151
|
Al Temimi AHK, van der Wekken-de Bruijne R, Proietti G, Guo H, Qian P, Mecinović J. γ-Thialysine versus Lysine: An Insight into the Epigenetic Methylation of Histones. Bioconjug Chem 2019; 30:1798-1804. [DOI: 10.1021/acs.bioconjchem.9b00313] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Abbas H. K. Al Temimi
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | | | - Giordano Proietti
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Hong Guo
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Ping Qian
- Chemistry and Material Science Faculty, Shandong Agricultural University, Tai’an 271018, P.R. China
| | - Jasmin Mecinović
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| |
Collapse
|
152
|
Petracca R, Bowen KA, McSweeney L, O'Flaherty S, Genna V, Twamley B, Devocelle M, Scanlan EM. Chemoselective Synthesis of N-Terminal Cysteinyl Thioesters via β,γ-C,S Thiol-Michael Addition. Org Lett 2019; 21:3281-3285. [PMID: 31017793 DOI: 10.1021/acs.orglett.9b01013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dehydroalanine (ΔAla) is a highly electrophilic residue that can react efficiently with sulfur nucleophiles to furnish cysteinyl analogues. Herein, we report an efficient synthesis of N-terminal cysteinyl thioesters, suitable for S, N-acyl transfer, based on β,γ-C,S thiol-Michael addition. Both ionic and radical-based methodologies were found to be efficient for this process.
Collapse
Affiliation(s)
- Rita Petracca
- School of Chemistry and Trinity Biomedical Sciences Institute (TBSI) , Trinity College Dublin, The University of Dublin , Dublin 2 , Ireland
| | - Katherine A Bowen
- School of Chemistry and Trinity Biomedical Sciences Institute (TBSI) , Trinity College Dublin, The University of Dublin , Dublin 2 , Ireland
| | - Lauren McSweeney
- School of Chemistry and Trinity Biomedical Sciences Institute (TBSI) , Trinity College Dublin, The University of Dublin , Dublin 2 , Ireland
| | - Siobhan O'Flaherty
- Department of Chemistry , Royal College of Surgeons in Ireland (RCSI) , Dublin , Ireland
| | - Vito Genna
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology , Joint IRB-BSC Program in Computational Biology, Baldiri-Reixac 10-12 , 08028 Barcelona , Spain
| | - Brendan Twamley
- School of Chemistry and Trinity Biomedical Sciences Institute (TBSI) , Trinity College Dublin, The University of Dublin , Dublin 2 , Ireland
| | - Marc Devocelle
- Department of Chemistry , Royal College of Surgeons in Ireland (RCSI) , Dublin , Ireland
| | - Eoin M Scanlan
- School of Chemistry and Trinity Biomedical Sciences Institute (TBSI) , Trinity College Dublin, The University of Dublin , Dublin 2 , Ireland
| |
Collapse
|
153
|
Yang B, Wang N, Schnier PD, Zheng F, Zhu H, Polizzi NF, Ittuveetil A, Saikam V, DeGrado WF, Wang Q, Wang PG, Wang L. Genetically Introducing Biochemically Reactive Amino Acids Dehydroalanine and Dehydrobutyrine in Proteins. J Am Chem Soc 2019; 141:7698-7703. [PMID: 31038942 DOI: 10.1021/jacs.9b02611] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Expansion of the genetic code with unnatural amino acids (Uaas) has significantly increased the chemical space available to proteins for exploitation. Due to the inherent limitation of translational machinery and the required compatibility with biological settings, function groups introduced via Uaas to date are restricted to chemically inert, bioorthogonal, or latent bioreactive groups. To break this barrier, here we report a new strategy enabling the specific incorporation of biochemically reactive amino acids into proteins. A latent bioreactive amino acid is genetically encoded at a position proximal to the target natural amino acid; they react via proximity-enabled reactivity, selectively converting the latter into a reactive residue in situ. Using this Genetically Encoded Chemical COnversion (GECCO) strategy and harnessing the sulfur-fluoride exchange (SuFEx) reaction between fluorosulfate-l-tyrosine and serine or threonine, we site-specifically generated the reactive dehydroalanine and dehydrobutyrine into proteins. GECCO works both inter- and intramolecularly, and is compatible with various proteins. We further labeled the resultant dehydroalanine-containing protein with thiol-saccharide to generate glycoprotein mimetics. GECCO represents a new solution for selectively introducing biochemically reactive amino acids into proteins and is expected to open new avenues for exploiting chemistry in live systems for biological research and engineering.
Collapse
Affiliation(s)
| | | | | | - Feng Zheng
- Hangzhou Research Institute of Technical Institute of Physics and Chemistry, Chinese Academy of Sciences , Hangzhou 310018 , China
| | - He Zhu
- Department of Chemistry and Center for Therapeutics and Diagnostics , Georgia State University , Atlanta , Georgia 30302 , United States
| | | | - Avinash Ittuveetil
- Department of Chemistry and Center for Therapeutics and Diagnostics , Georgia State University , Atlanta , Georgia 30302 , United States
| | - Varma Saikam
- Department of Chemistry and Center for Therapeutics and Diagnostics , Georgia State University , Atlanta , Georgia 30302 , United States
| | | | - Qian Wang
- Hangzhou Research Institute of Technical Institute of Physics and Chemistry, Chinese Academy of Sciences , Hangzhou 310018 , China
| | - Peng G Wang
- Department of Chemistry and Center for Therapeutics and Diagnostics , Georgia State University , Atlanta , Georgia 30302 , United States
| | | |
Collapse
|
154
|
Musselman CA, Kutateladze TG. Strategies for Generating Modified Nucleosomes: Applications within Structural Biology Studies. ACS Chem Biol 2019; 14:579-586. [PMID: 30817115 DOI: 10.1021/acschembio.8b01049] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Post-translational modifications on histone proteins play critical roles in the regulation of chromatin structure and all DNA-templated processes. Accumulating evidence suggests that these covalent modifications can directly alter chromatin structure, or they can modulate activities of chromatin-modifying and -remodeling factors. Studying these modifications in the context of the nucleosome, the basic subunit of chromatin, is thus of great interest; however, the generation of specifically modified nucleosomes remains challenging. This is especially problematic for most structural biology approaches in which a large amount of material is often needed. Here we discuss the strategies currently available for generation of these substrates. We in particular focus on novel ideas and discuss challenges in the application to structural biology studies.
Collapse
Affiliation(s)
- Catherine A. Musselman
- Department of Biochemistry, University of Iowa Carver College of Medicine, Iowa City, Iowa 52246, United States
| | - Tatiana G. Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, United States
| |
Collapse
|
155
|
Bogart JW, Bowers AA. Dehydroamino acids: chemical multi-tools for late-stage diversification. Org Biomol Chem 2019; 17:3653-3669. [PMID: 30849157 PMCID: PMC6637761 DOI: 10.1039/c8ob03155j] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
α,β-Dehydroamino acids (dhAAs) are noncanonical amino acids that are found in a wide array of natural products and can be easily installed into peptides and proteins. dhAAs exhibit remarkable synthetic flexibility, readily undergoing a number of reactions, such as polar and single-electron additions, transition metal catalyzed cross-couplings, and cycloadditions. Because of the relatively mild conditions required for many of these reactions, dhAAs are increasingly being used as orthogonal chemical handles for late-stage modification of biomolecules. Still, only a fraction of the chemical reactivity of dhAAs has been exploited in such biorthogonal applications. Herein, we provide an overview of the broad spectrum of chemical reactivity of dhAAs, with special emphasis on recent efforts to adapt such transformations for biomolecules such as natural products, peptides, and proteins. We also discuss examples of enzymes from natural product biosynthetic pathways that have been found to catalyze many similar reactions; these enzymes provide mild, regio- and stereoselective, biocatalytic alternatives for future development. We anticipate that the continued investigation of the innate reactivity of dhAAs will furnish a diverse portfolio dhAA-based chemistries for use in chemical biology and drug discovery.
