1
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Gless BH, Schmied SH, Bejder BS, Olsen CA. Förster Resonance Energy Transfer Assay for Investigating the Reactivity of Thioesters in Biochemistry and Native Chemical Ligation. JACS AU 2023; 3:1443-1451. [PMID: 37234128 PMCID: PMC10207088 DOI: 10.1021/jacsau.3c00095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 05/27/2023]
Abstract
Thioesters are considered to be "energy-rich" functional groups that are susceptible to attack by thiolate and amine nucleophiles while remaining hydrolytically stable at neutral pH, which enables thioester chemistry to take place in an aqueous medium. Thus, the inherent reactivity of thioesters enables their fundamental roles in biology and unique applications in chemical synthesis. Here, we investigate the reactivity of thioesters that mimic acyl-coenzyme A (CoA) species and S-acylcysteine modifications as well as aryl thioesters applied in chemical protein synthesis by native chemical ligation (NCL). We developed a fluorogenic assay format for the direct and continuous investigation of the rate of reaction between thioesters and nucleophiles (hydroxide, thiolate, and amines) under various conditions and were able to recapitulate previously reported reactivity of thioesters. Further, chromatography-based analyses of acetyl- and succinyl-CoA mimics revealed striking differences in their ability to acylate lysine side chains, providing insight into nonenzymatic protein acylation. Finally, we investigated key aspects of native chemical ligation reaction conditions. Our data revealed a profound effect of the tris-(2-carboxyethyl)phosphine (TCEP) commonly used in systems where thiol-thioester exchange occurs, including a potentially harmful hydrolysis side reaction. These data provide insight into the potential optimization of native chemical ligation chemistry.
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2
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Digal LD, Kirkeby EK, Austin MJ, Roberts AG. Design and Evaluation of Ambiphilic Aryl Thiol-Iminium-Based Molecules for Organocatalyzed Thioacyl Aminolysis. ACS OMEGA 2023; 8:9319-9325. [PMID: 36936301 PMCID: PMC10018527 DOI: 10.1021/acsomega.2c07586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Progress toward the design and synthesis of ambiphilic aryl thiol-iminium-based small molecules for organocatalyzed thioacyl aminolysis is reported. Here we describe the synthesis of a novel tetrahydroisoquinoline-derived scaffold, bearing both thiol and iminium functionalities, capable of promoting the transthioesterification and subsequent amine capture reactions necessary to achieve organocatalyzed thioacyl aminolysis. Model studies demonstrate the ability of this designed organocatalyst to deliver critical intermediates capable of undergoing these individual reactions necessary for the proposed process. Future design improvements and directions toward cysteine-independent organocatalyzed native chemical ligation are discussed.
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3
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Villamil V, Saiz C, Mahler G. Thioester deprotection using a biomimetic NCL approach. Front Chem 2022; 10:934376. [PMID: 36072700 PMCID: PMC9441695 DOI: 10.3389/fchem.2022.934376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/06/2022] [Indexed: 11/13/2022] Open
Abstract
The reversibility of the thiol-thioester linkage has been broadly employed in many fields of biochemistry (lipid synthesis) and chemistry (dynamic combinatorial chemistry and material science). When the transthioesterification is followed by a S-to-N acyl transfer to give an amide bond, it is called Native Chemical Ligation (NCL), a high-yield chemoselective process used for peptide synthesis. Recently, we described thioglycolic acid (TGA) as a useful reagent for thioester deprotection both in solution and anchored to a solid-support under mild conditions. Inspired by NCL, in this work, we extended this approach and explored the use of 2-aminothiols for the deprotection of thiols bearing an acyl group. The best results were obtained using cysteamine or L-cysteine in an aqueous buffer pH 8 at room temperature for 30 min. The described approach was useful for S-acetyl, S-butyryl, and S-benzoyl heterocycles deprotection with yields up to 84%. Employing this methodology, we prepared six new analogs 2 of mercaptomethyl bisthiazolidine 1, a useful inhibitor of a wide-range of Metallo-β-Lactamases (MBLs). Compared with the previous methodologies (TGA polymer supported and TGA in solution), the biomimetic deprotection herein described presents better performance with higher yields, shorter reaction times, less time-consuming operations, easier setup, and lower costs.
