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Ospina F, Schülke KH, Hammer SC. Biocatalytic Alkylation Chemistry: Building Molecular Complexity with High Selectivity. Chempluschem 2021; 87:e202100454. [PMID: 34821073 DOI: 10.1002/cplu.202100454] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/05/2021] [Indexed: 12/28/2022]
Abstract
Biocatalysis has traditionally been viewed as a field that primarily enables access to chiral centers. This includes the synthesis of chiral alcohols, amines and carbonyl compounds, often through functional group interconversion via hydrolytic or oxidation-reduction reactions. This limitation is partly being overcome by the design and evolution of new enzymes. Here, we provide an overview of a recently thriving research field that we summarize as biocatalytic alkylation chemistry. In the past 3-4 years, numerous new enzymes have been developed that catalyze sp3 C-C/N/O/S bond formations. These enzymes utilize different mechanisms to generate molecular complexity by coupling simple fragments with high activity and selectivity. In many cases, the engineered enzymes perform reactions that are difficult or impossible to achieve with current small-molecule catalysts such as organocatalysts and transition-metal complexes. This review further highlights that the design of new enzyme function is particularly successful when off-the-shelf synthetic reagents are utilized to access non-natural reactive intermediates. This underscores how biocatalysis is gradually moving to a field that build molecules through selective bond forming reactions.
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Affiliation(s)
- Felipe Ospina
- Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Kai H Schülke
- Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Stephan C Hammer
- Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
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Watkins-Dulaney EJ, Dunham NP, Straathof S, Turi S, Arnold FH, Buller AR. Asymmetric Alkylation of Ketones Catalyzed by Engineered TrpB. Angew Chem Int Ed Engl 2021; 60:21412-21417. [PMID: 34269506 DOI: 10.1002/anie.202106938] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Indexed: 11/12/2022]
Abstract
The β-subunit of tryptophan synthase (TrpB) catalyzes a PLP-mediated β-substitution reaction between indole and serine to form L-Trp. A succession of TrpB protein engineering campaigns to expand the enzyme's nucleophile substrate range has enabled the biocatalytic production of diverse non-canonical amino acids (ncAAs). Here, we show that ketone-derived enolates can serve as nucleophiles in the TrpB reaction to achieve the asymmetric alkylation of ketones, an outstanding challenge in synthetic chemistry. We engineered TrpB by directed evolution to catalyze the asymmetric alkylation of propiophenone and 2-fluoroacetophenone with a high degree of selectivity. In reactions with propiophenone, preference for the opposite product diastereomer emerges over the course of evolution, demonstrating that full control over the stereochemistry at the new chiral center can be achieved. The addition of this new reaction to the TrpB platform is a crucial first step toward the development of efficient methods to synthesize non-canonical prolines and other chirally dense nitrogen heterocycles.