Collapse
Affiliation(s)
- Jonathan W Bogart
- Division of Chemical Biology and Medicinal Chemistry Eshelman School of Pharmacy, and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
| | | |
Collapse
|
156
|
Voreakos K, Devel L, Georgiadis D. Late-Stage Diversification of Phosphinic Dehydroalanine Pseudopeptides Based on a Giese-Type Radical C-Alkylation Strategy. Org Lett 2019; 21:4397-4401. [PMID: 30933530 DOI: 10.1021/acs.orglett.9b00857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A straightforward, late-stage diversification strategy for the installation of side chains on readily accessible unsaturated phosphinopeptidic scaffolds based on a Giese-type addition of alkyl radicals has been investigated. Among different alternatives, the preferred methodology is operationally simple as it can be carried out in an open flask with no need for protection of acidic moieties. Direct application to the synthesis of SPPS-compatible building blocks or to longer peptides is also reported.
Collapse
Affiliation(s)
- Kostas Voreakos
- Department of Chemistry, Laboratory of Organic Chemistry , National and Kapodistrian University of Athens , Panepistimiopolis, Zografou , 15771 Athens , Greece
| | - Laurent Devel
- CEA, Institut des Sciences du Vivant Frédéric Joliot, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO) , Université Paris-Saclay , Gif-sur-Yvette 91190 , France
| | - Dimitris Georgiadis
- Department of Chemistry, Laboratory of Organic Chemistry , National and Kapodistrian University of Athens , Panepistimiopolis, Zografou , 15771 Athens , Greece
| |
Collapse
|
157
|
Ertl J, Ortiz‐Soto ME, Le TA, Bechold J, Shan J, Teßmar J, Engels B, Seibel J. Tuning the Product Spectrum of a Glycoside Hydrolase Enzyme by a Combination of Site‐Directed Mutagenesis and Tyrosine‐Specific Chemical Modification. Chemistry 2019; 25:6533-6541. [DOI: 10.1002/chem.201900576] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 02/22/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Julia Ertl
- Institut für Organische ChemieUniversität Würzburg Am Hubland 97074 Würzburg Germany
| | | | - Thien Anh Le
- Institut für Physikalische und Theoretische ChemieUniversität Würzburg Emil-Fischer Strasse 42 97074 Würzburg Germany
| | - Julian Bechold
- Institut für Organische ChemieUniversität Würzburg Am Hubland 97074 Würzburg Germany
| | - Junwen Shan
- Abteilung für Funktionswerkstoffe der Medizin und der ZahnheilkundeUniversitätsklinikum Würzburg Pleicherwall 2 97070 Würzburg Germany
| | - Jörg Teßmar
- Abteilung für Funktionswerkstoffe der Medizin und der ZahnheilkundeUniversitätsklinikum Würzburg Pleicherwall 2 97070 Würzburg Germany
| | - Bernd Engels
- Institut für Physikalische und Theoretische ChemieUniversität Würzburg Emil-Fischer Strasse 42 97074 Würzburg Germany
| | - Jürgen Seibel
- Institut für Organische ChemieUniversität Würzburg Am Hubland 97074 Würzburg Germany
| |
Collapse
|
158
|
Shin JA, Kim J, Lee H, Ha S, Lee HY. Cu(OTf)2-Promoted 1,4-Addition of Alkyl Bromides to Dehydroalanine. J Org Chem 2019; 84:4558-4565. [DOI: 10.1021/acs.joc.9b00369] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Jung-Ah Shin
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
- The Fourth R&D Institute-6, Agency for Defense Development, Daejeon 34186, Korea
| | - Jiheon Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Hongsoo Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Sura Ha
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Hee-Yoon Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| |
Collapse
|
159
|
Discovery of a pathway for terminal-alkyne amino acid biosynthesis. Nature 2019; 567:420-424. [DOI: 10.1038/s41586-019-1020-y] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 02/06/2019] [Indexed: 11/08/2022]
|
160
|
|
161
|
Pan M, Zheng Q, Ding S, Zhang L, Qu Q, Wang T, Hong D, Ren Y, Liang L, Chen C, Mei Z, Liu L. Chemical Protein Synthesis Enabled Mechanistic Studies on the Molecular Recognition of K27‐linked Ubiquitin Chains. Angew Chem Int Ed Engl 2019; 58:2627-2631. [DOI: 10.1002/anie.201810814] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 11/20/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Man Pan
- Tsinghua-Peking Center for Life SciencesMOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyCenter for Synthetic and Systems BiologyDepartment of ChemistryTsinghua University Beijing 100084 China
- State Key Laboratory of Chemical OncogenomicsKey Laboratory of Chemical Biologythe Graduate School at ShenzenTsinghua University Shenzen Guangdong 518055 China
| | - Qingyun Zheng
- Tsinghua-Peking Center for Life SciencesMOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyCenter for Synthetic and Systems BiologyDepartment of ChemistryTsinghua University Beijing 100084 China
| | - Shan Ding
- Biotechnology Research InstituteChinese Academy of Agricultural Science Beijing 100081 China
| | - Lujia Zhang
- Beijing Advanced Innovation Center for Structural BiologySchool of Life SciencesTsinghua University Beijing 100084 China
| | - Qian Qu
- Tsinghua-Peking Center for Life SciencesMOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyCenter for Synthetic and Systems BiologyDepartment of ChemistryTsinghua University Beijing 100084 China
| | - Tian Wang
- Tsinghua-Peking Center for Life SciencesMOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyCenter for Synthetic and Systems BiologyDepartment of ChemistryTsinghua University Beijing 100084 China
| | - Danning Hong
- Biotechnology Research InstituteChinese Academy of Agricultural Science Beijing 100081 China
| | - Yujing Ren
- Biotechnology Research InstituteChinese Academy of Agricultural Science Beijing 100081 China
| | - Lujun Liang
- Tsinghua-Peking Center for Life SciencesMOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyCenter for Synthetic and Systems BiologyDepartment of ChemistryTsinghua University Beijing 100084 China
| | - Chunlai Chen
- Beijing Advanced Innovation Center for Structural BiologySchool of Life SciencesTsinghua University Beijing 100084 China
| | - Ziqing Mei
- Biotechnology Research InstituteChinese Academy of Agricultural Science Beijing 100081 China
| | - Lei Liu
- Tsinghua-Peking Center for Life SciencesMOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyCenter for Synthetic and Systems BiologyDepartment of ChemistryTsinghua University Beijing 100084 China
- State Key Laboratory of Chemical OncogenomicsKey Laboratory of Chemical Biologythe Graduate School at ShenzenTsinghua University Shenzen Guangdong 518055 China
| |
Collapse
|
162
|
Pieters BJGE, Hintzen JCJ, Grobben Y, Al Temimi AHK, Kamps JJAG, Mecinović J. Installation of Trimethyllysine Analogs on Intact Histones via Cysteine Alkylation. Bioconjug Chem 2019; 30:952-958. [DOI: 10.1021/acs.bioconjchem.9b00065] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bas J. G. E. Pieters
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Jordi C. J. Hintzen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Yvonne Grobben
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Abbas H. K. Al Temimi
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Jos J. A. G. Kamps
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Jasmin Mecinović
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| |
Collapse
|
163
|
Pan M, Zheng Q, Ding S, Zhang L, Qu Q, Wang T, Hong D, Ren Y, Liang L, Chen C, Mei Z, Liu L. Chemical Protein Synthesis Enabled Mechanistic Studies on the Molecular Recognition of K27‐linked Ubiquitin Chains. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201810814] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Man Pan
- Tsinghua-Peking Center for Life SciencesMOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyCenter for Synthetic and Systems BiologyDepartment of ChemistryTsinghua University Beijing 100084 China
- State Key Laboratory of Chemical OncogenomicsKey Laboratory of Chemical Biologythe Graduate School at ShenzenTsinghua University Shenzen Guangdong 518055 China
| | - Qingyun Zheng
- Tsinghua-Peking Center for Life SciencesMOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyCenter for Synthetic and Systems BiologyDepartment of ChemistryTsinghua University Beijing 100084 China
| | - Shan Ding
- Biotechnology Research InstituteChinese Academy of Agricultural Science Beijing 100081 China
| | - Lujia Zhang
- Beijing Advanced Innovation Center for Structural BiologySchool of Life SciencesTsinghua University Beijing 100084 China
| | - Qian Qu
- Tsinghua-Peking Center for Life SciencesMOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyCenter for Synthetic and Systems BiologyDepartment of ChemistryTsinghua University Beijing 100084 China
| | - Tian Wang
- Tsinghua-Peking Center for Life SciencesMOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyCenter for Synthetic and Systems BiologyDepartment of ChemistryTsinghua University Beijing 100084 China
| | - Danning Hong
- Biotechnology Research InstituteChinese Academy of Agricultural Science Beijing 100081 China
| | - Yujing Ren
- Biotechnology Research InstituteChinese Academy of Agricultural Science Beijing 100081 China
| | - Lujun Liang
- Tsinghua-Peking Center for Life SciencesMOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyCenter for Synthetic and Systems BiologyDepartment of ChemistryTsinghua University Beijing 100084 China
| | - Chunlai Chen
- Beijing Advanced Innovation Center for Structural BiologySchool of Life SciencesTsinghua University Beijing 100084 China
| | - Ziqing Mei
- Biotechnology Research InstituteChinese Academy of Agricultural Science Beijing 100081 China
| | - Lei Liu
- Tsinghua-Peking Center for Life SciencesMOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyCenter for Synthetic and Systems BiologyDepartment of ChemistryTsinghua University Beijing 100084 China
- State Key Laboratory of Chemical OncogenomicsKey Laboratory of Chemical Biologythe Graduate School at ShenzenTsinghua University Shenzen Guangdong 518055 China
| |
Collapse
|
164
|
Sim J, Campbell MW, Molander GA. Synthesis of α-Fluoro-α-Amino Acid Derivatives via Photoredox-Catalyzed Carbofluorination. ACS Catal 2019; 9:1558-1563. [PMID: 31588366 DOI: 10.1021/acscatal.8b04284] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A mild, metal-free, regioselective carbofluorination of dehydroalanine derivatives has been developed. Alkyl radicals resulting from visible-light photoredox catalysis engage in a radical conjugate addition to dehydroalanine, with subsequent fluorination of the newly generated radical to afford an α-fluoro-α-amino acid. By using a highly oxidizing organic photocatalyst, this process incorporates non-stabilized primary, secondary, and tertiary alkyl radicals derived from commercially available alkyltrifluoroborates to furnish a wide range of fluorinated unnatural amino acids.
