1
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Novacek A, Ugaz B, Stephanopoulos N. Templating Peptide Chemistry with Nucleic Acids: Toward Artificial Ribosomes, Cell-Specific Therapeutics, and Novel Protein-Mimetic Architectures. Biomacromolecules 2024; 25:3865-3876. [PMID: 38860980 DOI: 10.1021/acs.biomac.4c00372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
In biology, nanomachines like the ribosome use nucleic acid templates to synthesize polymers in a sequence-specific, programmable fashion. Researchers have long been interested in using the programmable properties of nucleic acids to enhance chemical reactions via colocalization of reagents using complementary nucleic acid handles. In this review, we describe progress in using nucleic acid templates, handles, or splints to enhance the covalent coupling of peptides to other peptides or oligonucleotides. We discuss work in several areas: creating ribosome-mimetic systems, synthesizing bioactive peptides on DNA or RNA templates, linking peptides into longer molecules and bioactive antibody mimics, and scaffolding peptides to build protein-mimetic architectures. We close by highlighting the challenges that must be overcome in nucleic acid-templated peptide chemistry in two areas: making full-length, functional proteins from synthetic peptides and creating novel protein-mimetic architectures not possible through macromolecular folding alone.
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Affiliation(s)
- Alexandra Novacek
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85251, United States
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe Arizona 85251, United States
| | - Bryan Ugaz
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85251, United States
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe Arizona 85251, United States
| | - Nicholas Stephanopoulos
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85251, United States
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe Arizona 85251, United States
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2
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Barat A, Powner MW. Spontaneous Peptide Ligation Mediated by Cysteamine. JACS AU 2024; 4:1752-1757. [PMID: 38818061 PMCID: PMC11134366 DOI: 10.1021/jacsau.4c00243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 06/01/2024]
Abstract
The fundamental and universal nature of life's exploitation of peptides suggests they must have played a vital role during the onset of life, but their spontaneous chemoselective synthesis in water remains unknown. Aminonitriles (1) are widely accepted as prebiotic precursors of both amino acids and peptides, but they do not spontaneously polymerize in water to yield peptides. Here, we demonstrate that the simple prebiotically plausible aminothiol, cysteamine (5), participates in Strecker chemistry to furnish β-mercaptoethyl-α-aminonitriles (8) and β-mercaptoethyl-amino acids (16), which are predisposed to spontaneously form peptides in water. Intramolecular thiol catalyzed ligation is faster, higher-yielding, and more α-selective than previously reported prebiotic peptide ligation chemistries, enabling, for example, the highly regioselective α-ligation of Asp- and Glu-dinitriles in quantitative yields. Our findings suggest that cysteamine (5), the thiol bearing moiety of the universal thiol cofactor coenzyme A, may have played an important role in the selective chemical synthesis of prebiotic α-peptides.
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Affiliation(s)
- Abid Barat
- Department
of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Matthew W. Powner
- Department
of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
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3
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Jia X, Hao GL, Feng M, Jiang H, Wang SG, Huang L. Rh(III)-Catalyzed Diastereo- and Enantioselective Regiodivergent (Hetero)Arylamidation of (Homo)Allylic Sulfides. J Am Chem Soc 2024; 146:9768-9778. [PMID: 38545837 DOI: 10.1021/jacs.3c14041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
A rhodium-catalyzed 3-component conjunctive diastereo- and regioselective arylamidation of (homo)allylic sulfides, organon boronic acids, and dioxazolones is reported. These reactions deliver the 1,2-insertion and 2,1-insertion arylamidation products, respectively, for allylic sulfides and homoallylic sulfides. The enantioselective arylamidation of terminal and internal allylic sulfides is achieved, furnishing various 1,3-N,S compounds featuring one or two contiguous stereocenters in high yields and with high diastereo- and enantioselectivities. Mechanistic studies suggest a change in the turnover-limiting and selectivity-determining steps induced by the native and easily removable sulfide group.
