1
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Guo Y, Cheng L, Hu Y, Zhang M, Liu R, Wang Y, Jiang S, Xiao H. Biosynthesis of Halogenated Tryptophans for Protein Engineering Using Genetic Code Expansion. Chembiochem 2024:e202400366. [PMID: 38958600 DOI: 10.1002/cbic.202400366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 06/29/2024] [Accepted: 07/03/2024] [Indexed: 07/04/2024]
Abstract
Genetic Code Expansion technology offers significant potential in incorporating noncanonical amino acids into proteins at precise locations, allowing for the modulation of protein structures and functions. However, this technology is often limited by the need for costly and challenging-to-synthesize external noncanonical amino acid sources. In this study, we address this limitation by developing autonomous cells capable of biosynthesizing halogenated tryptophan derivatives and introducing them into proteins using Genetic Code Expansion technology. By utilizing inexpensive halide salts and different halogenases, we successfully achieve the selective biosynthesis of 6-chloro-tryptophan, 7-chloro-tryptophan, 6-bromo-tryptophan, and 7-bromo-tryptophan. These derivatives are introduced at specific positions with corresponding bioorthogonal aminoacyl-tRNA synthetase/tRNA pairs in response to the amber codon. Following optimization, we demonstrate the robust expression of proteins containing halogenated tryptophan residues in cells with the ability to biosynthesize these tryptophan derivatives. This study establishes a versatile platform for engineering proteins with various halogenated tryptophans.
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Affiliation(s)
- Yiming Guo
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas, 77005, U.S.A
| | - Linqi Cheng
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas, 77005, U.S.A
| | - Yu Hu
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas, 77005, U.S.A
| | - Mengxi Zhang
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas, 77005, U.S.A
| | - Rui Liu
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas, 77005, U.S.A
| | - Yixian Wang
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas, 77005, U.S.A
| | - Shiyu Jiang
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas, 77005, U.S.A
| | - Han Xiao
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas, 77005, U.S.A
- SynthX Center, Rice University, 6100 Main Street, Houston, Texas, 77005, U.S.A
- Department of Biosciences, Rice University, 6100 Main Street, Houston, Texas, 77005, U.S.A
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, Texas, 77005, USA
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2
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El-Maghrabey M, Kishikawa N, Kuroda N. Unique biomedical application of fluorescence derivatization based on palladium-catalyzed coupling reactions for HPLC analysis of pharmaceuticals and biomolecules. Biomed Chromatogr 2024; 38:e5857. [PMID: 38509750 DOI: 10.1002/bmc.5857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/31/2024] [Accepted: 02/13/2024] [Indexed: 03/22/2024]
Abstract
Palladium-catalyzed coupling reactions are versatile and powerful tools for the construction of carbon-carbon bonds in organic synthesis. Although these reactions have favorable features that proceed selectively in mild reaction conditions using aqueous organic solvents, no attention has been given to their application in the field of biomedical analysis. Therefore, we focused on these reactions and evaluated the scope and limitations of their analytical performance. In this review, we describe the pros and cons and future trends of fluorescence derivatization of pharmaceuticals and biomolecules based on palladium-catalyzed coupling reactions such as Suzuki-Miyaura coupling, Mizoroki-Heck coupling, and Sonogashira coupling reactions for HPLC analysis.
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Affiliation(s)
- Mahmoud El-Maghrabey
- Graduate School of Biomedical Sciences, Course of Pharmaceutical Sciences, Nagasaki University, Nagasaki, Japan
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Naoya Kishikawa
- Graduate School of Biomedical Sciences, Course of Pharmaceutical Sciences, Nagasaki University, Nagasaki, Japan
| | - Naotaka Kuroda
- Graduate School of Biomedical Sciences, Course of Pharmaceutical Sciences, Nagasaki University, Nagasaki, Japan
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3
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Ding XX, Ren BQ, Li BT, Pang ZJ, Xu YJ, Dong L. Pd(II)-Catalyzed β-C(sp 3)-H Alkynylation of Alanine in Di- and Tripeptides with Asn as an Endogenous Directing Group. J Org Chem 2024; 89:3390-3402. [PMID: 38377557 DOI: 10.1021/acs.joc.3c02823] [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: 02/22/2024]
Abstract
The introduction of alkyne moieties into peptides remains in demand as it represents a promising approach for further structural diversification of peptides. Herein, we describe the Pd(II)-catalyzed C(sp3)-H alkynylation of Ala-Asn-embedded di- and tripeptides using Asn as the endogenous lead group. In addition, a key building block for the glycopeptide Tyc4PG-14 and Tyc4PG-15 was produced by our methodology.