Collapse
Affiliation(s)
- Jaehoon Sim
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Mark W. Campbell
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Gary A. Molander
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| |
Collapse
|
165
|
Dinitroimidazoles as bifunctional bioconjugation reagents for protein functionalization and peptide macrocyclization. Nat Commun 2019; 10:142. [PMID: 30635561 PMCID: PMC6329768 DOI: 10.1038/s41467-018-08010-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 12/07/2018] [Indexed: 11/20/2022] Open
Abstract
Efficient and site-specific chemical modification of proteins under physiological conditions remains a challenge. Here we report that 1,4-dinitroimidazoles are highly efficient bifunctional bioconjugation reagents for protein functionalization and peptide macrocyclization. Under acidic to neutral aqueous conditions, 1,4-dinitroimidazoles react specifically with cysteines via a cine-substitution mechanism, providing rapid, stable and chemoselective protein bioconjugation. On the other hand, although unreactive towards amine groups under neutral aqueous conditions, 1,4-dinitroimidazoles react with lysines in organic solvents in the presence of base through a ring-opening & ring-close mechanism. The resulting cysteine- and lysine-(4-nitroimidazole) linkages exhibit stability superior to that of commonly employed maleimide-thiol conjugates. We demonstrate that 1,4-dinitroimidazoles can be applied in site-specific protein bioconjugation with functionalities such as fluorophores and bioactive peptides. Furthermore, a bisfunctional 1,4-dinitroimidazole derivative provides facile access to peptide macrocycles by crosslinking a pair of cysteine or lysine residues, including bicyclic peptides of complex architectures through highly controlled consecutive peptide macrocyclization. The selective formation of protein bioconjugates under physiological conditions is a challenging task. Here, the authors report that 1,4-dinitroimidazoles are reagents of choice for protein bioconjugation at either cysteine or lysine sites within short times and provide facile access to peptide macrocycles.
Collapse
|
166
|
Affiliation(s)
- Seiji SAKAMOTO
- Graduate School of Engineering, Department of Synthetic Chemistry and Biological Chemistry, Kyoto University
| | - Itaru HAMACHI
- Graduate School of Engineering, Department of Synthetic Chemistry and Biological Chemistry, Kyoto University
- ERATO Innovative Molecular Technology for Neuroscience Project, Japan Science and Technology Agency (JST)
| |
Collapse
|
167
|
Maaskant RV, Roelfes G. Bioorthogonal Metalloporphyrin-Catalyzed Selective Methionine Alkylation in the Lanthipeptide Nisin. Chembiochem 2019; 20:57-61. [PMID: 30246492 PMCID: PMC6680192 DOI: 10.1002/cbic.201800493] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Indexed: 12/30/2022]
Abstract
Bioorthogonal catalytic modification of ribosomally synthesized and post-translationally modified peptides (RiPPs) is a promising approach to obtaining novel antimicrobial peptides with improved properties and/or activities. Here, we present the serendipitous discovery of a selective and rapid method for the alkylation of methionines in the lanthipeptide nisin. Using carbenes, formed from water-soluble metalloporphyrins and diazoacetates, methionines are alkylated to obtain sulfonium ions. The formed sulfonium ions are stable, but can be further reacted to obtain functionalized methionine analogues, expanding the toolbox of chemical posttranslational modification even further.
Collapse
Affiliation(s)
- Ruben V. Maaskant
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Gerard Roelfes
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| |
Collapse
|
168
|
Perez-Rizquez C, Abian O, Palomo JM. Site-selective modification of tryptophan and protein tryptophan residues through PdNP bionanohybrid-catalysed C–H activation in aqueous media. Chem Commun (Camb) 2019; 55:12928-12931. [DOI: 10.1039/c9cc06971b] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
PdNP bionanohybrid catalyzed selective C–H bond arylation of tryptophan residues in proteins in aqueous media at room temperature.
Collapse
Affiliation(s)
| | - Olga Abian
- Instituto Aragonés de Ciencias de la Salud (IACS)
- Zaragoza
- Spain
- Institute of Biocomputation and Physics of Complex Systems (BIFI)
- Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI
| | - Jose M. Palomo
- Department of Biocatalysis
- Institute of Catalysis (ICP-CSIC)
- 28049 Madrid
- Spain
| |
Collapse
|
169
|
Tamura T, Hamachi I. Chemistry for Covalent Modification of Endogenous/Native Proteins: From Test Tubes to Complex Biological Systems. J Am Chem Soc 2018; 141:2782-2799. [DOI: 10.1021/jacs.8b11747] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Tomonori Tamura
- Graduate School of Engineering, Department of Synthetic Chemistry and Biological Chemistry, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Graduate School of Engineering, Department of Synthetic Chemistry and Biological Chemistry, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- ERATO, Japan Science and Technology Agency (JST), 5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| |
Collapse
|
170
|
Allan C, Kosar M, Burr CV, Mackay CL, Duncan RR, Hulme AN. A Catch-and-Release Approach to Selective Modification of Accessible Tyrosine Residues. Chembiochem 2018; 19:2443-2447. [PMID: 30212615 DOI: 10.1002/cbic.201800532] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Indexed: 01/25/2023]
Abstract
The tyrosine side chain is amphiphilic leading to significant variations in the surface exposure of tyrosine residues in the folded structure of a native sequence protein. This variability can be exploited to give residue-selective functionalization of a protein substrate by using a highly reactive diazonium group tethered to an agarose-based resin. This novel catch-and-release approach to protein modification has been demonstrated for proteins with accessible tyrosine residues, which are compared with a control group of proteins in which there are no accessible tyrosine residues. MS analysis of the modified proteins showed that functionalization was highly selective, but reactivity was further attenuated by the electrostatic environment of any individual residue. Automated screening of PDB structures allows identification of potential candidates for selective modification by comparison with the accessibility of the tyrosine residue in a benchmark peptide (GYG).