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Affiliation(s)
- Ella J Watkins-Dulaney
- Division of Biology and Biological Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA, 91125, USA
| | - Noah P Dunham
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA, 91125, USA
| | - Sabine Straathof
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA, 91125, USA
| | - Soma Turi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA, 91125, USA
| | - Frances H Arnold
- Division of Biology and Biological Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA, 91125, USA.,Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA, 91125, USA
| | - Andrew R Buller
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI, 53706, USA
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Watkins‐Dulaney EJ, Dunham NP, Straathof S, Turi S, Arnold FH, Buller AR. Asymmetric Alkylation of Ketones Catalyzed by Engineered TrpB. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Ella J. Watkins‐Dulaney
- Division of Biology and Biological Engineering California Institute of Technology, MC 210-41 1200 E. California Boulevard Pasadena CA 91125 USA
| | - Noah P. Dunham
- Division of Chemistry and Chemical Engineering California Institute of Technology, MC 210-41 1200 E. California Boulevard Pasadena CA 91125 USA
| | - Sabine Straathof
- Division of Chemistry and Chemical Engineering California Institute of Technology, MC 210-41 1200 E. California Boulevard Pasadena CA 91125 USA
| | - Soma Turi
- Division of Chemistry and Chemical Engineering California Institute of Technology, MC 210-41 1200 E. California Boulevard Pasadena CA 91125 USA
| | - Frances H. Arnold
- Division of Biology and Biological Engineering California Institute of Technology, MC 210-41 1200 E. California Boulevard Pasadena CA 91125 USA
- Division of Chemistry and Chemical Engineering California Institute of Technology, MC 210-41 1200 E. California Boulevard Pasadena CA 91125 USA
| | - Andrew R. Buller
- Department of Chemistry University of Wisconsin—Madison 1101 University Avenue Madison WI 53706 USA
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Watkins-Dulaney E, Straathof S, Arnold F. Tryptophan Synthase: Biocatalyst Extraordinaire. Chembiochem 2021; 22:5-16. [PMID: 32677310 PMCID: PMC7935429 DOI: 10.1002/cbic.202000379] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/15/2020] [Indexed: 12/23/2022]
Abstract
Tryptophan synthase (TrpS) has emerged as a paragon of noncanonical amino acid (ncAA) synthesis and is an ideal biocatalyst for synthetic and biological applications. TrpS catalyzes an irreversible, C-C bond-forming reaction between indole and serine to make l-tryptophan; native TrpS complexes possess fairly broad specificity for indole analogues, but are difficult to engineer to extend substrate scope or to confer other useful properties due to allosteric constraints and their heterodimeric structure. Directed evolution freed the catalytically relevant TrpS β-subunit (TrpB) from allosteric regulation by its TrpA partner and has enabled dramatic expansion of the enzyme's substrate scope. This review examines the long and storied career of TrpS from the perspective of its application in ncAA synthesis and biocatalytic cascades.
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Affiliation(s)
- Ella Watkins-Dulaney
- Division of Biology and Biological Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Sabine Straathof
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Frances Arnold
- Division of Biology and Biological Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA 91125, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA 91125, USA
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Abstract
Pd-mediated reactions have emerged as a powerful tool for the site-selective and bioorthogonal late-stage diversification of amino acids, peptides and related compounds. Indole moieties of tryptophan derivatives are susceptible to C2 H-activation, whereas halogenated aromatic amino acids such as halophenylalanines or halotryptophans provide a broad spectrum of different functionalisations. The compatibility of transition-metal-catalysed cross-couplings with functional groups in peptides, other biologically active compounds and even proteins has been demonstrated. This Review primarily compiles the application of different cross-coupling reactions to modify halotryptophans, halotryptophan containing peptides or halogenated, biologically active compounds derived from tryptophan. Modern approaches use regio- and stereoselective biocatalytic strategies to generate halotryptophans and derivatives on a preparative scale. The combination of bio- and chemocatalysis in cascade reactions is given by the biocompatibility and bioorthogonality of Pd-mediated reactions.
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Affiliation(s)
- Hendrik Gruß
- Organische und Bioorganische ChemieFakultät für ChemieUniversität BielefeldUniversitätsstraße 2533615BielefeldGermany
| | - Norbert Sewald
- Organische und Bioorganische ChemieFakultät für ChemieUniversität BielefeldUniversitätsstraße 2533615BielefeldGermany
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Watkins EJ, Almhjell PJ, Arnold FH. Direct Enzymatic Synthesis of a Deep-Blue Fluorescent Noncanonical Amino Acid from Azulene and Serine. Chembiochem 2019; 21:80-83. [PMID: 31513332 DOI: 10.1002/cbic.201900497] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Indexed: 12/21/2022]
Abstract
We report a simple, one-step enzymatic synthesis of the blue fluorescent noncanonical amino acid β-(1-azulenyl)-l-alanine (AzAla). By using an engineered tryptophan synthase β-subunit (TrpB), stereochemically pure AzAla can be synthesized at scale starting from commercially available azulene and l-serine. Mutation of a universally conserved catalytic glutamate in the active site to glycine has only a modest effect on native activity with indole but abolishes activity on azulene, suggesting that this glutamate activates azulene for nucleophilic attack by stabilization of the aromatic ion.