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Affiliation(s)
- Xing-Xing Ding
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu, Sichuan 610066, China
| | - Bo-Quan Ren
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu, Sichuan 610066, China
| | - Bing-Tong Li
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Zhao-Jiong Pang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Yan-Jun Xu
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu, Sichuan 610066, China
| | - Lin Dong
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
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4
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Montua N, Thye P, Hartwig P, Kühle M, Sewald N. Enzymatic Peptide and Protein Bromination: The BromoTrp Tag. Angew Chem Int Ed Engl 2024; 63:e202314961. [PMID: 38009455 DOI: 10.1002/anie.202314961] [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: 10/05/2023] [Revised: 11/21/2023] [Accepted: 11/24/2023] [Indexed: 11/28/2023]
Abstract
Bio-orthogonal reactions for modification of proteins and unprotected peptides are of high value in chemical biology. The combination of enzymatic halogenation with transition metal-catalyzed cross-coupling provides a feasible approach for the modification of proteins and unprotected peptides. By a semirational protein engineering approach, variants of the tryptophan 6-halogenase Thal were identified that enable efficient bromination of peptides with a C-terminal tryptophan residue. The substrate scope was explored using di-, tri-, and tetrapeptide arrays, leading to the identification of an optimized peptide tag we named BromoTrp tag. This tag was introduced into three model proteins. Preparative scale post-translational bromination was possible with only a single cultivation and purification step using the brominating E. coli coexpression system Brocoli. Palladium-catalyzed Suzuki-Miyaura cross-coupling of the bromoarene was achieved with Pd nanoparticle catalysts at 37 °C, highlighting the rich potential of this strategy for bio-orthogonal functionalization and conjugation.
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Affiliation(s)
- Nicolai Montua
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Paula Thye
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Pia Hartwig
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Matthias Kühle
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Norbert Sewald
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
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5
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Besse C, Niemann HH, Sewald N. Increasing the Stability of Flavin-Dependent Halogenases by Disulfide Engineering. Chembiochem 2024; 25:e202300700. [PMID: 37917145 DOI: 10.1002/cbic.202300700] [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: 10/13/2023] [Revised: 10/27/2023] [Accepted: 11/02/2023] [Indexed: 11/03/2023]
Abstract
Flavin-dependent halogenases allow halogenation of electron-rich aromatic compounds under mild reaction conditions even at electronically unfavored positions with high regioselectivity. In order to expand the application of halogenases, the enzymes need to be improved in terms of stability and efficiency. A previous study with the tryptophan 6-halogenase Thal demonstrated that thermostable Thal variants tend to form dimers in solution while the wild type is present as a monomer. Based on this a dimeric Thal variant was generated that is covalently linked by disulfide bonds. Introducing two cysteine residues at the dimer interface resulted in the variant Thal CC with significantly increased thermostability (▵T50 =15.7 K) and stability over time at elevated temperature compared to the wild type. By introducing the homologous mutations into the tryptophan 5-halogenase PyrH, we were able to show that the stabilization by covalent dimerization can also be transferred to other halogenases. Moreover, it was possible to further increase the thermostability of PyrH by inserting cysteine mutations at alternative sites of the dimer interface.