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Affiliation(s)
- Valentina Villamil
- Laboratorio de Química Farmacéutica (DQO), Facultad de Química, Universidad de la República, Montevideo, Uruguay
- Graduate Program in Chemistry, Facultad de Química, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - Cecilia Saiz
- Laboratorio de Química Farmacéutica (DQO), Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Graciela Mahler
- Laboratorio de Química Farmacéutica (DQO), Facultad de Química, Universidad de la República, Montevideo, Uruguay
- *Correspondence: Graciela Mahler,
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4
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Shi YM, Hirschmann M, Shi YN, Bode HB. Cleavage Off-Loading and Post-assembly-Line Conversions Yield Products with Unusual Termini during Biosynthesis. ACS Chem Biol 2022; 17:2221-2228. [PMID: 35860925 PMCID: PMC9396620 DOI: 10.1021/acschembio.2c00367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Piscibactins and photoxenobactins are metallophores and
virulence
factors, whose biosynthetic gene cluster, termed pxb, is the most prevalent polyketide synthase/non-ribosomal peptide
synthetase hybrid cluster across entomopathogenic bacteria. They are
structurally similar to yersiniabactin, which contributes to the virulence
of the human pathogen Yersinia pestis. However, the pxb-derived products feature various
chain lengths and unusual carboxamide, thiocarboxylic acid, and dithioperoxoate
termini, which are rarely found in thiotemplated biosyntheses. Here,
we characterize the pxb biosynthetic logic by gene
deletions, site-directed mutagenesis, and isotope labeling experiments.
Notably, we propose that it involves (1) heterocyclization domains
with various catalytic efficiencies catalyzing thiazoline and amide/thioester
bond formation and (2) putative C–N and C–S bond cleavage
off-loading manners, which lead to products with different chain lengths
and usual termini. Additionally, the post-assembly-line spontaneous
conversions of the biosynthetic end product contribute to production
titers of the other products in the culture medium. This study broadens
our knowledge of thiotemplated biosynthesis and how bacterial host
generate a chemical arsenal.
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Affiliation(s)
- Yi-Ming Shi
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany.,Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Merle Hirschmann
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Yan-Ni Shi
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany.,Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Helge B Bode
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany.,Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany.,Chemical Biology, Department of Chemistry, Philipps University Marburg, 35043 Marburg, Germany.,Senckenberg Gesellschaft für Naturforschung, 60325 Frankfurt am Main, Germany
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5
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Cicek E, Monard G, Sungur FA. Molecular Mechanism of Protein Arginine Deiminase 2: A Study Involving Multiple Microsecond Long Molecular Dynamics Simulations. Biochemistry 2022; 61:1286-1297. [PMID: 35737372 PMCID: PMC9260958 DOI: 10.1021/acs.biochem.2c00158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptidylarginine deiminase 2 (PAD2) is a Ca2+-dependent enzyme that catalyzes the conversion of protein arginine residues to citrulline. This kind of structural modification in histone molecules may affect gene regulation, leading to effects that may trigger several diseases, including breast cancer, which makes PAD2 an attractive target for anticancer drug development. To design new effective inhibitors to control activation of PAD2, improving our understanding of the molecular mechanisms of PAD2 using up-to-date computational techniques is essential. We have designed five different PAD2-substrate complex systems based on varying protonation states of the active site residues. To search the conformational space broadly, multiple independent molecular dynamics simulations of the complexes have been performed. In total, 50 replica simulations have been performed, each of 1 μs, yielding a total simulation time of 50 μs. Our findings identify that the protonation states of Cys647, Asp473, and His471 are critical for the binding and localization of the N-α-benzoyl-l-arginine ethyl ester substrate within the active site. A novel mechanism for enzyme activation is proposed according to near attack conformers. This represents an important step in understanding the mechanism of citrullination and developing PAD2-inhibiting drugs for the treatment of breast cancer.