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Affiliation(s)
- Xiaoyan Jia
- State Key Laboratory of Pulp and Paper Engineering and Key Laboratory of Functional Molecular Engineering of Guangdong Province in School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, P. R. China
| | - Gui-Lin Hao
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, P. R. China
| | - Mengxia Feng
- State Key Laboratory of Pulp and Paper Engineering and Key Laboratory of Functional Molecular Engineering of Guangdong Province in School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, P. R. China
| | - Huanfeng Jiang
- State Key Laboratory of Pulp and Paper Engineering and Key Laboratory of Functional Molecular Engineering of Guangdong Province in School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, P. R. China
| | - Shou-Guo Wang
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, P. R. China
| | - Liangbin Huang
- State Key Laboratory of Pulp and Paper Engineering and Key Laboratory of Functional Molecular Engineering of Guangdong Province in School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, P. R. China
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4
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Schrems M, Kravchuk AV, Niederacher G, Exler F, Bello C, Becker CFW. Light-Cleavable Auxiliary for Diselenide-Selenoester Ligations of Peptides and Proteins. Chemistry 2023; 29:e202301253. [PMID: 37265454 PMCID: PMC10946927 DOI: 10.1002/chem.202301253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/24/2023] [Accepted: 06/02/2023] [Indexed: 06/03/2023]
Abstract
Diselenide-selenoester ligations are increasingly used for the synthesis of proteins. Excellent ligation rates, even at low concentrations, in combination with mild and selective deselenization conditions can overcome some of the most severe challenges in chemical protein synthesis. Herein, the versatile multicomponent synthesis and application of a new ligation auxiliary that combines a photocleavable scaffold with the advantages of selenium-based ligation strategies are presented. Its use was investigated with respect to different ligation junctions and describe a novel para-methoxybenzyl deprotection reaction for the selenol moiety. The glycine-based auxiliary enabled successful synthesis of the challenging target protein G-CSF.
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Affiliation(s)
- Maximilian Schrems
- Institute of Biological ChemistryFaculty of ChemistryUniversity of ViennaWähringer Str. 381090ViennaAustria
- Vienna Doctoral School in Chemistry (DoSChem)University of ViennaWähringer Str. 421090ViennaAustria
| | - Alexander V. Kravchuk
- Institute of Biological ChemistryFaculty of ChemistryUniversity of ViennaWähringer Str. 381090ViennaAustria
| | - Gerhard Niederacher
- Institute of Biological ChemistryFaculty of ChemistryUniversity of ViennaWähringer Str. 381090ViennaAustria
| | - Florian Exler
- Institute of Biological ChemistryFaculty of ChemistryUniversity of ViennaWähringer Str. 381090ViennaAustria
| | - Claudia Bello
- Interdepartmental Research Unit of Peptide and Protein Chemistry and BiologyDepartment of Chemistry “Ugo Schiff”University of Florencevia della Lastruccia 1350019Sesto FiorentinoItaly
| | - Christian F. W. Becker
- Institute of Biological ChemistryFaculty of ChemistryUniversity of ViennaWähringer Str. 381090ViennaAustria
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5
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Trunschke S, Piemontese E, Fuchs O, Abboud S, Seitz O. Enhancing Auxiliary-Mediated Native Chemical Ligation at Challenging Junctions with Pyridine Scaffolds. Chemistry 2022; 28:e202202065. [PMID: 36097325 PMCID: PMC10091703 DOI: 10.1002/chem.202202065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Indexed: 12/13/2022]
Abstract
To expand the scope of native chemical ligation (NCL) beyond reactions at cysteine, ligation auxiliaries are appended to the peptide N-terminus. After the introduction of a pyridine-containing auxiliary, which provided access to challenging junctions (proline or β-branched amino acids), we herein probe the role of the pyridine-ring nitrogen. We observed side reactions leading to preliminary auxiliary loss. We describe a new easy to attach β-mercapto-β-(4-methoxy-2-pyridinyl)-ethyl (MMPyE) auxiliary, which 1) has increased stability; 2) enables NCL at sterically encumbered junctions (e. g., Leu-Val); and 3) allows removal under mildly basic (pH 8.5) conditions was introduced. The synthesis of a 120 aa long peptide containing eight MUC5AC tandem repeats via ligation of two 60mers demonstrates the usefulness. Making use of hitherto unexplored NCL to tyrosine, the MMPyE auxiliary provided access to a head-to-tail-cyclized 21-mer peptide and a His6 -tagged hexaphosphorylated peptide comprising 6 heptapeptide repeats of the RNA polymerase II C-terminal domain.