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Affiliation(s)
- Caroline Besse
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Hartmut H Niemann
- Structural Biochemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Norbert Sewald
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
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6
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Milne N, Sáez-Sáez J, Nielsen AM, Dyekjaer JD, Rago D, Kristensen M, Wulff T, Borodina I. Engineering Saccharomyces cerevisiae for the de novo Production of Halogenated Tryptophan and Tryptamine Derivatives. ChemistryOpen 2023; 12:e202200266. [PMID: 36929157 PMCID: PMC10068768 DOI: 10.1002/open.202200266] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/28/2023] [Indexed: 03/18/2023] Open
Abstract
The indole scaffold is a recurring structure in multiple bioactive heterocycles and natural products. Substituted indoles like the amino acid tryptophan serve as a precursor for a wide range of natural products with pharmaceutical or agrochemical applications. Inspired by the versatility of these compounds, medicinal chemists have for decades exploited indole as a core structure in the drug discovery process. With the aim of tuning the properties of lead drug candidates, regioselective halogenation of the indole scaffold is a common strategy. However, chemical halogenation is generally expensive, has a poor atom economy, lacks regioselectivity, and generates hazardous waste streams. As an alternative, in this work we engineer the industrial workhorse Saccharomyces cerevisiae for the de novo production of halogenated tryptophan and tryptamine derivatives. Functional expression of bacterial tryptophan halogenases together with a partner flavin reductase and a tryptophan decarboxylase resulted in the production of halogenated tryptophan and tryptamine with chlorine or bromine. Furthermore, by combining tryptophan halogenases, production of di-halogenated molecules was also achieved. Overall, this works paves the road for the production of new-to-nature halogenated natural products in yeast.
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Affiliation(s)
- Nicholas Milne
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.,Octarine Bio ApS, Lersø Parkallé 42, 1. Sal, 2100, Copenhagen, Denmark
| | - Javier Sáez-Sáez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Annette Munch Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.,Octarine Bio ApS, Lersø Parkallé 42, 1. Sal, 2100, Copenhagen, Denmark
| | - Jane Dannow Dyekjaer
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Daniela Rago
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Mette Kristensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Tune Wulff
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
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7
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Halogenation of Peptides and Proteins Using Engineered Tryptophan Halogenase Enzymes. Biomolecules 2022; 12:biom12121841. [PMID: 36551269 PMCID: PMC9775415 DOI: 10.3390/biom12121841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/05/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
Halogenation of bioactive peptides via incorporation of non-natural amino acid derivatives during chemical synthesis is a common strategy to enhance functionality. Bacterial tyrptophan halogenases efficiently catalyze regiospecific halogenation of the free amino acid tryptophan, both in vitro and in vivo. Expansion of their substrate scope to peptides and proteins would facilitate highly-regulated post-synthesis/expression halogenation. Here, we demonstrate novel in vitro halogenation (chlorination and bromination) of peptides by select halogenase enzymes and identify the C-terminal (G/S)GW motif as a preferred substrate. In a first proof-of-principle experiment, we also demonstrate chemo-catalyzed derivatization of an enzymatically chlorinated peptide, albeit with low efficiency. We further rationally derive PyrH halogenase mutants showing improved halogenation of the (G/S)GW motif, both as a free peptide and when genetically fused to model proteins with efficiencies up to 90%.
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8
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Koiwa D, Ohira M, Hiramatsu T, Abe H, Kawamoto T, Ishihara Y, Ignacio B, Mansour N, Romoff T. Rapid and efficient syntheses of tryptophans using a continuous-flow quaternization-substitution reaction of gramines with a chiral nucleophilic glycine equivalent. Org Biomol Chem 2022; 20:8331-8340. [PMID: 36250233 DOI: 10.1039/d2ob01682f] [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: 06/16/2023]
Abstract
A continuous-flow quaternization reaction of gramines with MeI (<1 min) followed by a substitution reaction with a chiral nucleophilic glycine-derived Ni-complex (S)-2 (<1 min) has successfully been developed to afford the corresponding alkylated Ni-complexes 3 in good yields with excellent diastereoselectivity, based on the results of a one-pot quaternization-substitution reaction of gramines with (S)-2 in a batch process. The continuous-flow process allowed the safe and efficient scale-up synthesis of 3j (84% yield, 99% de, 540 g h-1) to give 7-azatryptophan derivative (S)-4j readily by an acid-catalyzed hydrolysis reaction followed by protection with an Fmoc group. The present method for the rapid and efficient syntheses of enantiopure unnatural tryptophan derivatives from various gramines and (S)-2 will be useful to further promote peptide and protein drug discovery and development research.