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Affiliation(s)
- Erdem Cicek
- Informatics Institute, Computational Science and Engineering, Istanbul Technical University, TR-34469 Istanbul, Turkey
| | - Gerald Monard
- Université de Lorraine, CNRS, LPCT, F-54000 Nancy, France
| | - Fethiye Aylin Sungur
- Informatics Institute, Computational Science and Engineering, Istanbul Technical University, TR-34469 Istanbul, Turkey
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6
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Fuchs O, Trunschke S, Hanebrink H, Reimann M, Seitz O. Enabling Cysteine-Free Native Chemical Ligation at Challenging Junctions with a Ligation Auxiliary Capable of Base Catalysis. Angew Chem Int Ed Engl 2021; 60:19483-19490. [PMID: 34165893 PMCID: PMC8457107 DOI: 10.1002/anie.202107158] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Indexed: 12/14/2022]
Abstract
Ligation auxiliaries are used in chemical protein synthesis to extend the scope of native chemical ligation (NCL) beyond cysteine. However, auxiliary-mediated ligations at sterically demanding junctions have been difficult. Often the thioester intermediate formed in the thiol exchange step of NCL accumulates because the subsequent S→N acyl transfer is extremely slow. Here we introduce the 2-mercapto-2-(pyridin-2-yl)ethyl (MPyE) group as the first auxiliary designed to aid the ligation reaction by catalysis. Notably, the MPyE auxiliary provides useful rates even for junctions containing proline or a β-branched amino acid. Quantum chemical calculations suggest that the pyridine nitrogen acts as an intramolecular base in a rate-determining proton transfer step. The auxiliary is prepared in two steps and conveniently introduced by reductive alkylation. Auxiliary cleavage is induced upon treatment with TCEP/morpholine in presence of a MnII complex as radical starter. The synthesis of a de novo designed 99mer peptide and an 80 aa long MUC1 peptide demonstrates the usefulness of the MPyE auxiliary.
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Affiliation(s)
- Olaf Fuchs
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| | - Sebastian Trunschke
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| | - Hendrik Hanebrink
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| | - Marc Reimann
- Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Oliver Seitz
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
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7
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Ein zur Basenkatalyse befähigtes Ligationsauxiliar ermöglicht die cysteinfreie native chemische Ligation an anspruchsvollen Verknüpfungsstellen. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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8
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Shigenaga A. Theoretical study on reaction mechanism of phosphate-catalysed N-S acyl transfer of N-sulfanylethylanilide (SEAlide). Org Biomol Chem 2020; 18:9706-9711. [PMID: 33237096 DOI: 10.1039/d0ob01968b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
C-Terminally thioesterificated peptides are essential building blocks for chemical protein synthesis. To date, many acyl transfer auxiliaries have been developed to enable facile preparation of peptide thioesters. We previously developed an N-sulfanylethylanilide (SEAlide) auxiliary, which causes an N-S acyl transfer reaction upon addition of phosphate salt to convert a C-terminal amide to a thioester. The mechanism of how phosphate triggers the reaction is speculative, and the details are unknown. In this study, the mechanism by which phosphate promotes acyl transfer is discussed based on density functional theory (DFT) calculations and non-covalent interaction (NCI) analysis. As a result, although the notion that phosphate acts as an acid-base catalyst, as speculated in our previous study, was correct, it became clear that two competing reaction pathways exist: a previously proposed stepwise pathway and a concerted one. Furthermore, calculation was performed in the presence of various additives other than phosphate to uncover the effect of the additives on the stability of transition states.
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Affiliation(s)
- Akira Shigenaga
- Faculty of Pharmacy and Pharmaceutical Sciences, Fukuyama University, Hiroshima 729-0292, Japan.
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9
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10
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Aksakal S, Liu R, Aksakal R, Becer CR. Nitroxide-mediated polymerisation of thioacrylates and their transformation into poly(acrylamide)s. Polym Chem 2020. [DOI: 10.1039/c9py01129c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Nitroxide mediated polymers of thioacrylates can be transformed into poly(acrylamide)s.