Collapse
Affiliation(s)
- Christopher Allan
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - Miroslav Kosar
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - Christina V Burr
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - C Logan Mackay
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - Rory R Duncan
- Institute of Biological Chemistry, Biophysics and Bioengineering, David Brewster Building, Heriot-Watt University, Edinburgh, EH14 4AS, UK
| | - Alison N Hulme
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, UK
| |
Collapse
|
171
|
Bartoccini F, Mari M, Retini M, Bartolucci S, Piersanti G. Organocatalytic Aza-Friedel-Crafts/Lactonization Domino Reaction of Naphthols and Phenols with 2-Acetamidoacrylate to Naphtho- and Benzofuranones Bearing a Quaternary Center at the C3 Position. J Org Chem 2018; 83:12275-12283. [PMID: 30191715 DOI: 10.1021/acs.joc.8b01774] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
N-Acetyl ketimine generated from methyl 2-acetamidoacrylate was explored to develop an unprecedented domino aza-Friedel-Crafts/lactonization reaction with naphthols and phenols (including 5-hydroxyindoles). This novel method requires a catalyst loading of only 5 mol % of a phosphoric acid catalyst and provides a new series of 3-NHAc-naphtho- and benzofuranone derivatives bearing tetra-substituted stereogenic centers in moderate-to-good yields. The enantioselective variant using BINOL-derived phosphoric acids was also explored with 1-naphthol, providing the desired product with moderate enantioselectivities (up to 99:1 following recrystallization).
Collapse
Affiliation(s)
- Francesca Bartoccini
- Department of Biomolecular Sciences , University of Urbino "Carlo Bo" , P.zza Rinascimento 6 , 61029 Urbino , PU , Italy
| | - Michele Mari
- Department of Biomolecular Sciences , University of Urbino "Carlo Bo" , P.zza Rinascimento 6 , 61029 Urbino , PU , Italy
| | - Michele Retini
- Department of Biomolecular Sciences , University of Urbino "Carlo Bo" , P.zza Rinascimento 6 , 61029 Urbino , PU , Italy
| | - Silvia Bartolucci
- Department of Biomolecular Sciences , University of Urbino "Carlo Bo" , P.zza Rinascimento 6 , 61029 Urbino , PU , Italy
| | - Giovanni Piersanti
- Department of Biomolecular Sciences , University of Urbino "Carlo Bo" , P.zza Rinascimento 6 , 61029 Urbino , PU , Italy
| |
Collapse
|
172
|
Bertoldo JB, Terenzi H, Hüttelmaier S, Bernardes GJL. Posttranslational Chemical Mutagenesis: To Reveal the Role of Noncatalytic Cysteine Residues in Pathogenic Bacterial Phosphatases. Biochemistry 2018; 57:6144-6152. [DOI: 10.1021/acs.biochem.8b00639] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jean B. Bertoldo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
- Institut für Molekulare Medizin, Medizinische Fakultät, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Stra 3a, 06108 Halle, Germany
| | - Hernán Terenzi
- Centro de Biologia Molecular Estrutural, Departamento de Bioquímica, Universidade Federal de Santa Catarina, 88040-970 Florianópolis, SC, Brazil
| | - Stefan Hüttelmaier
- Institut für Molekulare Medizin, Medizinische Fakultät, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Stra 3a, 06108 Halle, Germany
| | - Gonçalo J. L. Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| |
Collapse
|
173
|
Taylor MT, Nelson JE, Suero MG, Gaunt MJ. A protein functionalization platform based on selective reactions at methionine residues. Nature 2018; 562:563-568. [PMID: 30323287 PMCID: PMC6203954 DOI: 10.1038/s41586-018-0608-y] [Citation(s) in RCA: 167] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 08/21/2018] [Indexed: 11/12/2022]
Abstract
Nature has a remarkable ability to carry out site-selective post-translational modification of proteins, therefore enabling a marked increase in their functional diversity1. Inspired by this, chemical tools have been developed for the synthetic manipulation of protein structure and function, and have become essential to the continued advancement of chemical biology, molecular biology and medicine. However, the number of chemical transformations that are suitable for effective protein functionalization is limited, because the stringent demands inherent to biological systems preclude the applicability of many potential processes2. These chemical transformations often need to be selective at a single site on a protein, proceed with very fast reaction rates, operate under biologically ambient conditions and should provide homogeneous products with near-perfect conversion2-7. Although many bioconjugation methods exist at cysteine, lysine and tyrosine, a method targeting a less-explored amino acid would considerably expand the protein functionalization toolbox. Here we report the development of a multifaceted approach to protein functionalization based on chemoselective labelling at methionine residues. By exploiting the electrophilic reactivity of a bespoke hypervalent iodine reagent, the S-Me group in the side chain of methionine can be targeted. The bioconjugation reaction is fast, selective, operates at low-micromolar concentrations and is complementary to existing bioconjugation strategies. Moreover, it produces a protein conjugate that is itself a high-energy intermediate with reactive properties and can serve as a platform for the development of secondary, visible-light-mediated bioorthogonal protein functionalization processes. The merger of these approaches provides a versatile platform for the development of distinct transformations that deliver information-rich protein conjugates directly from the native biomacromolecules.
Collapse
Affiliation(s)
| | | | - Marcos G Suero
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Matthew J Gaunt
- Department of Chemistry, University of Cambridge, Cambridge, UK.
| |
Collapse
|
174
|
Post-translational site-selective protein backbone α-deuteration. Nat Chem Biol 2018; 14:955-963. [DOI: 10.1038/s41589-018-0128-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 07/19/2018] [Indexed: 01/29/2023]
|
175
|
Khan RKM, Zhao Y, Scully TD, Buchwald SL. Catalytic Arylhydroxylation of Dehydroalanine in Continuous Flow for Simple Access to Unnatural Amino Acids. Chemistry 2018; 24:15215-15218. [DOI: 10.1002/chem.201804094] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Indexed: 11/09/2022]
Affiliation(s)
- R. Kashif M. Khan
- Department of ChemistryMassachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
| | - Yang Zhao
- Department of ChemistryMassachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
| | - Tal D. Scully
- Department of ChemistryMassachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
| | - Stephen L. Buchwald
- Department of ChemistryMassachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
| |
Collapse
|
176
|
Aycock RA, Pratt CJ, Jui NT. Aminoalkyl Radicals as Powerful Intermediates for the Synthesis of Unnatural Amino Acids and Peptides. ACS Catal 2018. [DOI: 10.1021/acscatal.8b03031] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- R. Adam Aycock
- Department of Chemistry and Winship Cancer Institute, Emory University, Atlanta, Georgia 30322, United States
| | - Cameron J. Pratt
- Department of Chemistry and Winship Cancer Institute, Emory University, Atlanta, Georgia 30322, United States
| | - Nathan T. Jui
- Department of Chemistry and Winship Cancer Institute, Emory University, Atlanta, Georgia 30322, United States
| |
Collapse
|
177
|
Abstract
The conjugation of biomolecules can impart materials with the bioactivity necessary to modulate specific cell behaviors. While the biological roles of particular polypeptide, oligonucleotide, and glycan structures have been extensively reviewed, along with the influence of attachment on material structure and function, the key role played by the conjugation strategy in determining activity is often overlooked. In this review, we focus on the chemistry of biomolecule conjugation and provide a comprehensive overview of the key strategies for achieving controlled biomaterial functionalization. No universal method exists to provide optimal attachment, and here we will discuss both the relative advantages and disadvantages of each technique. In doing so, we highlight the importance of carefully considering the impact and suitability of a particular technique during biomaterial design.
Collapse
Affiliation(s)
- Christopher D. Spicer
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles Väg 2, Stockholm, Sweden
| | - E. Thomas Pashuck
- NJ
Centre for Biomaterials, Rutgers University, 145 Bevier Road, Piscataway, New Jersey United States
| | - Molly M. Stevens
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles Väg 2, Stockholm, Sweden
- Department
of Materials, Department of Bioengineering, and Institute of Biomedical Engineering, Imperial College London, Exhibition Road, London, United Kingdom
| |
Collapse
|
178
|
De Leon CA, Lang G, Saavedra MI, Pratt MR. Simple and Efficient Preparation of O- and S-GlcNAcylated Amino Acids through InBr 3-Catalyzed Synthesis of β- N-Acetylglycosides from Commercially Available Reagents. Org Lett 2018; 20:5032-5035. [PMID: 30088936 DOI: 10.1021/acs.orglett.8b02182] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The facile synthesis of serine, threonine, and cysteine β-glycosides using commercially available peracetylated β- N-acetylglucosamine (β-Ac4GlcNAc) and catalytic amounts of indium bromide (InBr3) is described. This method involves only inexpensive reagents that require no further modification or special handling. The reagents are simply mixed, dissolved, and refluxed to afford the GlcNAcylated amino acids in great yields (70-80%). This operationally simple procedure should facilitate the study of O-GlcNAcylation without necessitating expertise in synthetic carbohydrate chemistry.