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Affiliation(s)
- Daichi Koiwa
- Research & Development Division, Hamari Chemicals, Ltd, 1-19-40, Nankokita, Suminoe-ku, Osaka, 559-0034, Japan.
| | - Masayuki Ohira
- Research & Development Division, Hamari Chemicals, Ltd, 1-19-40, Nankokita, Suminoe-ku, Osaka, 559-0034, Japan.
| | - Takahiro Hiramatsu
- Research & Development Division, Hamari Chemicals, Ltd, 1-19-40, Nankokita, Suminoe-ku, Osaka, 559-0034, Japan.
| | - Hidenori Abe
- Research & Development Division, Hamari Chemicals, Ltd, 1-19-40, Nankokita, Suminoe-ku, Osaka, 559-0034, Japan.
| | - Tetsuji Kawamoto
- Research & Development Division, Hamari Chemicals, Ltd, 1-19-40, Nankokita, Suminoe-ku, Osaka, 559-0034, Japan.
| | - Yuji Ishihara
- Research & Development Division, Hamari Chemicals, Ltd, 1-19-40, Nankokita, Suminoe-ku, Osaka, 559-0034, Japan.
| | - Bernardo Ignacio
- Hamari Chemicals USA, Inc., 11558 Sorrento Valley Rd Suite 3, San Diego, California, 92121, USA
| | - Noel Mansour
- Hamari Chemicals USA, Inc., 11558 Sorrento Valley Rd Suite 3, San Diego, California, 92121, USA
| | - Todd Romoff
- Hamari Chemicals USA, Inc., 11558 Sorrento Valley Rd Suite 3, San Diego, California, 92121, USA
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9
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Sabadasch V, Dirksen M, Fandrich P, Hellweg T. Multifunctional Core-Shell Microgels as Pd-Nanoparticle Containing Nanoreactors With Enhanced Catalytic Turnover. Front Chem 2022; 10:889521. [PMID: 35692683 PMCID: PMC9185801 DOI: 10.3389/fchem.2022.889521] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 04/21/2022] [Indexed: 11/26/2022] Open
Abstract
In this work, we present core-shell microgels with tailor-made architecture and properties for the incorporation of palladium nanoparticles. The microgel core consists of poly-N-isopropylacrylamide (PNIPAM) copolymerized with methacrylic acid (MAc) as anchor point for the incorporation of palladium nanoparticles. The microgel shell is prepared by copolymerization of NIPAM and the UV-sensitive comonomer 2-hydroxy-4-(methacryloyloxy)-benzophenone (HMABP). The obtained core-shell architecture was analyzed by means of photon correlation spectroscopy, while the incorporated amount of HMABP was further confirmed via Fourier transform infrared spectroscopy. Subsequently, the microgel system was used for loading with palladium nanoparticles and their size and localization were investigated by transmission electron microscopy. The catalytic activity of the monodisperse palladium nanoparticles was tested by reduction of 4-nitrophenol to 4-aminophenol. The obtained reaction rate constants for the core-shell system showed enhanced activity compared to the Pd-loaded bare core system. Furthermore, it was possible to recycle the catalyst several times. Analysis via transmission electron microscopy revealed, that the incorporated palladium nanoparticles emerged undamaged after the reaction and subsequent purification process since no aggregation or loss in size was observed.