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Affiliation(s)
- Suzan Aksakal
- Polymer Chemistry Laboratory
- School of Engineering and Materials Science
- Queen Mary University of London
- London
- UK
| | - Renjie Liu
- Polymer Chemistry Laboratory
- School of Engineering and Materials Science
- Queen Mary University of London
- London
- UK
| | - Resat Aksakal
- Polymer Chemistry Laboratory
- School of Engineering and Materials Science
- Queen Mary University of London
- London
- UK
| | - C. Remzi Becer
- Polymer Chemistry Laboratory
- School of Engineering and Materials Science
- Queen Mary University of London
- London
- UK
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11
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Du Y, Xu Y, Qi C, Wang C. Mechanistic study on the Knorr pyrazole synthesis-thioester generation reaction. Tetrahedron Lett 2019. [DOI: 10.1016/j.tetlet.2019.06.053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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12
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Jiang YY, Zhu L, Fan X, Zhang Q, Fu YJ, Li H, Hu B, Bi S. A computational study on H 2S release and amide formation from thionoesters and cysteine. Org Biomol Chem 2019; 17:5771-5778. [PMID: 31135017 DOI: 10.1039/c9ob00854c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The recognition of the biological activity of H2S has drawn much attention to the development of biocompatible H2S release reactions. Thiol-, particularly cysteine-triggered systems which mimic the enzymatic conversion of cysteine or homocysteine to H2S have been intensively reported recently. Herein, a density functional theory (DFT) study was performed to address the reaction mechanism of H2S release and potential amide bond formation from thionoesters and cysteine to gain deeper mechanistic insights. Three possible mechanisms were considered and we found that the one starting from the nucleophilic addition of the ionized mercapto of cysteine on thionoester to generate a dithioester intermediate (Path A) is kinetically favored over the others starting from the nucleophilic addition of the amine of cysteine to generate thionoamide intermediates (Paths B and C). Dithioester then undergoes intramolecular nucleophilic addition of an amine group and the rate-limiting water-assisted proton transfer to generate a cyclic thiol intermediate, and finally affords H2S and dihydrothiazole via water-assisted elimination. The hydrolysis of thionoamide or dihydrothiazole to produce amide is highly difficult under neutral conditions but is operative under strong basic conditions, which explains the experimental observation that dihydrothiazole rather than amide is the major product. Meanwhile, the ring opening reaction of the cyclic thiol intermediate to form the more stable thionoamide is detrimental to H2S release and becomes competitive under basic conditions.
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Affiliation(s)
- Yuan-Ye Jiang
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, People's Republic of China.
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13
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Agouridas V, El Mahdi O, Diemer V, Cargoët M, Monbaliu JCM, Melnyk O. Native Chemical Ligation and Extended Methods: Mechanisms, Catalysis, Scope, and Limitations. Chem Rev 2019; 119:7328-7443. [DOI: 10.1021/acs.chemrev.8b00712] [Citation(s) in RCA: 243] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Vangelis Agouridas
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Ouafâa El Mahdi
- Faculté Polydisciplinaire de Taza, University Sidi Mohamed Ben Abdellah, BP 1223 Taza Gare, Morocco
| | - Vincent Diemer
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Marine Cargoët
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Jean-Christophe M. Monbaliu
- Center for Integrated Technology and Organic Synthesis, Department of Chemistry, University of Liège, Building B6a, Room 3/16a, Sart-Tilman, B-4000 Liège, Belgium
| | - Oleg Melnyk
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
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14
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Bi S, Liu P, Ling B, Yuan X, Jiang Y. Mechanism of N-to-S acyl transfer of N-(2-hydroxybenzyl) cysteine derivatives and origin of phenol acceleration effect. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2017.11.043] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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15