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Affiliation(s)
- Sebastian Trunschke
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| | - Emanuele Piemontese
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| | - Olaf Fuchs
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| | - Skander Abboud
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| | - Oliver Seitz
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
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6
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Bilbrough T, Piemontese E, Seitz O. Dissecting the role of protein phosphorylation: a chemical biology toolbox. Chem Soc Rev 2022; 51:5691-5730. [PMID: 35726784 DOI: 10.1039/d1cs00991e] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Protein phosphorylation is a crucial regulator of protein and cellular function, yet, despite identifying an enormous number of phosphorylation sites, the role of most is still unclear. Each phosphoform, the particular combination of phosphorylations, of a protein has distinct and diverse biological consequences. Aberrant phosphorylation is implicated in the development of many diseases. To investigate their function, access to defined protein phosphoforms is essential. Materials obtained from cells often are complex mixtures. Recombinant methods can provide access to defined phosphoforms if site-specifically acting kinases are known, but the methods fail to provide homogenous material when several amino acid side chains compete for phosphorylation. Chemical and chemoenzymatic synthesis has provided an invaluable toolbox to enable access to previously unreachable phosphoforms of proteins. In this review, we selected important tools that enable access to homogeneously phosphorylated protein and discuss examples that demonstrate how they can be applied. Firstly, we discuss the synthesis of phosphopeptides and proteins through chemical and enzymatic means and their advantages and limitations. Secondly, we showcase illustrative examples that applied these tools to answer biological questions pertaining to proteins involved in signal transduction, control of transcription, neurodegenerative diseases and aggregation, apoptosis and autophagy, and transmembrane proteins. We discuss the opportunities and challenges in the field.
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Affiliation(s)
- Tim Bilbrough
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany.
| | - Emanuele Piemontese
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 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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Lamb C, Shi J, Wilden JD, Macmillan D. Novel electrochemically-mediated peptide dethiylation in processes relevant to native chemical ligation. Org Biomol Chem 2022; 20:7343-7350. [DOI: 10.1039/d2ob01499h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here we explore electrochemical dethiylation in processes relevant to Native Chemical Ligation (NCL). NCL’s reliance on the redox active amino acid cysteine and β-mercaptoamine derivatives suggests a potential role for...