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10
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Sabadasch V, Fandrich P, Annegarn M, Hellweg T. Effect of Methacrylic Acid in PNNPAM Microgels on the Catalytic Activity of Embedded Palladium Nanoparticles. MACROMOL CHEM PHYS 2022. [DOI: 10.1002/macp.202200045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Viktor Sabadasch
- Physical and Biophysical Chemistry Bielefeld University Bielefeld 33615 Germany
| | - Pascal Fandrich
- Physical and Biophysical Chemistry Bielefeld University Bielefeld 33615 Germany
| | - Marco Annegarn
- Physical and Biophysical Chemistry Bielefeld University Bielefeld 33615 Germany
| | - Thomas Hellweg
- Physical and Biophysical Chemistry Bielefeld University Bielefeld 33615 Germany
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11
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Sabadasch V, Dachwitz S, Hellweg T, Sewald N, Hannappel Y. Acrylamide-Based Pd-Nanoparticle Carriers as Smart Catalysts for the Suzuki–Miyaura Cross-Coupling of Amino Acids. SYNTHESIS-STUTTGART 2022. [DOI: 10.1055/a-1782-4224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
AbstractPolyacrylamide-based waterborne microgels were prepared with copolymerized carboxylic acid and tertiary amine moieties. The colloidal gels were loaded with palladium nanoparticles and utilized for the Suzuki–Miyaura cross-coupling of amino acids and peptides. The thermoresponsive properties of the prepared microgels were characterized by means of photon correlation spectroscopy (PCS) at solvent conditions of the catalytic reaction. The localization and morphology of the incorporated nanoparticles were characterized with transmission electron microscopy (TEM). Palladium-catalyzed Suzuki–Miyaura cross-coupling of N
α-Boc-4-iodophenylalanine and N
α-Boc-7-bromotryptophan with phenylboronic acid was carried out under ambient atmosphere in water at 20, 37, and 60 °C, respectively. The properties of the thermoresponsive microgel showed a strong influence on the reactivity and selectivity towards the respective substrate. For the amine containing microgels, a recyclability for up to four cycles without loss in activity could be realized. Furthermore, the systems showed good catalytic activity regarding Suzuki–Miyaura cross-coupling of halogenated amino acids in selected tri- and tetrapeptides.
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Affiliation(s)
- Viktor Sabadasch
- Department of Chemistry, Physical and Biophysical Chemistry, Bielefeld University
| | - Steffen Dachwitz
- Department of Chemistry, Organic and Bioorganic Chemistry, Bielefeld University
| | - Thomas Hellweg
- Department of Chemistry, Physical and Biophysical Chemistry, Bielefeld University
- BINAS - Bielefeld Institute for Biophysics and Nanoscience, Bielefeld University
| | - Norbert Sewald
- Department of Chemistry, Organic and Bioorganic Chemistry, Bielefeld University
| | - Yvonne Hannappel
- Department of Chemistry, Physical and Biophysical Chemistry, Bielefeld University
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12
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Brittain WDG, Coxon CR. Perfluoroaryl and Perfluoroheteroaryl Reagents as Emerging New Tools for Peptide Synthesis, Modification and Bioconjugation. Chemistry 2022; 28:e202103305. [PMID: 34762323 PMCID: PMC9299879 DOI: 10.1002/chem.202103305] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Indexed: 12/30/2022]
Abstract
Peptides and proteins are becoming increasingly valuable as medicines, diagnostic agents and as tools for biomedical sciences. Much of this has been underpinned by the emergence of new methods for the manipulation and augmentation of native biomolecules. Perfluoroaromatic reagents are perhaps one of the most diverse and exciting tools with which to modify peptides and proteins, due principally to their nucleophilic substitution chemistry, high electron deficiency and the ability for their reactivity to be tuned towards specific nucleophiles. As discussed in this minireview, in recent years, perfluoroaromatic reagents have found applications as protecting groups or activating groups in peptide synthesis and as orthogonal handles for peptide modification. Furthermore, they have applications in chemoselective 'tagging', stapling and bioconjugation of peptides and proteins, as well as tuning of 'drug-like' properties. This review will also explore possible future applications of these reagents in biological chemistry.