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Jiang YY, Liu TT, Zhang RX, Xu ZY, Sun X, Bi S. Mechanism and Rate-Determining Factors of Amide Bond Formation through Acyl Transfer of Mixed Carboxylic–Carbamic Anhydrides: A Computational Study. J Org Chem 2018; 83:2676-2685. [DOI: 10.1021/acs.joc.7b03107] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Yuan-Ye Jiang
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, People’s Republic of China
| | - Tian-Tian Liu
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, People’s Republic of China
| | - Rui-Xue Zhang
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, People’s Republic of China
| | - Zhong-Yan Xu
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, People’s Republic of China
| | - Xue Sun
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, People’s Republic of China
| | - Siwei Bi
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, People’s Republic of China
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16
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Tersa M, Raich L, Albesa-Jové D, Trastoy B, Prandi J, Gilleron M, Rovira C, Guerin ME. The Molecular Mechanism of Substrate Recognition and Catalysis of the Membrane Acyltransferase PatA from Mycobacteria. ACS Chem Biol 2018; 13:131-140. [PMID: 29185694 DOI: 10.1021/acschembio.7b00578] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Glycolipids play a central role in a variety of important biological processes in all living organisms. PatA is a membrane acyltransferase involved in the biosynthesis of phosphatidyl-myo-inositol mannosides (PIMs), key structural elements, and virulence factors of Mycobacterium tuberculosis. PatA catalyzes the transfer of a palmitoyl moiety from palmitoyl-CoA to the 6-position of the mannose ring linked to the 2-position of inositol in PIM1/PIM2. We report here the crystal structure of PatA in the presence of 6-O-palmitoyl-α-d-mannopyranoside, unraveling the acceptor binding mechanism. The acceptor mannose ring localizes in a cavity at the end of a surface-exposed long groove where the active site is located, whereas the palmitate moiety accommodates into a hydrophobic pocket deeply buried in the α/β core of the protein. Both fatty acyl chains of the PIM2 acceptor are essential for the reaction to take place, highlighting their critical role in the generation of a competent active site. By the use of combined structural and quantum-mechanics/molecular-mechanics (QM/MM) metadynamics, we unravel the catalytic mechanism of PatA at the atomic-electronic level. Our study provides a detailed structural rationale for a stepwise reaction, with the generation of a tetrahedral transition state for the rate-determining step. Finally, the crystal structure of PatA in the presence of β-d-mannopyranose and palmitate suggests an inhibitory mechanism for the enzyme, providing exciting possibilities for inhibitor design and the discovery of chemotherapeutic agents against this major human pathogen.
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Affiliation(s)
- Montse Tersa
- Structural Biology
Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Lluís Raich
- Departament
de Química Inorgànica i Orgànica (Secció
de Química Orgànica) and IQTCUB, Universitat de Barcelona, 08028 Barcelona, Spain
| | - David Albesa-Jové
- Structural Biology
Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
- Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas - Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain
- Departamento de
Bioquímica, Universidad del País Vasco, Leioa, Spain
- IKERBASQUE, Basque Foundation for Science, 48013, Bilbao, Spain
| | - Beatriz Trastoy
- Structural Biology
Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Jacques Prandi
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 205 route de Narbonne, F-31077 Toulouse, France
| | - Martine Gilleron
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 205 route de Narbonne, F-31077 Toulouse, France
| | - Carme Rovira
- Departament
de Química Inorgànica i Orgànica (Secció
de Química Orgànica) and IQTCUB, Universitat de Barcelona, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08020 Barcelona, Spain
| | - Marcelo E. Guerin
- Structural Biology
Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
- Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas - Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain
- Departamento de
Bioquímica, Universidad del País Vasco, Leioa, Spain
- IKERBASQUE, Basque Foundation for Science, 48013, Bilbao, Spain
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17
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Abstract
Inspired by the uniqueness and ubiquity of thioesters in nature, much attention has been paid to thioester functionalized materials, yielding applications ranging from responsive polymers to bioconjugates and (bio)degradable polymers.
