: Polyketide biosynthetic pathways have been engineered to generate natural product analogs for over two decades. However, manipulation of modular type I polyketide synthases (PKSs) to make unnatural metabolites commonly results in attenuated yields or entirely inactive pathways, and the mechanistic basis for compromised production is rarely elucidated since rate-limiting or inactive domain(s) remain unidentified. Accordingly, we synthesized and assayed a series of modified pikromycin (Pik) pentaketides that mimic early pathway engineering to probe the substrate tolerance of the PikAIII-TE module in vitro. Truncated pentaketides were processed with varying efficiencies to corresponding macrolactones, while pentaketides with epimerized chiral centers were poorly processed by PikAIII-TE and failed to generate 12-membered ring products. Isolation and identification of extended but prematurely offloaded shunt products suggested that the Pik thioesterase (TE) domain has limited substrate flexibility and functions as a gatekeeper in the processing of -
THIOL OXIDATION a Slippery Slope the Oxidation of Thiols — Molecules RSH Oxidation May Proceed Too Predominates
RESEARCH HIGHLIGHTS Nature Reviews Chemistry | Published online 25 Jan 2017; doi:10.1038/s41570-016-0013 THIOL OXIDATION A slippery slope The oxidation of thiols — molecules RSH oxidation may proceed too predominates. Here, the maximum of the form RSH — can afford quickly for intermediates like RSOH rate constants indicate the order − − − These are many products. From least to most to be spotted and may also afford of reactivity: RSO > RS >> RSO2 . common oxidized, these include disulfides intractable mixtures. Addressing When the reactions are carried out (RSSR), as well as sulfenic (RSOH), the first problem, Chauvin and Pratt in methanol-d , the obtained kinetic reactions, 1 sulfinic (RSO2H) and sulfonic slowed the reactions down by using isotope effect values (kH/kD) are all but have (RSO3H) acids. Such chemistry “very sterically bulky thiols, whose in the range 1.1–1.2, indicating that historically is pervasive in nature, in which corresponding sulfenic acids were no acidic proton is transferred in the been very disulfide bonds between cysteine known to be isolable but were yet rate-determining step. Rather, the residues stabilize protein structures, to be thoroughly explored in terms oxidations involve a specific base- difficult to and where thiols and thiolates often of reactivity”. The second problem catalysed mechanism wherein an study undergo oxidation by H2O2 or O2 in was tackled by modifying the model acid–base equilibrium precedes the order to protect important biological system, 9-mercaptotriptycene, by rate-determining nucleophilic attack − − − structures from damage. Among including a fluorine substituent to of RS , RSO or RSO2 on H2O2. the oxidation products, sulfenic serve as a spectroscopic handle. -
Using Dynamic Combinatorial Chemistry to Construct Novel Thioester and Disulfide Lipids
Using dynamic combinatorial chemistry to construct novel thioester and disulfide lipids A dissertation submitted to the University of Manchester for the degree of MSc by Research Chemistry In the Faculty of Science and Engineering 2017 Jack A. Yung School of Chemistry Table of Contents List of figures, tables and equations 5 Symbols and abbreviations 10 Abstract 12 Declaration 13 Copyright statement 13 Acknowledgements 14 The author 14 Chapter 1. Introduction 15 1.1 The cell membrane 16 1.1.1 Function and composition 16 1.2 Membrane lipids 16 1.2.1 Lipid classification 16 1.2.2 Amphiphiles 17 1.2.3 Glycolipids 17 1.2.4 Sterols 18 1.2.5 Phospholipids 19 1.3 Lipid vesicles 20 1.3.1 Supramolecular self-assembly 20 1.3.2 Interaction free energies 21 1.3.3 Framework for the theory of self-assembly 22 1.3.4 Micelles 23 1.3.5 Lipid bilayers 24 1.3.6 Vesicles 25 1.3.7 Phase-transition temperature 27 1.4 Amphiphilic building blocks 27 1.5 Thioesters 29 1.5.1 Thioester reactivity 29 1.5.2 Trans-thioesterification 30 1.5.3 Thioester exchange reactions in DCC 31 1.6 Disulfides 32 2 1.6.1 Disulfide reactivity 32 1.6.2 Thiol-disulfide interchange reactions 32 1.6.3 Disulfide exchange reactions in DCC 33 1.7 Pre-biotic lipids 34 1.7.1 Sources of pre-biotic organic compounds 34 1.7.2 The first pre-biotic membrane structure 36 1.7.3 The role of sulfur in pre-biotic chemistry 36 1.8 Artificially designed vesicles 37 1.8.1 Applications of artificially designed vesicles 37 1.8.2 Zeta-potential 37 1.8.3 Vesicle design 38 1.9 Targets 39 1.9.1 Aims 39 Chapter 2. -