Collapse
|
179
|
Jbara M, Laps S, Morgan M, Kamnesky G, Mann G, Wolberger C, Brik A. Palladium prompted on-demand cysteine chemistry for the synthesis of challenging and uniquely modified proteins. Nat Commun 2018; 9:3154. [PMID: 30089783 PMCID: PMC6082840 DOI: 10.1038/s41467-018-05628-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 07/16/2018] [Indexed: 01/12/2023] Open
Abstract
Organic chemistry allows for the modification and chemical preparation of protein analogues for various studies. The thiolate side chain of the Cys residue has been a key functionality in these ventures. In order to generate complex molecular targets, there is a particular need to incorporate orthogonal protecting groups of the thiolated amino acids to control the directionality of synthesis and modification site. Here, we demonstrate the tuning of palladium chemoselectivity in aqueous medium for on-demand deprotection of several Cys-protecting groups that are useful in protein synthesis and modification. These tools allow the preparation of highly complex analogues as we demonstrate in the synthesis of the copper storage protein and selectively modified peptides with multiple Cys residues. We also report the synthesis of an activity-based probe comprising ubiquitinated histone H2A and its incorporation into nucleosomes and demonstrate its reactivity with deubiquitinating enzyme to generate a covalent nucleosome-enzyme complex.
Collapse
Affiliation(s)
- Muhammad Jbara
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200008, Israel
| | - Shay Laps
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200008, Israel
| | - Michael Morgan
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD, 21205-2185, USA
| | - Guy Kamnesky
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200008, Israel
| | - Guy Mann
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200008, Israel
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD, 21205-2185, USA
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200008, Israel.
| |
Collapse
|
180
|
de Bruijn AD, Roelfes G. Chemical Modification of Dehydrated Amino Acids in Natural Antimicrobial Peptides by Photoredox Catalysis. Chemistry 2018; 24:11314-11318. [PMID: 29939448 PMCID: PMC6099298 DOI: 10.1002/chem.201803144] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Indexed: 12/29/2022]
Abstract
Dehydroalanine (Dha) and dehydrobutyrine (Dhb) are remarkably versatile non-canonical amino acids often found in antimicrobial peptides. This work presents the selective modification of Dha and Dhb in antimicrobial peptides through photocatalytic activation of organoborates under the influence of visible light. Ir(dF(CF3 )ppy)2 (dtbbpy)PF6 was used as a photoredox catalyst in aqueous solutions for the modification of thiostrepton and nisin. The mild conditions and high selectivity for the dehydrated residues show that photoredox catalysis is a promising tool for the modification of peptide-derived natural products.
Collapse
Affiliation(s)
- A. Dowine de Bruijn
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Gerard Roelfes
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| |
Collapse
|
181
|
Nadal S, Raj R, Mohammed S, Davis BG. Synthetic post-translational modification of histones. Curr Opin Chem Biol 2018; 45:35-47. [DOI: 10.1016/j.cbpa.2018.02.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 01/17/2018] [Accepted: 02/10/2018] [Indexed: 12/14/2022]
|
182
|
Tajima K, Katoh T, Suga H. Genetic code expansion via integration of redundant amino acid assignment by finely tuning tRNA pools. Curr Opin Chem Biol 2018; 46:212-218. [PMID: 30072241 DOI: 10.1016/j.cbpa.2018.07.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 05/23/2018] [Accepted: 07/13/2018] [Indexed: 10/28/2022]
Abstract
In all translation systems, the genetic code assigns codons to amino acids as building blocks of polypeptides, defining their chemical, structural and physiological properties. The canonical genetic code, however, utilizes only 20 proteinogenic amino acids redundantly encoded in 61 codons. In order to expand the building block repertoire, this redundancy was reduced by tuning composition of the transfer RNA (tRNA) mixture in vitro. Depletion of particular tRNAs from the total tRNA mixture or its reconstitution with in vitro-transcribed tRNASNNs (S = C or G, N = U, C, A or G) divided a codon box to encode two amino acids, expanding the repertoire to 23. The expanded genetic codes may benefit analysis of cellular regulatory pathways and drug screening.
Collapse
Affiliation(s)
- Kenya Tajima
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayuki Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| |
Collapse
|
183
|
de Bruijn AD, Roelfes G. Catalytic Modification of Dehydroalanine in Peptides and Proteins by Palladium-Mediated Cross-Coupling. Chemistry 2018; 24:12728-12733. [PMID: 29923249 PMCID: PMC6146911 DOI: 10.1002/chem.201802846] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 06/18/2018] [Indexed: 11/16/2022]
Abstract
Dehydroalanine (Dha) is a remarkably versatile non‐canonical amino acid often found in antimicrobial peptides. Herein, we present the catalytic modification of Dha by a palladium‐mediated cross‐coupling reaction. By using Pd(EDTA)(OAc)2 as water‐soluble catalyst, a variety of arylboronic acids was coupled to the dehydrated residues in proteins and peptides, such as Nisin. The cross‐coupling reaction gave both the Heck product, in which the sp2‐hybridisation of the α‐carbon is retained, as well as the conjugated addition product. The reaction can be performed under mild aqueous conditions, which makes this method an attractive addition to the palette of bio‐orthogonal catalytic methods.
Collapse
Affiliation(s)
- A Dowine de Bruijn
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| |
Collapse
|
184
|
Chen H, Zhang Y, Li QQ, Zhao YF, Chen YX, Li YM. De Novo Design To Synthesize Lanthipeptides Involving Cascade Cysteine Reactions: SapB Synthesis as an Example. J Org Chem 2018; 83:7528-7533. [PMID: 29893565 DOI: 10.1021/acs.joc.8b00259] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Lanthipeptides are a family of ribosomally synthesized peptides that have crucial biological functions. However, due to their complicated structures, the total synthesis of lanthipeptides is challenging. Here, a novel strategy to construct lanthipeptides is described, which involves cascade reactions of cysteine, including Cys disalkylation elimination, Michael reaction, and native chemical ligation. We utilized this strategy to synthesize lanthipeptide SapB as an example. This methodology has the potential to obtain lanthipeptides and their analogues for biological research and drug discovery.
Collapse
Affiliation(s)
- Huai Chen
- Key Lab of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry , Tsinghua University , Beijing 100084 , P.R. China
| | - Yuan Zhang
- Key Lab of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry , Tsinghua University , Beijing 100084 , P.R. China
| | - Qian-Qian Li
- Key Lab of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry , Tsinghua University , Beijing 100084 , P.R. China
| | - Yu-Fen Zhao
- Key Lab of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry , Tsinghua University , Beijing 100084 , P.R. China
| | - Yong-Xiang Chen
- Key Lab of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry , Tsinghua University , Beijing 100084 , P.R. China
| | - Yan-Mei Li
- Key Lab of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry , Tsinghua University , Beijing 100084 , P.R. China.,Beijing Institute for Brain Disorders , Beijing 100069 , P.R. China
| |
Collapse
|
185
|
Site-selective installation of an electrophilic handle on proteins for bioconjugation. Bioorg Med Chem 2018; 26:3060-3064. [DOI: 10.1016/j.bmc.2018.02.028] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 02/14/2018] [Accepted: 02/16/2018] [Indexed: 02/02/2023]
|
186
|
Ortiz-Soto ME, Ertl J, Mut J, Adelmann J, Le TA, Shan J, Teßmar J, Schlosser A, Engels B, Seibel J. Product-oriented chemical surface modification of a levansucrase (SacB) via an ene-type reaction. Chem Sci 2018; 9:5312-5321. [PMID: 30009003 PMCID: PMC6009436 DOI: 10.1039/c8sc01244j] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 05/18/2018] [Indexed: 12/29/2022] Open
Abstract
Carbohydrate processing enzymes are sophisticated tools of living systems that have evolved to execute specific reactions on sugars. Here we present for the first time the site-selective chemical modification of exposed tyrosine residues in SacB, a levansucrase from Bacillus megaterium (Bm-LS) for enzyme engineering purposes via an ene-type reaction. Bm-LS is unable to sustain the synthesis of high molecular weight (HMW) levan (a fructose polymer) due to protein-oligosaccharide dissociation events occurring at an early stage during polymer elongation. We switched the catalyst from levan-like oligosaccharide synthesis to the efficient production of a HMW fructan polymer through the covalent addition of a flexible chemical side-chain that fluctuates over the central binding cavity of the enzyme preventing premature oligosaccharide disengagement.