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8
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Houska R, Stutz MB, Seitz O. Expanding the scope of native chemical ligation - templated small molecule drug synthesis via benzanilide formation. Chem Sci 2021; 12:13450-13457. [PMID: 34777764 PMCID: PMC8528049 DOI: 10.1039/d1sc00513h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 09/10/2021] [Indexed: 12/15/2022] Open
Abstract
We describe a reaction system that enables the synthesis of Bcr–Abl tyrosine kinase inhibitors (TKI) via benzanilide formation in water. The reaction is based on native chemical ligation (NCL). In contrast to previous applications, we used the NCL chemistry to establish aromatic rather than aliphatic amide bonds in coupling reactions between benzoyl and o-mercaptoaniline fragments. The method was applied for the synthesis of thiolated ponatinib and GZD824 derivatives. Acid treatment provided benzothiazole structures, which opens opportunities for diversification. Thiolation affected the affinity for Abl1 kinase only moderately. Of note, a ponatinib-derived benzothiazole also showed nanomolar affinity. NCL-enabled benzanilide formation may prove useful for fragment-based drug discovery. To show that benzanilide synthesis can be put under the control of a template, we connected the benzoyl and o-mercaptoaniline fragments to DNA and peptide nucleic acid (PNA) oligomers. Complementary RNA templates enabled adjacent binding of reactive conjugates triggering a rapid benzoyl transfer from a thioester-linked DNA conjugate to an o-mercaptoaniline-DNA or -PNA conjugate. We evaluated the influence of linker length and unpaired spacer nucleotides within the RNA template on the product yield. The data suggest that nucleic acid-templated benzanilide formation could find application in the establishment of DNA-encoded combinatorial libraries (DEL). The templated native chemical ligation between benzoyl thioesters and o-mercaptoaniline fragments proceeds in water and provides benzanilides that have nanomolar affinity for Abl1 kinase.![]()
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Affiliation(s)
- Richard Houska
- Department of Chemistry, Humboldt-Universität zu Berlin Brook-Taylor-Strasse 2 12489 Berlin Germany
| | - Marvin Björn Stutz
- Department of Chemistry, Humboldt-Universität zu Berlin Brook-Taylor-Strasse 2 12489 Berlin Germany
| | - Oliver Seitz
- Department of Chemistry, Humboldt-Universität zu Berlin Brook-Taylor-Strasse 2 12489 Berlin Germany
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9
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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: 19] [Impact Index Per Article: 6.3] [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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10
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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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11
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Abboud SA, Aucagne V. An optimized protocol for the synthesis of N-2-hydroxybenzyl-cysteine peptide crypto-thioesters. Org Biomol Chem 2020; 18:8199-8208. [PMID: 33034311 DOI: 10.1039/d0ob01737j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We herein report a robust upgraded synthetic protocol for the synthesis of N-Hnb-Cys crypto-thioester peptides, useful building blocks for segment-based chemical protein synthesis through native chemical ligation. We recently observed the formation of an isomeric co-product when using a different solid support than the originally-reported one, thus hampering the general applicability of the methodology. We undertook a systematic study to characterize this compound and identify the parameters favouring its formation. We show here that epimerization from l- to d-cysteine occurred during the key solid-supported reductive amination step. We also observed the formation of imidazolidinones by-products arising from incomplete reduction of the imine. Structural characterization combined with the deciphering of underlying reaction mechanisms allowed us to optimize conditions that abolished the formation of all these side-products.
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Affiliation(s)
- Skander A Abboud
- Centre de Biophysique Moléculaire, CNRS UPR 4301, Rue Charles Sadron, 45071, Orléans cedex 2, France.
| | - Vincent Aucagne
- Centre de Biophysique Moléculaire, CNRS UPR 4301, Rue Charles Sadron, 45071, Orléans cedex 2, France.
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12
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Nakatsu K, Hayashi G, Okamoto A. Toolbox for chemically synthesized histone proteins. Curr Opin Chem Biol 2020; 58:10-19. [DOI: 10.1016/j.cbpa.2020.04.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/13/2020] [Accepted: 04/16/2020] [Indexed: 01/28/2023]
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13
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14
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Enhancing native chemical ligation for challenging chemical protein syntheses. Curr Opin Chem Biol 2020; 58:37-44. [PMID: 32745915 DOI: 10.1016/j.cbpa.2020.04.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/01/2020] [Accepted: 04/01/2020] [Indexed: 02/01/2023]
Abstract
Native chemical ligation has enabled the chemical synthesis of proteins for a wide variety of applications (e.g., mirror-image proteins). However, inefficiencies of this chemoselective ligation in the context of large or otherwise challenging protein targets can limit the practical scope of chemical protein synthesis. In this review, we focus on recent developments aimed at enhancing and expanding native chemical ligation for challenging protein syntheses. Chemical auxiliaries, use of selenium chemistry, and templating all enable ligations at otherwise suboptimal junctions. The continuing development of these tools is making the chemical synthesis of large proteins increasingly accessible.