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Affiliation(s)
| | - Christopher R. Coxon
- EaStChem School of ChemistryThe University of Edinburgh Joseph Black BuildingDavid Brewster RoadEdinburghEH9 3FJUK
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13
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Gruß H, Feiner RC, Mseya R, Schröder DC, Jewgiński M, Müller KM, Latajka R, Marion A, Sewald N. Peptide stapling by late-stage Suzuki–Miyaura cross-coupling. Beilstein J Org Chem 2022; 18:1-12. [PMID: 35047078 PMCID: PMC8744458 DOI: 10.3762/bjoc.18.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 12/09/2021] [Indexed: 12/19/2022] Open
Abstract
The development of peptide stapling techniques to stabilise α-helical secondary structure motifs of peptides led to the design of modulators of protein–protein interactions, which had been considered undruggable for a long time. We disclose a novel approach towards peptide stapling utilising macrocyclisation by late-stage Suzuki–Miyaura cross-coupling of bromotryptophan-containing peptides of the catenin-binding domain of axin. Optimisation of the linker length in order to find a compromise between both sufficient linker rigidity and flexibility resulted in a peptide with an increased α-helicity and enhanced binding affinity to its native binding partner β-catenin. An increased proteolytic stability against proteinase K has been demonstrated.
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Affiliation(s)
- Hendrik Gruß
- Department of Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Rebecca C Feiner
- Department of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Ridhiwan Mseya
- Department of Chemistry, Middle East Technical University, 06800, Ankara, Turkey
| | - David C Schröder
- Department of Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Michał Jewgiński
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wrocław, Poland
| | - Kristian M Müller
- Department of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Rafał Latajka
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wrocław, Poland
| | - Antoine Marion
- Department of Chemistry, Middle East Technical University, 06800, Ankara, Turkey
| | - Norbert Sewald
- Department of Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
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14
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Abstract
Biocatalysis has an enormous impact on chemical synthesis. The waves in which biocatalysis has developed, and in doing so changed our perception of what organic chemistry is, were reviewed 20 and 10 years ago. Here we review the consequences of these waves of development. Nowadays, hydrolases are widely used on an industrial scale for the benign synthesis of commodity and bulk chemicals and are fully developed. In addition, further enzyme classes are gaining ever increasing interest. Particularly, enzymes catalysing selective C-C-bond formation reactions and enzymes catalysing selective oxidation and reduction reactions are solving long-standing synthetic challenges in organic chemistry. Combined efforts from molecular biology, systems biology, organic chemistry and chemical engineering will establish a whole new toolbox for chemistry. Recent developments are critically reviewed.
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Affiliation(s)
- Ulf Hanefeld
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, The Netherlands.
| | - Frank Hollmann
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, The Netherlands.
| | - Caroline E Paul
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, The Netherlands.
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15
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Abstract
Over the past few decades, the use of transition metal nanoparticles (NPs) in catalysis has attracted much attention and their use in C–C bond forming reactions constitutes one of their most important applications. A huge variety of metal NPs, which have showed high catalytic activity for C–C bond forming reactions, have been developed up to now. Many kinds of stabilizers, such as inorganic materials, magnetically recoverable materials, porous materials, organic–inorganic composites, carbon materials, polymers, and surfactants have been utilized to develop metal NPs catalysts. This review classified and outlined the categories of metal NPs by the type of support.