Collapse
Affiliation(s)
- Maria Elena Ortiz-Soto
- Institut für Organische Chemie , Universität Würzburg , Am Hubland , 97074 Würzburg , Germany .
| | - Julia Ertl
- Institut für Organische Chemie , Universität Würzburg , Am Hubland , 97074 Würzburg , Germany .
| | - Jürgen Mut
- Institut für Organische Chemie , Universität Würzburg , Am Hubland , 97074 Würzburg , Germany .
| | - Juliane Adelmann
- Institut für Organische Chemie , Universität Würzburg , Am Hubland , 97074 Würzburg , Germany .
| | - Thien Anh Le
- Institut für Physikalische und Theoretische Chemie , Universität Würzburg , Emil-Fischer Strasse 42 , 97074 Würzburg , Germany
| | - Junwen Shan
- Abteilung für Funktionswerkstoffe der Medizin und der Zahnheilkunde , Universitätsklinikum Würzburg , Pleicherwall 2 , D-97070 Würzburg , Germany
| | - Jörg Teßmar
- Abteilung für Funktionswerkstoffe der Medizin und der Zahnheilkunde , Universitätsklinikum Würzburg , Pleicherwall 2 , D-97070 Würzburg , Germany
| | - Andreas Schlosser
- Rudolf-Virchow-Zentrum für Experimentelle Biomedizin , Universität Würzburg , Josef-Schneider Str. 2, Haus D15 , 97080 Würzburg , Germany
| | - Bernd Engels
- Institut für Physikalische und Theoretische Chemie , Universität Würzburg , Emil-Fischer Strasse 42 , 97074 Würzburg , Germany
| | - Jürgen Seibel
- Institut für Organische Chemie , Universität Würzburg , Am Hubland , 97074 Würzburg , Germany .
| |
Collapse
|
187
|
Kinetically guided radical-based synthesis of C(sp 3)-C(sp 3) linkages on DNA. Proc Natl Acad Sci U S A 2018; 115:E6404-E6410. [PMID: 29946037 DOI: 10.1073/pnas.1806900115] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
DNA-encoded libraries (DEL)-based discovery platforms have recently been widely adopted in the pharmaceutical industry, mainly due to their powerful diversity and incredible number of molecules. In the two decades since their disclosure, great strides have been made to expand the toolbox of reaction modes that are compatible with the idiosyncratic aqueous, dilute, and DNA-sensitive parameters of this system. However, construction of highly important C(sp3)-C(sp3) linkages on DNA through cross-coupling remains unexplored. In this article, we describe a systematic approach to translating standard organic reactions to a DEL setting through the tactical combination of kinetic analysis and empirical screening with information captured from data mining. To exemplify this model, implementation of the Giese addition to forge high value C-C bonds on DNA was studied, which represents a radical-based synthesis in DEL.
Collapse
|
188
|
Abstract
Protein lysine methylation is a distinct posttranslational modification that causes minimal changes in the size and electrostatic status of lysine residues. Lysine methylation plays essential roles in regulating fates and functions of target proteins in an epigenetic manner. As a result, substrates and degrees (free versus mono/di/tri) of protein lysine methylation are orchestrated within cells by balanced activities of protein lysine methyltransferases (PKMTs) and demethylases (KDMs). Their dysregulation is often associated with neurological disorders, developmental abnormalities, or cancer. Methyllysine-containing proteins can be recognized by downstream effector proteins, which contain methyllysine reader domains, to relay their biological functions. While numerous efforts have been made to annotate biological roles of protein lysine methylation, limited work has been done to uncover mechanisms associated with this modification at a molecular or atomic level. Given distinct biophysical and biochemical properties of methyllysine, this review will focus on chemical and biochemical aspects in addition, recognition, and removal of this posttranslational mark. Chemical and biophysical methods to profile PKMT substrates will be discussed along with classification of PKMT inhibitors for accurate perturbation of methyltransferase activities. Semisynthesis of methyllysine-containing proteins will also be covered given the critical need for these reagents to unambiguously define functional roles of protein lysine methylation.
Collapse
Affiliation(s)
- Minkui Luo
- Chemical Biology Program , Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States.,Program of Pharmacology, Weill Graduate School of Medical Science , Cornell University , New York , New York 10021 , United States
| |
Collapse
|
189
|
Spears RJ, Brabham RL, Budhadev D, Keenan T, McKenna S, Walton J, Brannigan JA, Brzozowski AM, Wilkinson AJ, Plevin M, Fascione MA. Site-selective C-C modification of proteins at neutral pH using organocatalyst-mediated cross aldol ligations. Chem Sci 2018; 9:5585-5593. [PMID: 30061990 PMCID: PMC6049525 DOI: 10.1039/c8sc01617h] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 05/31/2018] [Indexed: 12/30/2022] Open
Abstract
An organocatalyst-mediated protein aldol ligation (OPAL) affords C–C linked bioconjugates at neutral pH.
The bioconjugation of proteins with small molecules has proved an invaluable strategy for probing and perturbing biological mechanisms. The general use of chemical methods for protein functionalisation can be limited however by the requirement for complicated reaction partners to be present in large excess, and harsh conditions which are incompatible with many protein scaffolds. Herein we describe a site-selective organocatalyst-mediated protein aldol ligation (OPAL) that affords stable carbon–carbon linked bioconjugates at neutral pH. OPAL enables rapid modification of proteins using simple aldehyde probes in minimal excess, and is utilised here in the affinity tagging of proteins in cell lysate. Furthermore we demonstrate that the β-hydroxy aldehyde OPAL product can be functionalised again at neutral pH in a tandem organocatalyst-mediated oxime ligation. This tandem strategy is showcased in the ‘chemical mimicry’ of a previously inaccessible natural dual post-translationally modified protein integral to the pathogenesis of the neglected tropical disease Leishmaniasis.
Collapse
Affiliation(s)
- Richard J Spears
- Department of Chemistry , University of York , York , YO10 5DD , UK .
| | - Robin L Brabham
- Department of Chemistry , University of York , York , YO10 5DD , UK .
| | - Darshita Budhadev
- Department of Chemistry , University of York , York , YO10 5DD , UK .
| | - Tessa Keenan
- Department of Chemistry , University of York , York , YO10 5DD , UK .
| | - Sophie McKenna
- Department of Chemistry , University of York , York , YO10 5DD , UK .
| | - Julia Walton
- Department of Chemistry , University of York , York , YO10 5DD , UK .
| | - James A Brannigan
- Department of Chemistry , University of York , York , YO10 5DD , UK .
| | | | | | - Michael Plevin
- Department of Biology , University of York , York , YO10 5DD , UK
| | - Martin A Fascione
- Department of Chemistry , University of York , York , YO10 5DD , UK .
| |
Collapse
|
190
|
Abstract
Chemical tools are transforming our understanding of biomolecules and living systems. Included in this group are bioorthogonal reagents-functional groups that are inert to most biological species, but can be selectively ligated with complementary probes, even in live cells and whole organisms. Applications of these tools have revealed fundamental new insights into biomolecule structure and function-information often beyond the reach of genetic approaches. In many cases, the knowledge gained from bioorthogonal probes has enabled new questions to be asked and innovative research to be pursued. Thus, the continued development and application of these tools promises to both refine our view of biological systems and facilitate new discoveries. Despite decades of achievements in bioorthogonal chemistry, limitations remain. Several reagents are too large or insufficiently stable for use in cellular environments. Many bioorthogonal groups also cross-react with one another, restricting them to singular tasks. In this Account, we describe our work to address some of the voids in the bioorthogonal toolbox. Our efforts to date have focused on small reagents with a high degree of tunability: cyclopropenes, triazines, and cyclopropenones. These motifs react selectively with complementary reagents, and their unique features are enabling new pursuits in biology. The Account is organized by common themes that emerged in our development of novel bioorthogonal reagents and reactions. First, natural product structures can serve as valuable starting points for probe design. Cyclopropene, triazine, and cyclopropenone motifs are all found in natural products, suggesting that they would be metabolically stable and compatible with a variety of living systems. Second, fine-tuning bioorthogonal reagents is essential for their successful translation to biological systems. Different applications demand different types of probes; thus, generating a collection of tools that span a continuum of reactivities and stabilities remains an important goal. We have used both computational analyses and mechanistic studies to guide the optimization of various cyclopropene and triazine probes. Along the way, we identified reagents that are chemoselective but best suited for in vitro work. Others are selective and robust enough for use in living organisms. The last section of this Account highlights the need for the continued pursuit of new reagents and reactions. Challenges exist when bioorthogonal chemistries must be used in concert, given that many exploit similar mechanisms and cannot be used simultaneously. Such limitations have precluded certain multicomponent labeling studies and other biological applications. We have relied on mechanistic and computational insights to identify mutually orthogonal sets of reactions, in addition to exploring unique genres of reactivity. The continued development of mechanistically distinct, biocompatible reactions will further diversify the bioorthogonal reaction portfolio for examining biomolecules.