Variations in the Structure and Reactivity of Thioester Functionalized Self-Assembled Monolayers and Their Use for Controlled Surface Modification
Variations in the structure and reactivity of thioester functionalized self-assembled monolayers and their use for controlled surface modification Inbal Aped, Yacov Mazuz and Chaim N. Sukenik* Full Research Paper Open Access Address: Beilstein J. Nanotechnol. 2012, 3, 213–220. Department of Chemistry and Institute for Nanotechnology and doi:10.3762/bjnano.3.24 Advanced Materials, Bar-Ilan University, Ramat-Gan, Israel 52900 Received: 01 December 2011 Email: Accepted: 10 February 2012 Chaim N. Sukenik* - [email protected] Published: 09 March 2012 * Corresponding author This article is part of the Thematic Series "Self-assembly at solid surfaces". Keywords: siloxane-anchored self-assembled monolayers; sulfonated interfaces; Guest Editors: S. R. Cohen and J. Sagiv surface chemistry © 2012 Aped et al; licensee Beilstein-Institut. License and terms: see end of document. Abstract Thioester-functionalized, siloxane-anchored, self-assembled monolayers provide a powerful tool for controlling the chemical and physical properties of surfaces. The thioester moiety is relatively stable to long-term storage and its structure can be systematically varied so as to provide a well-defined range of reactivity and wetting properties. The oxidation of thioesters with different-chain- length acyl groups allows for very hydrophobic surfaces to be transformed into very hydrophilic, sulfonic acid-bearing, surfaces. Systematic variation in the length of the polymethylene chain has also allowed us to examine how imbedding reaction sites at various depths in a densely packed monolayer changes their reactivity. π-Systems (benzene and thiophene) conjugated to the thioester carbonyl enable the facile creation of photoreactive surfaces that are able to use light of different wavelengths. -
Thiolated Polymers: Stability of Thiol Moieties Under Different Storage Conditions
Scientia Pharmaceutica (Sci. Pharm.) 70, 331-339 (2002) 0 Osterreichische Apotheker-Verlagsgesellschaftm.b.H., Wien, Printed in Austria Thiolated polymers: Stability of thiol moieties under different storage conditions A. ~ernko~-schnijrchi*,M.D. ~ornof'*,C.E. ~ast'and N. ~angoth' 'institute of Pharmaceutical Technology and Biopharmaceutics, Center of Pharmacy, University of Vienna, Althanstr. 14, 1090 Vienna, Austria 2~romaPharma GmbH, lndustriezeile 6, 2100 Leobendorf, Austria Abstract: The purpose of this study was to evaluate the stability of thiolated polymers - so-called thiomers. A polycarbophil-cysteine conjugate and a chitosan-thioglycolic acid conjugate were chosen as representative anionic and cationic thiomer. The thiol group bearing compounds L-cysteine and thioglycolic acid were introduced to polycarbophil and chitosan, respectively with a coupling reaction mediated by a carbodiimide. The resulting thiolated polymers were freeze-dried and the amount of thiol groups on the thiomer was determined spectrophotometrically. Each kind of polymer was directly used or compressed into 1 mg matrix-tablets. Polymers were stored for a period of six months at four different storage conditions, namely at -20°C (56% relative humidity; RH), 4°C (53% RH), at 20°C (70% RH), and at 22°C (25% RH). Samples were taken after 6 months to determine the formation of disulfide bonds and the remaining thiol groups on the polymer. When the polycarbophil-cysteine and chitosan-thioglycolic acid conjugate were stored as powder a decrease of free thiol groups was observed only after storage at 20°C and 70% RH. Both polymers were found to be stable under all storage conditions when compressed into matrix tablets. -
In This Handout, All of Our Functional Groups Are Presented As Condensed Line Formulas, 2D and 3D Formulas and with Nomenclature Prefixes and Suffixes (If Present)