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15
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Mueller LK, Baumruck AC, Zhdanova H, Tietze AA. Challenges and Perspectives in Chemical Synthesis of Highly Hydrophobic Peptides. Front Bioeng Biotechnol 2020; 8:162. [PMID: 32195241 PMCID: PMC7064641 DOI: 10.3389/fbioe.2020.00162] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/18/2020] [Indexed: 12/31/2022] Open
Abstract
Solid phase peptide synthesis (SPPS) provides the possibility to chemically synthesize peptides and proteins. Applying the method on hydrophilic structures is usually without major drawbacks but faces extreme complications when it comes to "difficult sequences." These includes the vitally important, ubiquitously present and structurally demanding membrane proteins and their functional parts, such as ion channels, G-protein receptors, and other pore-forming structures. Standard synthetic and ligation protocols are not enough for a successful synthesis of these challenging sequences. In this review we highlight, summarize and evaluate the possibilities for synthetic production of "difficult sequences" by SPPS, native chemical ligation (NCL) and follow-up protocols.
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Affiliation(s)
- Lena K. Mueller
- Clemens-Schöpf Institute of Organic Chemistry and Biochemistry, Darmstadt University of Technology, Darmstadt, Germany
| | - Andreas C. Baumruck
- Clemens-Schöpf Institute of Organic Chemistry and Biochemistry, Darmstadt University of Technology, Darmstadt, Germany
| | - Hanna Zhdanova
- Department of Chemistry and Molecular Biology, Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Alesia A. Tietze
- Department of Chemistry and Molecular Biology, Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
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16
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Chu GC, Hua X, Zuo C, Chen CC, Meng XB, Zhang Z, Fu Y, Shi J, Li YM. Efficient Semi-Synthesis of Atypical Ubiquitin Chains and Ubiquitin-Based Probes Forged by Thioether Isopeptide Bonds. Chemistry 2019; 25:16668-16675. [PMID: 31625216 DOI: 10.1002/chem.201904010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/16/2019] [Indexed: 01/24/2023]
Abstract
The development of powerful and general methods to acquire ubiquitin (Ub) chains has prompted the deciphering of Ub-mediated processes. Herein, the cysteine-aminoethylation assisted chemical ubiquitination (CAACU) strategy is extended and improved to enable the efficient semi-synthesis of atypical Ub chain analogues and Ub-based probes. Combining the Cys aminoethylation and the auxiliary-mediated protein ligation, several linkage- and length-defined atypical Ub chains including di-Ubs, K27C-linked tri-Ub, K11/K48C-branched tri-Ub, and even the SUMOlated Ub are successfully prepared from recombinantly expressed starting materials at about a 9-20 mg L-1 expression level. In addition, the utility of this strategy is demonstrated with the synthesis of a novel non-hydrolyzable di-Ub PA probe, which may provide a new useful tool for the mechanistic studies of deubiquitinase (DUB) recognition.