Collapse
|
191
|
Mukai T, Sevostyanova A, Suzuki T, Fu X, Söll D. Eine einfache Methode zur Produktion von Selenoproteinen. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201713215] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Takahito Mukai
- Department of Molecular Biophysics and Biochemistry Yale University New Haven CT 06520 USA
| | - Anastasia Sevostyanova
- Department of Molecular Biophysics and Biochemistry Yale University New Haven CT 06520 USA
| | - Tateki Suzuki
- Department of Molecular Biophysics and Biochemistry Yale University New Haven CT 06520 USA
| | - Xian Fu
- Department of Molecular Biophysics and Biochemistry Yale University New Haven CT 06520 USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry Yale University New Haven CT 06520 USA
- Department of Chemistry Yale University New Haven CT 06520 USA
| |
Collapse
|
192
|
Mukai T, Sevostyanova A, Suzuki T, Fu X, Söll D. A Facile Method for Producing Selenocysteine-Containing Proteins. Angew Chem Int Ed Engl 2018; 57:7215-7219. [PMID: 29631320 DOI: 10.1002/anie.201713215] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/20/2018] [Indexed: 01/14/2023]
Abstract
Selenocysteine (Sec, U) confers new chemical properties on proteins. Improved tools are thus required that enable Sec insertion into any desired position of a protein. We report a facile method for synthesizing selenoproteins with multiple Sec residues by expanding the genetic code of Escherichia coli. We recently discovered allo-tRNAs, tRNA species with unusual structure, that are as efficient serine acceptors as E. coli tRNASer . Ser-allo-tRNA was converted into Sec-allo-tRNA by Aeromonas salmonicida selenocysteine synthase (SelA). Sec-allo-tRNA variants were able to read through five UAG codons in the fdhF mRNA coding for E. coli formate dehydrogenase H, and produced active FDHH with five Sec residues in E. coli. Engineering of the E. coli selenium metabolism along with mutational changes in allo-tRNA and SelA improved the yield and purity of recombinant human glutathione peroxidase 1 (to over 80 %). Thus, our allo-tRNAUTu system offers a new selenoprotein engineering platform.
Collapse
Affiliation(s)
- Takahito Mukai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Anastasia Sevostyanova
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Tateki Suzuki
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Xian Fu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.,Department of Chemistry, Yale University, New Haven, CT, 06520, USA
| |
Collapse
|
193
|
Liu J, Cheng R, Rozovsky S. Synthesis and semisynthesis of selenopeptides and selenoproteins. Curr Opin Chem Biol 2018; 46:41-47. [PMID: 29723718 DOI: 10.1016/j.cbpa.2018.04.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/09/2018] [Accepted: 04/16/2018] [Indexed: 11/19/2022]
Abstract
The versatile chemistry of the genetically encoded amino acid selenocysteine (Sec) is employed in Nature to expand the reactivity of enzymes. In addition to, its role in biology, Sec is used in protein engineering to modify folding, stability, and reactivity of proteins, to introduce conjugations and to facilitate reactions. However, due to limitations related to Sec's insertion mechanism in Nature, much of the production of Sec containing peptides and proteins relies on synthesis and semisynthesis. Here, we review recent advances that have enabled the assembly of complicated selenoproteins, including novel uses of protecting groups for solid phase peptide synthesis, rapid selenoester driven chemical ligations and versatile expressed protein ligations.
Collapse
Affiliation(s)
- Jun Liu
- University of California, San Francisco, Department of Pharmaceutical Chemistry, 555 Mission Bay Blvd. South, San Francisco, CA 94158, United States.
| | - Rujin Cheng
- University of Delaware, Department of Chemistry and Biochemistry, Newark, DE 19716, United States
| | - Sharon Rozovsky
- University of Delaware, Department of Chemistry and Biochemistry, Newark, DE 19716, United States.
| |
Collapse
|
194
|
Abstract
Exciting new technological developments have pushed the boundaries of structural biology, and have enabled studies of biological macromolecules and assemblies that would have been unthinkable not long ago. Yet, the enhanced capabilities of structural biologists to pry into the complex molecular world have also placed new demands on the abilities of protein engineers to reproduce this complexity into the test tube. With this challenge in mind, we review the contents of the modern molecular engineering toolbox that allow the manipulation of proteins in a site-specific and chemically well-defined fashion. Thus, we cover concepts related to the modification of cysteines and other natural amino acids, native chemical ligation, intein and sortase-based approaches, amber suppression, as well as chemical and enzymatic bio-conjugation strategies. We also describe how these tools can be used to aid methodology development in X-ray crystallography, nuclear magnetic resonance, cryo-electron microscopy and in the studies of dynamic interactions. It is our hope that this monograph will inspire structural biologists and protein engineers alike to apply these tools to novel systems, and to enhance and broaden their scope to meet the outstanding challenges in understanding the molecular basis of cellular processes and disease.
Collapse
|
195
|
Oliveira BL, Guo Z, Bernardes GJL. Inverse electron demand Diels-Alder reactions in chemical biology. Chem Soc Rev 2018; 46:4895-4950. [PMID: 28660957 DOI: 10.1039/c7cs00184c] [Citation(s) in RCA: 641] [Impact Index Per Article: 106.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The emerging inverse electron demand Diels-Alder (IEDDA) reaction stands out from other bioorthogonal reactions by virtue of its unmatchable kinetics, excellent orthogonality and biocompatibility. With the recent discovery of novel dienophiles and optimal tetrazine coupling partners, attention has now been turned to the use of IEDDA approaches in basic biology, imaging and therapeutics. Here we review this bioorthogonal reaction and its promising applications for live cell and animal studies. We first discuss the key factors that contribute to the fast IEDDA kinetics and describe the most recent advances in the synthesis of tetrazine and dienophile coupling partners. Both coupling partners have been incorporated into proteins for tracking and imaging by use of fluorogenic tetrazines that become strongly fluorescent upon reaction. Selected notable examples of such applications are presented. The exceptional fast kinetics of this catalyst-free reaction, even using low concentrations of coupling partners, make it amenable for in vivo radiolabelling using pretargeting methodologies, which are also discussed. Finally, IEDDA reactions have recently found use in bioorthogonal decaging to activate proteins or drugs in gain-of-function strategies. We conclude by showing applications of the IEDDA reaction in the construction of biomaterials that are used for drug delivery and multimodal imaging, among others. The use and utility of the IEDDA reaction is interdisciplinary and promises to revolutionize chemical biology, radiochemistry and materials science.