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Affiliation(s)
- Suzan Aksakal
- Polymer Chemistry Laboratories
- School of Engineering and Materials Science
- Queen Mary University of London
- London
- UK
| | - Resat Aksakal
- Polymer Chemistry Laboratories
- School of Engineering and Materials Science
- Queen Mary University of London
- London
- UK
| | - C. Remzi Becer
- Polymer Chemistry Laboratories
- School of Engineering and Materials Science
- Queen Mary University of London
- London
- UK
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18
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Jiang YY, Liu TT, Sun X, Xu ZY, Fan X, Zhu L, Bi S. Computational study of the mechanism of amide bond formation via CS2-releasing 1,3-acyl transfer. Org Biomol Chem 2018; 16:5808-5815. [DOI: 10.1039/c8ob01338a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A systematic computational study on CS2-releasing 1,3-acyl transfer was performed for the first time and provided deeper mechanistic insights.
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Affiliation(s)
- Yuan-Ye Jiang
- School of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu 273165
- People's Republic of China
| | - Tian-Tian Liu
- School of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu 273165
- People's Republic of China
| | - Xue Sun
- School of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu 273165
- People's Republic of China
| | - Zhong-Yan Xu
- School of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu 273165
- People's Republic of China
| | - Xia Fan
- School of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu 273165
- People's Republic of China
| | - Ling Zhu
- School of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu 273165
- People's Republic of China
| | - Siwei Bi
- School of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu 273165
- People's Republic of China
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19
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Kent S. Chemical protein synthesis: Inventing synthetic methods to decipher how proteins work. Bioorg Med Chem 2017; 25:4926-4937. [DOI: 10.1016/j.bmc.2017.06.020] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 06/07/2017] [Accepted: 06/13/2017] [Indexed: 12/15/2022]
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20
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Jiang YY, Zhu L, Man X, Liang Y, Bi S. Mechanism of trifluoroacetic-acid-promoted N-to-S acyl transfer of enamides. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.05.099] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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21
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Aromatic thiol-mediated cleavage of N-O bonds enables chemical ubiquitylation of folded proteins. Nat Commun 2016; 7:12979. [PMID: 27680493 PMCID: PMC5056422 DOI: 10.1038/ncomms12979] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 08/22/2016] [Indexed: 01/01/2023] Open
Abstract
Access to protein substrates homogenously modified by ubiquitin (Ub) is critical for biophysical and biochemical investigations aimed at deconvoluting the myriad biological roles for Ub. Current chemical strategies for protein ubiquitylation, however, employ temporary ligation auxiliaries that are removed under harsh denaturing conditions and have limited applicability. We report an unprecedented aromatic thiol-mediated N–O bond cleavage and its application towards native chemical ubiquitylation with the ligation auxiliary 2-aminooxyethanethiol. Our interrogation of the reaction mechanism suggests a disulfide radical anion as the active species capable of cleaving the N–O bond. The successful semisynthesis of full-length histone H2B modified by the small ubiquitin-like modifier-3 (SUMO-3) protein further demonstrates the generalizability and compatibility of our strategy with folded proteins. Chemical approaches to site-specifically ubiquitylate a target protein allow investigation of the biochemical effects of this modification, but they often destabilize the protein. Here, the authors report on a synthetic conjugation strategy that leads to protein ubiquitylation in non-denaturing conditions.
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Abstract
The present review offers an overview of nonclassical (e.g., with no pre- or in situ activation of a carboxylic acid partner) approaches for the construction of amide bonds. The review aims to comprehensively discuss relevant work, which was mainly done in the field in the last 20 years. Organization of the data follows a subdivision according to substrate classes: catalytic direct formation of amides from carboxylic and amines ( section 2 ); the use of carboxylic acid surrogates ( section 3 ); and the use of amine surrogates ( section 4 ). The ligation strategies (NCL, Staudinger, KAHA, KATs, etc.) that could involve both carboxylic acid and amine surrogates are treated separately in section 5 .