In this handout, all of our functional groups are presented as condensed line formulas, 2D and 3D formulas and with nomenclature prefixes and suffixes (if present). Organic names are built on a foundation of alkanes, alkenes and alkynes. Those examples are presented first and you need to know those rules. The strategies can be found in Chapter 4 of our textbook (alkanes: pages 93-98, cycloalkanes 102-104, alkenes: pages 104-110, alkynes: pages 112-113 and combinations of all of them 113-115). After introducing examples of alkanes, alkenes, alkynes and combinations of them, the functional groups are presented in order of priority. A few nomenclature examples are provided for each of the functional groups. Examples of the various functional groups are presented on pages 115-135 in the textbook. Two overview pages are on pages 136-137. Some functional groups have a suffix name when they are the highest priority functional group and a prefix name when they are not the highest priority group, and these are added to the skeletal names with identifying numbers and stereochemistry terms (E and Z for alkenes, R and S for chiral centers and cis and trans for rings). Several low priority functional groups only have a prefix name. A few additional special patterns are shown on pages 98-102. The only way to learn this topic is practice (over and over). The best practice approach is to actually write out the names (on an extra piece of paper or on a white board, and then do it again). The same functional groups are used throughout the entire course. -
215-216 HH W12-Notes-Ch 15
Chem 215 F12 Notes Notes – Dr. Masato Koreeda - Page 1 of 17. Date: October 5, 2012 Chapter 15: Carboxylic Acids and Their Derivatives and 21.3 B, C/21.5 A “Acyl-Transfer Reactions” I. Introduction Examples: note: R could be "H" R Z R O H R O R' ester O carboxylic acid O O an acyl group bonded to R X R S acid halide* R' an electronegative atom (Z) thioester O X = halogen O R' R, R', R": alkyl, alkenyl, alkynyl, R O R' R N or aryl group R" amide O O O acid anhydride one of or both of R' and R" * acid halides could be "H" R F R Cl R Br R I O O O O acid fluoride acid chloride acid bromide acid iodide R Z sp2 hybridized; trigonal planar making it relatively "uncrowded" O The electronegative O atom polarizes the C=O group, making the C=O carbon "electrophilic." Resonance contribution by Z δ * R Z R Z R Z R Z C C C C O O O δ O hybrid structure The basicity and size of Z determine how much this resonance structure contributes to the hybrid. * The more basic Z is, the more it donates its electron pair, and the more resonance structure * contributes to the hybrid. similar basicity O R' Cl OH OR' NR'R" Trends in basicity: O weakest increasing basiciy strongest base base Check the pKa values of the conjugate acids of these bases. Chem 215 F12 Notes Notes –Dr. Masato Koreeda - Page 2 of 17. -
Synthesis and Characterization of Functionalized Poly(Arylene Ether Sulfone)S Using Click Chemistry
Wright State University CORE Scholar Browse all Theses and Dissertations Theses and Dissertations 2016 Synthesis and Characterization of Functionalized Poly(arylene ether sulfone)s using Click Chemistry Kavitha Neithikunta Wright State University Follow this and additional works at: https://corescholar.libraries.wright.edu/etd_all Part of the Chemistry Commons Repository Citation Neithikunta, Kavitha, "Synthesis and Characterization of Functionalized Poly(arylene ether sulfone)s using Click Chemistry" (2016). Browse all Theses and Dissertations. 1650. https://corescholar.libraries.wright.edu/etd_all/1650 This Thesis is brought to you for free and open access by the Theses and Dissertations at CORE Scholar. It has been accepted for inclusion in Browse all Theses and Dissertations by an authorized administrator of CORE Scholar. For more information, please contact [email protected]. SYNTHESIS AND CHARACTERIZATION OF FUNCTIONALIZED POLY (ARYLENE ETHER SULFONE)S USING CLICK CHEMSITRY A thesis submitted in partial fulfilment of the requirements for the degree of Master of Science By Kavitha Neithikunta B.sc Osmania University, 2010 2016 Wright State University WRIGHT STATE UNIVERSITY GRADUATE SCHOOL August 26, 2016 I HEREBY RECOMMEND THAT THE THESIS PREPARED UNDER MYSUPERVISION BY Kavitha Neithikunta ENTITLED Synthesis and Characterization of Functionalized Poly(arylene ether sulfone)s using Click chemistry BE ACCEPTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF Master of Science __________________________ Eric Fossum, Ph.D. Thesis Advisor ___________________________ David Grossie, Ph.D. Chair, Department of Chemistry Committee on Final Examination ____________________________ Eric Fossum, Ph.D. _____________________________ Daniel M. Ketcha, Ph.D. _____________________________ William A. Feld, Ph.D. _______________________________ Robert E. W. Fyffe, Ph.D Vice President for Research and Dean of the Graduate School ABSTRACT Neithikunta, Kavitha M.S., Department of Chemistry, Wright State University, 2016.