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Affiliation(s)
- Guo-Chao Chu
- Department of Chemistry, University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Xiao Hua
- Department of Chemistry, University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Chong Zuo
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for, Major Diseases of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui, 230009, P. R. China
| | - Chen-Chen Chen
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for, Major Diseases of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui, 230009, P. R. China
| | - Xian-Bin Meng
- National Protein Science Technology Center, Tsinghua University, Beijing, 100084, P. R. China
| | - Zhongping Zhang
- Institute of Intelligent Machines, Chinese Academy of Sciences, Hefei, Anhui, 230031, P. R. China
| | - Yao Fu
- Department of Chemistry, University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Jing Shi
- Department of Chemistry, University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Yi-Ming Li
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for, Major Diseases of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui, 230009, P. R. China
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17
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LU D, Yin H, Wang S, Tang F, Huang W, Wang P. Chemical Synthesis of the Homogeneous Granulocyte-Macrophage Colony-Stimulating Factor Through Se-Auxiliary-Mediated Ligation. J Org Chem 2019; 85:1652-1660. [DOI: 10.1021/acs.joc.9b02232] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Dan LU
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Hongli Yin
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Siyao Wang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Feng Tang
- CAS Key Laboratory of Receptor Research, CAS Center for Excellence in Molecular Cell Science, Center for Biotherapeutics Discovery Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Wei Huang
- CAS Key Laboratory of Receptor Research, CAS Center for Excellence in Molecular Cell Science, Center for Biotherapeutics Discovery Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Ping Wang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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18
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Seitz O. Templated chemistry for bioorganic synthesis and chemical biology. J Pept Sci 2019; 25:e3198. [PMID: 31309674 PMCID: PMC6771651 DOI: 10.1002/psc.3198] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 05/27/2019] [Accepted: 05/27/2019] [Indexed: 12/24/2022]
Abstract
In light of the 2018 Max Bergmann Medal, this review discusses advancements on chemical biology-driven templated chemistry developed in the author's laboratories. The focused review introduces the template categories applied to orient functional units such as functional groups, chromophores, biomolecules, or ligands in space. Unimolecular templates applied in protein synthesis facilitate fragment coupling of unprotected peptides. Templating via bimolecular assemblies provides control over proximity relationships between functional units of two molecules. As an instructive example, the coiled coil peptide-templated labelling of receptor proteins on live cells will be shown. Termolecular assemblies provide the opportunity to put the proximity of functional units on two (bio)molecules under the control of a third party molecule. This allows the design of conditional bimolecular reactions. A notable example is DNA/RNA-triggered peptide synthesis. The last section shows how termolecular and multimolecular assemblies can be used to better characterize and understand multivalent protein-ligand interactions.
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Affiliation(s)
- Oliver Seitz
- Department of ChemistryHumboldt University BerlinBerlinGermany
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19
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Yin H, Lu D, Wang S, Wang P. Development of Powerful Auxiliary-Mediated Ligation To Facilitate Rapid Protein Assembly. Org Lett 2019; 21:5138-5142. [PMID: 31247759 DOI: 10.1021/acs.orglett.9b01737] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Here, we describe an Se-auxiliary mediated ligation protocol capable of rapid native chemical ligations at sterically hindered junctions, followed by in situ auxiliary cleavage under neutral conditions without affecting unprotected Cys residues. This auxiliary, which is prepared from phenyl acetaldehyde in one step, can be conveniently attached to the N-terminal region of a peptide via a reductive amination or coupling reaction. We demonstrated this methodology by synthesizing two protein samples.
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Affiliation(s)
- Hongli Yin
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , P.R. China
| | - Dan Lu
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , P.R. China
| | - Siyao Wang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , P.R. China
| | - Ping Wang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , P.R. China
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20
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Chu GC, Pan M, Li J, Liu S, Zuo C, Tong ZB, Bai JS, Gong Q, Ai H, Fan J, Meng X, Huang YC, Shi J, Deng H, Tian C, Li YM, Liu L. Cysteine-Aminoethylation-Assisted Chemical Ubiquitination of Recombinant Histones. J Am Chem Soc 2019; 141:3654-3663. [PMID: 30758956 DOI: 10.1021/jacs.8b13213] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Histone ubiquitination affects the structure and function of nucleosomes through tightly regulated dynamic reversible processes. The efficient preparation of ubiquitinated histones and their analogs is important for biochemical and biophysical studies on histone ubiquitination. Here, we report the CAACU (cysteine-aminoethylation assisted chemical ubiquitination) strategy for the efficient synthesis of ubiquitinated histone analogs. The key step in the CAACU strategy is the installation of an N-alkylated 2-bromoethylamine derivative into a recombinant histone through cysteine aminoethylation, followed by native chemical ligation assisted by Seitz's auxiliary to produce mono- and diubiquitin (Ub) and small ubiquitin-like modifier (SUMO) modified histone analogs. This approach enables the rapid production of modified histones from recombinant proteins at about 1.5-6 mg/L expression. The thioether-containing isopeptide bonds in the products are chemically stable and bear only one atomic substitution in the structure, compared to their native counterparts. The ubiquitinated histone analogs prepared by CAACU can be readily reconstituted into nucleosomes and selectively recognized by relevant interacting proteins. The thioether-containing isopeptide bonds can also be recognized and hydrolyzed by deubiquitinases (DUBs). Cryo-electron microscopy (cryo-EM) of the nucleosome containing H2BKC34Ub indicated that the obtained CAACU histones were of good quality for structural studies. Collectively, this work exemplifies the utility of the CAACU strategy for the simple and efficient production of homogeneous ubiquitinated and SUMOylated histones for biochemical and biophysical studies.