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Affiliation(s)
- Renata Marcia de Figueiredo
- Institut Charles Gerhardt de Montpellier (ICGM), UMR 5253-CNRS-UM-ENSCM, Ecole Nationale Supérieure de Chimie , 8 rue de l'Ecole Normale, 34296 Montpellier Cedex 5, France
| | - Jean-Simon Suppo
- Institut Charles Gerhardt de Montpellier (ICGM), UMR 5253-CNRS-UM-ENSCM, Ecole Nationale Supérieure de Chimie , 8 rue de l'Ecole Normale, 34296 Montpellier Cedex 5, France
| | - Jean-Marc Campagne
- Institut Charles Gerhardt de Montpellier (ICGM), UMR 5253-CNRS-UM-ENSCM, Ecole Nationale Supérieure de Chimie , 8 rue de l'Ecole Normale, 34296 Montpellier Cedex 5, France
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23
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Ali Shah MI, Xu ZY, Liu L, Jiang YY, Shi J. Mechanism for the enhanced reactivity of 4-mercaptoprolyl thioesters in native chemical ligation. RSC Adv 2016. [DOI: 10.1039/c6ra13793h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Ring-strain-precluded strategy benefiting from entropy effects and n → π* orbital interaction, enhances the reactivity of C-terminal prolyl thioesters in NCL.
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Affiliation(s)
| | - Zhe-Yuan Xu
- Collaborative Innovation Center of Chemistry for Energy Materials
- CAS Key Laboratory of Urban Pollutant Conversion
- Department of Chemistry
- University of Science and Technology of China
- Hefei 230026
| | - Lei Liu
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- China
| | - Yuan-Ye Jiang
- Collaborative Innovation Center of Chemistry for Energy Materials
- CAS Key Laboratory of Urban Pollutant Conversion
- Department of Chemistry
- University of Science and Technology of China
- Hefei 230026
| | - Jing Shi
- Collaborative Innovation Center of Chemistry for Energy Materials
- CAS Key Laboratory of Urban Pollutant Conversion
- Department of Chemistry
- University of Science and Technology of China
- Hefei 230026
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Sun XH, Yu HZ, Pei SQ, Dang ZM. Theoretical investigations on the thiol–thioester exchange steps of different thioesters. CHINESE CHEM LETT 2015. [DOI: 10.1016/j.cclet.2015.07.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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25
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Tian Y, Wang L, Shi J, Yu HZ. Desulfurization Mechanism of Cysteine in Synthesis of Polypeptides. CHINESE J CHEM PHYS 2015. [DOI: 10.1063/1674-0068/28/cjcp1501009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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26
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Panda SS, Jones RA, Hall CD, Katritzky AR. Applications of Chemical Ligation in Peptide Synthesis via Acyl Transfer. Top Curr Chem (Cham) 2015; 362:229-65. [PMID: 25805142 DOI: 10.1007/128_2014_608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
The utility of native chemical ligation (NCL) in the solution or solid phase synthesis of peptides, cyclic peptides, glycopeptides, and neoglycoconjugates is reviewed. In addition, the mechanistic details of inter- or intra-molecular NCLs are discussed from experimental and computational points of view.
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Affiliation(s)
- Siva S Panda
- Department of Chemistry, Center for Heterocyclic Compounds, University of Florida, Gainesville, FL, 32611-7200, USA,
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27
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Stuhr-Hansen N, Bork N, Strømgaard K. Mechanistic insight into benzenethiol catalyzed amide bond formations from thioesters and primary amines. Org Biomol Chem 2014; 12:5745-51. [DOI: 10.1039/c4ob00073k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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Panda SS, Oliferenko AA, Marwani HM, Katritzky AR. Effects of preorganization and hydrogen bonding on intramolecular chemical ligation of (N)-and (O)-acyl isopeptides. MENDELEEV COMMUNICATIONS 2014. [DOI: 10.1016/j.mencom.2014.03.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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29
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Yu H, Wang C, Yang Y, Dang ZM. Mechanistic Study on Rh-Catalyzed Stereoselective CC/CH Activation oftert-Cyclobutanols. Chemistry 2014; 20:3839-48. [DOI: 10.1002/chem.201303249] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2013] [Revised: 11/30/2013] [Indexed: 12/23/2022]
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30
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Verzele D, Madder A. Patchwork protein chemistry: a practitioner's treatise on the advances in synthetic peptide stitchery. Chembiochem 2014; 14:1032-48. [PMID: 23775826 DOI: 10.1002/cbic.201200775] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Indexed: 12/22/2022]
Abstract
With the study of peptides and proteins at the heart of many scientific endeavors, the omics era heralded a multitude of opportunities for chemists and biologists alike. Across the interface with life sciences, peptide chemistry plays an indispensable role, and progress made over the past decades now allows proteins to be treated as molecular patchworks stitched together through synthetic tailoring. The continuous elaboration of sophisticated strategies notwithstanding, Merrifield's solid-phase methodology remains a cornerstone of chemical protein design. Although the non-practitioner might misjudge peptide synthesis as trivial, routine, or dull given its long history, we comment here on its many advances, obstacles, and prospects from a practitioner's point of view. While sharing our perspectives through thematic highlights across the literature, this treatise provides an interpretive overview as a guide to novices, and a recap for specialists.