Collapse
Affiliation(s)
- B L Oliveira
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Z Guo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - G J L Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK. and Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, Lisboa, 1649-028, Portugal.
| |
Collapse
|
196
|
White CJ, Bode JW. PEGylation and Dimerization of Expressed Proteins under Near Equimolar Conditions with Potassium 2-Pyridyl Acyltrifluoroborates. ACS CENTRAL SCIENCE 2018; 4:197-206. [PMID: 29532019 PMCID: PMC5833003 DOI: 10.1021/acscentsci.7b00432] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Indexed: 05/27/2023]
Abstract
The covalent conjugation of large, functionalized molecules remains a frontier in synthetic chemistry, as it requires rapid, chemoselective reactions. The potassium acyltrifluoroborate (KAT)-hydroxylamine amide-forming ligation shows promise for conjugations of biomolecules under aqueous, acidic conditions, but the variants reported to date are not suited to ligations at micromolar concentrations. We now report that 2-pyridyl KATs display significantly enhanced ligation kinetics over their aryl counterparts. Following their facile, one-step incorporation onto the termini of polyethylene glycol (PEG) chains, we show that 2-pyridyl KATs can be applied to the construction of protein-polymer conjugates in excellent (>95%) yield. Four distinct expressed, folded proteins equipped with a hydroxylamine could be PEGylated with 2-20 kDa 2-pyridyl mPEG KATs in high yield and with near-equimolar amounts of coupling partners. Furthermore, the use of a bis 2-pyridyl PEG KAT enables the covalent homodimerization of proteins with good conversion. The 2-pyridyl KAT ligation offers an effective alternative to conventional protein-polymer conjugation by operating under aqueous acidic conditions well suited for the handling of folded proteins.
Collapse
Affiliation(s)
- Christopher J. White
- Laboratorium für Organische Chemie,
Department of Chemistry and Applied Biosciences, ETH Zürich, 8093, Zürich, Switzerland
| | - Jeffrey W. Bode
- Laboratorium für Organische Chemie,
Department of Chemistry and Applied Biosciences, ETH Zürich, 8093, Zürich, Switzerland
| |
Collapse
|
197
|
Zheng Q, Fang H, Liu W. Post-translational modifications involved in the biosynthesis of thiopeptide antibiotics. Org Biomol Chem 2018; 15:3376-3390. [PMID: 28358161 DOI: 10.1039/c7ob00466d] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thiopeptide antibiotics are a class of typical ribosomally synthesized and post-translationally modified peptides (RiPPs) with complex chemical structures that are difficult to construct via chemical synthesis. To date, more than 100 thiopeptides have been discovered, and most of these compounds exhibit remarkable biological activities, such as antibacterial, antitumor and immunosuppressive activities. Therefore, studies of the biosynthesis of thiopeptides can contribute to the development of new drug leads and facilitate the understanding of the complex post-translational modifications (PTMs) of peptides and/or proteins. Since the biosynthetic gene clusters of thiopeptides were first discovered in 2009, several research studies regarding the biochemistry and enzymology of thiopeptide biosyntheses have been reported, indicating that their characteristic framework is constructed via a cascade of common PTMs and that additional specific PTMs diversify the molecules. In this review, we primarily summarize recent advances in understanding the biosynthesis of thiopeptide antibiotics and propose some potential applications based on our insights into the biosynthetic logic and machinery.
Collapse
Affiliation(s)
- Qingfei Zheng
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
| | | | | |
Collapse
|
198
|
Romero O, de las Rivas B, Lopez-Tejedor D, Palomo JM. Effect of Site-Specific Peptide-Tag Labeling on the Biocatalytic Properties of Thermoalkalophilic Lipase from Geobacillus thermocatenulatus. Chembiochem 2018; 19:369-378. [DOI: 10.1002/cbic.201700466] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Oscar Romero
- Department of Biocatalysis; Institute of Catalysis (CSIC); Marie Curie 2 Cantoblanco CampusUAM 28049 Madrid Spain
| | - Blanca de las Rivas
- Laboratorio de Biotecnología Microbiana; Instituto de Ciencia y Tecnología de alimentos y Nutrición (ICTAN-CSIC); José Antonio Novais, 10 28040 Madrid Spain
| | - David Lopez-Tejedor
- Department of Biocatalysis; Institute of Catalysis (CSIC); Marie Curie 2 Cantoblanco CampusUAM 28049 Madrid Spain
| | - Jose M. Palomo
- Department of Biocatalysis; Institute of Catalysis (CSIC); Marie Curie 2 Cantoblanco CampusUAM 28049 Madrid Spain
| |
Collapse
|
199
|
Freedy A, Matos MJ, Boutureira O, Corzana F, Guerreiro A, Akkapeddi P, Somovilla VJ, Rodrigues T, Nicholls K, Xie B, Jiménez-Osés G, Brindle KM, Neves AA, Bernardes GJL. Chemoselective Installation of Amine Bonds on Proteins through Aza-Michael Ligation. J Am Chem Soc 2017; 139:18365-18375. [PMID: 29206031 PMCID: PMC5799870 DOI: 10.1021/jacs.7b10702] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Indexed: 12/30/2022]
Abstract
Chemical modification of proteins is essential for a variety of important diagnostic and therapeutic applications. Many strategies developed to date lack chemo- and regioselectivity as well as result in non-native linkages that may suffer from instability in vivo and adversely affect the protein's structure and function. We describe here the reaction of N-nucleophiles with the amino acid dehydroalanine (Dha) in a protein context. When Dha is chemically installed in proteins, the addition of a wide-range N-nucleophiles enables the rapid formation of amine linkages (secondary and tertiary) in a chemoselective manner under mild, biocompatible conditions. These new linkages are stable at a wide range of pH values (pH 2.8 to 12.8), under reducing conditions (biological thiols such as glutathione) and in human plasma. This method is demonstrated for three proteins and is shown to be fully compatible with disulfide bridges, as evidenced by the selective modification of recombinant albumin that displays 17 structurally relevant disulfides. The practicability and utility of our approach is further demonstrated by the construction of a chemically modified C2A domain of Synaptotagmin-I protein that retains its ability to preferentially bind to apoptotic cells at a level comparable to the native protein. Importantly, the method was useful for building a homogeneous antibody-drug conjugate with a precise drug-to-antibody ratio of 2. The kinase inhibitor crizotinib was directly conjugated to Dha through its piperidine motif, and its antibody-mediated intracellular delivery results in 10-fold improvement of its cancer cell-killing efficacy. The simplicity and exquisite site-selectivity of the aza-Michael ligation described herein allows the construction of stable secondary and tertiary amine-linked protein conjugates without affecting the structure and function of biologically relevant proteins.
Collapse
Affiliation(s)
- Allyson
M. Freedy
- Department
of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K.
| | - Maria J. Matos
- Department
of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K.
| | - Omar Boutureira
- Department
of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K.
| | - Francisco Corzana
- Department
of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K.
- Departamento
de Química, Centro de Investigación en Síntesis
Química, Universidad de La Rioja, 26006 Logroño, Spain
| | - Ana Guerreiro
- Instituto
de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Padma Akkapeddi
- Instituto
de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Víctor J. Somovilla
- Department
of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K.
- Departamento
de Química, Centro de Investigación en Síntesis
Química, Universidad de La Rioja, 26006 Logroño, Spain
| | - Tiago Rodrigues
- Instituto
de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Karl Nicholls
- Albumedix
Ltd., Castle Court, 59
Castle Boulevard, NG7 1FD Nottingham, U.K.
| | - Bangwen Xie
- Li
Ka Shing Centre, Cancer Research UK Cambridge
Institute, Robinson Way, CB2 0RE Cambridge, U.K.
| | - Gonzalo Jiménez-Osés
- Departamento
de Química, Centro de Investigación en Síntesis
Química, Universidad de La Rioja, 26006 Logroño, Spain
| | - Kevin M. Brindle
- Departamento
de Química, Centro de Investigación en Síntesis
Química, Universidad de La Rioja, 26006 Logroño, Spain
- Li
Ka Shing Centre, Cancer Research UK Cambridge
Institute, Robinson Way, CB2 0RE Cambridge, U.K.
| | - André A. Neves
- Li
Ka Shing Centre, Cancer Research UK Cambridge
Institute, Robinson Way, CB2 0RE Cambridge, U.K.
| | - Gonçalo J. L. Bernardes
- Department
of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K.
- Instituto
de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| |
Collapse
|
200
|
Mousa R, Notis Dardashti R, Metanis N. Selen und Selenocystein in der Proteinchemie. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706876] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Reem Mousa
- The Institute of Chemistry; The Hebrew University of Jerusalem; Edmond J. Safra, Givat Ram Jerusalem 91904 Israel
| | - Rebecca Notis Dardashti
- The Institute of Chemistry; The Hebrew University of Jerusalem; Edmond J. Safra, Givat Ram Jerusalem 91904 Israel
| | - Norman Metanis
- The Institute of Chemistry; The Hebrew University of Jerusalem; Edmond J. Safra, Givat Ram Jerusalem 91904 Israel
| |
Collapse
|