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Romero E, Jones BS, Hogg BN, Rué Casamajo A, Hayes MA, Flitsch SL, Turner NJ, Schnepel C. Enzymkatalysierte späte Modifizierungen: Besser spät als nie. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 133:16962-16993. [PMID: 38505660 PMCID: PMC10946893 DOI: 10.1002/ange.202014931] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 01/15/2021] [Indexed: 03/21/2024]
Abstract
AbstractDie Enzymkatalyse gewinnt zunehmend an Bedeutung in der Synthesechemie. Die durch Bioinformatik und Enzym‐Engineering stetig wachsende Zahl von Biokatalysatoren eröffnet eine große Vielfalt selektiver Reaktionen. Insbesondere für späte Funktionalisierungsreaktionen ist die Biokatalyse ein geeignetes Werkzeug, das oftmals der konventionellen De‐novo‐Synthese überlegen ist. Enzyme haben sich als nützlich erwiesen, um funktionelle Gruppen direkt in komplexe Molekülgerüste einzuführen sowie für die rasche Diversifizierung von Substanzbibliotheken. Biokatalytische Oxyfunktionalisierungen, Halogenierungen, Methylierungen, Reduktionen und Amidierungen sind von besonderem Interesse, da diese Strukturmotive häufig in Pharmazeutika vertreten sind. Dieser Aufsatz gibt einen Überblick über die Stärken und Schwächen der enzymkatalysierten späten Modifizierungen durch native und optimierte Enzyme in der Synthesechemie. Ebenso werden wichtige Beispiele in der Wirkstoffentwicklung hervorgehoben.
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Affiliation(s)
- Elvira Romero
- Compound Synthesis and ManagementDiscovery Sciences, BioPharmaceuticals R&DAstraZenecaGötheborgSchweden
| | - Bethan S. Jones
- School of ChemistryThe University of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNVereinigtes Königreich
| | - Bethany N. Hogg
- School of ChemistryThe University of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNVereinigtes Königreich
| | - Arnau Rué Casamajo
- School of ChemistryThe University of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNVereinigtes Königreich
| | - Martin A. Hayes
- Compound Synthesis and ManagementDiscovery Sciences, BioPharmaceuticals R&DAstraZenecaGötheborgSchweden
| | - Sabine L. Flitsch
- School of ChemistryThe University of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNVereinigtes Königreich
| | - Nicholas J. Turner
- School of ChemistryThe University of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNVereinigtes Königreich
| | - Christian Schnepel
- School of ChemistryThe University of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNVereinigtes Königreich
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Romero E, Jones BS, Hogg BN, Rué Casamajo A, Hayes MA, Flitsch SL, Turner NJ, Schnepel C. Enzymatic Late-Stage Modifications: Better Late Than Never. Angew Chem Int Ed Engl 2021; 60:16824-16855. [PMID: 33453143 PMCID: PMC8359417 DOI: 10.1002/anie.202014931] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 01/15/2021] [Indexed: 12/16/2022]
Abstract
Enzyme catalysis is gaining increasing importance in synthetic chemistry. Nowadays, the growing number of biocatalysts accessible by means of bioinformatics and enzyme engineering opens up an immense variety of selective reactions. Biocatalysis especially provides excellent opportunities for late-stage modification often superior to conventional de novo synthesis. Enzymes have proven to be useful for direct introduction of functional groups into complex scaffolds, as well as for rapid diversification of compound libraries. Particularly important and highly topical are enzyme-catalysed oxyfunctionalisations, halogenations, methylations, reductions, and amide bond formations due to the high prevalence of these motifs in pharmaceuticals. This Review gives an overview of the strengths and limitations of enzymatic late-stage modifications using native and engineered enzymes in synthesis while focusing on important examples in drug development.