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Affiliation(s)
- Dieter Verzele
- Organic and Biomimetic Chemistry Research Group, Department of Organic Chemistry, Faculty of Sciences, Ghent University, Krijgslaan 281 (S4), 9000 Ghent, Belgium.
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31
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Yu H, Lu Q, Dang Z, Fu Y. Mechanistic Study of the Rhodium-Catalyzed [3+2+2] Carbocyclization of Alkenylidenecyclopropanes with Alkynes. Chem Asian J 2013; 8:2262-73. [DOI: 10.1002/asia.201300575] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Indexed: 01/06/2023]
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32
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Monbaliu JCM, Dive G, Stevens CV, Katritzky AR. Governing Parameters of Long-Range Intramolecular S-to-N Acyl Transfers within (S)-Acyl Isopeptides. J Chem Theory Comput 2013; 9:927-34. [DOI: 10.1021/ct300830k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Jean-Christophe M. Monbaliu
- Center for Heterocyclic Compounds,
Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
- Department of Sustainable Organic
Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, B-9000 Ghent, Belgium
| | - Georges Dive
- Center of Protein Engineering,
Institut de Chimie, University of Liège, Bâtiment B.6, B-4000 Sart Tilman, Liège, Belgium
| | - Christian V. Stevens
- Department of Sustainable Organic
Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, B-9000 Ghent, Belgium
| | - Alan R. Katritzky
- Center for Heterocyclic Compounds,
Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
- Chemistry Department, King Abdulaziz University, Jeddah, 21589 Saudi Arabia
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33
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Moyal T, Hemantha HP, Siman P, Refua M, Brik A. Highly efficient one-pot ligation and desulfurization. Chem Sci 2013. [DOI: 10.1039/c3sc50239b] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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34
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Wang C, Yu HZ, Fu Y, Guo QX. Mechanism of arylboronic acid-catalyzed amidation reaction between carboxylic acids and amines. Org Biomol Chem 2013; 11:2140-6. [DOI: 10.1039/c3ob27367a] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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35
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36
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Monbaliu JCM, Katritzky AR. Recent trends in Cys- and Ser/Thr-based synthetic strategies for the elaboration of peptide constructs. Chem Commun (Camb) 2012; 48:11601-22. [DOI: 10.1039/c2cc34434c] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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37
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Thomas GL, Hsieh YSY, Chun CKY, Cai ZL, Reimers JR, Payne RJ. Peptide ligations accelerated by N-terminal aspartate and glutamate residues. Org Lett 2011; 13:4770-3. [PMID: 21830797 DOI: 10.1021/ol2017356] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A novel application of intramolecular base catalysis confers enhanced reaction rates for aminolysis ligations between peptide thioesters and peptides bearing N-terminal aspartate or glutamate residues. The broad scope of this process and its application in the total synthesis of the diabetes drug exenatide is demonstrated.
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Affiliation(s)
- Gemma L Thomas
- School of Chemistry, The University of Sydney, NSW 2006, Australia
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