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Affiliation(s)
- Guo-Chao Chu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry , Tsinghua University , Beijing 100084 , China.,School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes , Hefei University of Technology , Hefei 230009 , China
| | - Man Pan
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry , Tsinghua University , Beijing 100084 , China
| | | | | | - Chong Zuo
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry , Tsinghua University , Beijing 100084 , China.,School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes , Hefei University of Technology , Hefei 230009 , China
| | - Ze-Bin Tong
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry , Tsinghua University , Beijing 100084 , China.,School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes , Hefei University of Technology , Hefei 230009 , China
| | - Jing-Si Bai
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes , Hefei University of Technology , Hefei 230009 , China
| | | | - Huasong Ai
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry , Tsinghua University , Beijing 100084 , China
| | | | - Xianbin Meng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences , Tsinghua University , Beijing 100084 , China
| | - Yi-Chao Huang
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry , Tsinghua University , Beijing 100084 , China
| | | | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences , Tsinghua University , Beijing 100084 , China
| | | | - Yi-Ming Li
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes , Hefei University of Technology , Hefei 230009 , China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry , Tsinghua University , Beijing 100084 , China
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21
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Recent advances in the chemical synthesis and semi-synthesis of poly-ubiquitin-based proteins and probes. Sci China Chem 2019. [DOI: 10.1007/s11426-018-9401-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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22
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Kent SBH. Novel protein science enabled by total chemical synthesis. Protein Sci 2018; 28:313-328. [PMID: 30345579 DOI: 10.1002/pro.3533] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 10/12/2018] [Accepted: 10/15/2018] [Indexed: 01/01/2023]
Abstract
Chemical synthesis is a well-established method for the preparation in the research laboratory of multiple-tens-of-milligram amounts of correctly folded, high purity protein molecules. Chemically synthesized proteins enable a broad spectrum of novel protein science. Racemic mixtures consisting of d-protein and l-protein enantiomers facilitate crystallization and determination of protein structures by X-ray diffraction. d-Proteins enable the systematic development of unnatural mirror image protein molecules that bind with high affinity to natural protein targets. The d-protein form of a therapeutic target can also be used to screen natural product libraries to identify novel small molecule leads for drug development. Proteins with novel polypeptide chain topologies including branched, circular, linear-loop, and interpenetrating polypeptide chains can be constructed by chemical synthesis. Medicinal chemistry can be applied to optimize the properties of therapeutic protein molecules. Chemical synthesis has been used to redesign glycoproteins and for the a priori design and construction of covalently constrained novel protein scaffolds not found in nature. Versatile and precise labeling of protein molecules by chemical synthesis facilitates effective application of advanced physical methods including multidimensional nuclear magnetic resonance and time-resolved FTIR for the elucidation of protein structure-activity relationships. The chemistries used for total synthesis of proteins have been adapted to making artificial molecular devices and protein-inspired nanomolecular constructs. Research to develop mirror image life in the laboratory is in its very earliest stages, based on the total chemical synthesis of d-protein forms of polymerase enzymes.
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Affiliation(s)
- Stephen B H Kent
- Department of Chemistry and Department of Biochemistry and Molecular Biology; Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois, 60637
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