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Affiliation(s)
- Elvira Romero
- Compound Synthesis and ManagementDiscovery Sciences, BioPharmaceuticals R&DAstraZenecaGothenburgSweden
| | - Bethan S. Jones
- School of ChemistryThe University of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNUnited Kingdom
| | - Bethany N. Hogg
- School of ChemistryThe University of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNUnited Kingdom
| | - Arnau Rué Casamajo
- School of ChemistryThe University of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNUnited Kingdom
| | - Martin A. Hayes
- Compound Synthesis and ManagementDiscovery Sciences, BioPharmaceuticals R&DAstraZenecaGothenburgSweden
| | - Sabine L. Flitsch
- School of ChemistryThe University of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNUnited Kingdom
| | - Nicholas J. Turner
- School of ChemistryThe University of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNUnited Kingdom
| | - Christian Schnepel
- School of ChemistryThe University of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNUnited Kingdom
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Kemker I, Schröder DC, Feiner RC, Müller KM, Marion A, Sewald N. Tuning the Biological Activity of RGD Peptides with Halotryptophans†. J Med Chem 2020; 64:586-601. [PMID: 33356253 DOI: 10.1021/acs.jmedchem.0c01536] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
An array of l- and d-halotryptophans with different substituents at the indole moiety was synthesized employing either enzymatic halogenation by halogenases or incorporation of haloindoles using tryptophan synthase. Introduction of these Trp derivatives into RGD peptides as a benchmark system was performed to investigate their influence on bioactivity. Halotryptophan-containing RGD peptides display increased affinity toward integrin αvβ3 and enhanced selectivity over integrin α5β1. In addition, bromotryptophan was exploited as a platform for late-stage diversification by Suzuki-Miyaura cross-coupling (SMC), resulting in new-to-nature biaryl motifs. These peptides show enhanced affinity toward αvβ3, good affinity to αvβ8, and remarkable selectivity over α5β1 and αIIbβ3 while featuring fluorogenic properties. Their feasibility as a probe was demonstrated in vitro. Extensive molecular dynamics simulations were undertaken to elucidate NMR and high-performance liquid chromatography (HPLC) data for these late-stage diversified cyclic RGD peptides and to further characterize their conformational preferences.
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Affiliation(s)
- Isabell Kemker
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - David C Schröder
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Rebecca C Feiner
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Kristian M Müller
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Antoine Marion
- Department of Chemistry, Middle East Technical University, Kimya Bölümü Üniversiteler Mah., Çankaya, 06800 Ankara, Turkey
| | - Norbert Sewald
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany.,Department of Chemistry, Middle East Technical University, Kimya Bölümü Üniversiteler Mah., Çankaya, 06800 Ankara, Turkey
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Dachwitz S, Duwe DH, Wang YH, Gruß H, Hannappel Y, Hellweg T, Sewald N. Suzuki-Miyaura Cross-Coupling of Bromotryptophan Derivatives at Ambient Temperature. Chemistry 2020; 26:16357-16364. [PMID: 32639079 PMCID: PMC7756874 DOI: 10.1002/chem.202002454] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/23/2020] [Indexed: 02/06/2023]
Abstract
Mild reaction conditions are highly desirable for bio‐orthogonal side chain derivatizations of amino acids, peptides or proteins due to the sensitivity of these substrates. Transition metal catalysed cross‐couplings such as Suzuki–Miyaura reactions are highly versatile, but usually require unfavourable reaction conditions, in particular, when applied with aryl bromides. Ligand‐free solvent‐stabilised Pd‐nanoparticles represent an efficient and sustainable alternative to conventional phosphine‐based catalysts, because the cross‐coupling can be performed at considerably lower temperature. We report on the application of such a highly reactive heterogeneous catalyst for the Suzuki–Miyaura cross‐coupling of brominated tryptophan derivatives. The solvent‐stabilised Pd‐nanoparticles are even more efficient than the literature‐known ADHP‐Pd precatalyst. Interestingly, the latter also leads to the formation of quasi‐homogeneous Pd‐nanoparticles as the catalytic species. One advantage of our approach is the compatibility with aqueous and aerobic conditions at near‐ambient temperatures and short reaction times of only 2 h. The influence of different Nα‐protecting groups, boronic acids as well as the impact of different amino acid side chains in bromotryptophan‐containing peptides has been studied. Notably, a surprising acceleration of the catalysis was observed when palladium‐coordinating side chains were present in proximal positions.
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Affiliation(s)
- Steffen Dachwitz
- Department of Chemistry, Organic and Bioorganic Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Dario H Duwe
- Department of Chemistry, Organic and Bioorganic Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Yating Hong Wang
- Department of Chemistry, Organic and Bioorganic Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Hendrik Gruß
- Department of Chemistry, Organic and Bioorganic Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Yvonne Hannappel
- Department of Chemistry, Physical Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Thomas Hellweg
- Department of Chemistry, Physical Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Norbert Sewald
- Department of Chemistry, Organic and Bioorganic Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
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