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Affiliation(s)
- Ella J Watkins
- Division of Biology and Biological Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA, 91125, USA
| | - Patrick J Almhjell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA, 91125, USA
| | - Frances H Arnold
- Division of Biology and Biological Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA, 91125, USA.,Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA, 91125, USA
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Pubill‐Ulldemolins C, Sharma SV, Cartmell C, Zhao J, Cárdenas P, Goss RJM. Heck Diversification of Indole-Based Substrates under Aqueous Conditions: From Indoles to Unprotected Halo-tryptophans and Halo-tryptophans in Natural Product Derivatives. Chemistry 2019; 25:10866-10875. [PMID: 31125453 PMCID: PMC6772188 DOI: 10.1002/chem.201901327] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/21/2019] [Indexed: 12/17/2022]
Abstract
The blending of synthetic chemistry with biosynthetic processes provides a powerful approach to synthesis. Biosynthetic halogenation and synthetic cross-coupling have great potential to be used together, for small molecule generation, access to natural product analogues and as a tool for chemical biology. However, to enable enhanced generality of this approach, further synthetic tools are needed. Though considerable research has been invested in the diversification of phenylalanine and tyrosine, functionalisation of tryptophans thorough cross-coupling has been largely neglected. Tryptophan is a key residue in many biologically active natural products and peptides; in proteins it is key to fluorescence and dominates protein folding. To this end, we have explored the Heck cross-coupling of halo-indoles and halo-tryptophans in water, showing broad reaction scope. We have demonstrated the ability to use this methodology in the functionalisation of a brominated antibiotic (bromo-pacidamycin), as well as a marine sponge metabolite, barettin.
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Affiliation(s)
- Cristina Pubill‐Ulldemolins
- Department of Chemistry and BSRCUniversity of St AndrewsSt AndrewsKY16 9STUK
- Present address: Department of ChemistrySchool of Life SciencesUniversity of SussexBrightonBN19QJUK
| | - Sunil V. Sharma
- Department of Chemistry and BSRCUniversity of St AndrewsSt AndrewsKY16 9STUK
| | | | - Jinlian Zhao
- Department of Chemistry and BSRCUniversity of St AndrewsSt AndrewsKY16 9STUK
| | - Paco Cárdenas
- Pharmacognosy, Department of Medicinal ChemistryUppsala UniversityUppsala75123Sweden
| | - Rebecca J. M. Goss
- Department of Chemistry and BSRCUniversity of St AndrewsSt AndrewsKY16 9STUK
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McDonald AD, Perkins LJ, Buller AR. Facile in Vitro Biocatalytic Production of Diverse Tryptamines. Chembiochem 2019; 20:1939-1944. [PMID: 30864270 PMCID: PMC6800669 DOI: 10.1002/cbic.201900069] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/08/2019] [Indexed: 01/01/2023]
Abstract
Tryptamines are a medicinally important class of small molecules that serve as precursors to more complex, clinically used indole alkaloid natural products. Typically, tryptamine analogues are prepared from indoles through multistep synthetic routes. In the natural world, the desirable tryptamine synthon is produced in a single step by l-tryptophan decarboxylases (TDCs). However, no TDCs are known to combine high activity and substrate promiscuity, which might enable a practical biocatalytic route to tryptamine analogues. We have now identified the TDC from Ruminococcus gnavus as the first highly active and promiscuous member of this enzyme family. RgnTDC performs up to 96 000 turnovers and readily accommodates tryptophan analogues with substituents at the 4, 5, 6, and 7 positions, as well as alternative heterocycles, thus enabling the facile biocatalytic synthesis of >20 tryptamine analogues. We demonstrate the utility of this enzyme in a two-step biocatalytic sequence with an engineered tryptophan synthase to afford an efficient, cost-effective route to tryptamines from commercially available indole starting materials.
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Affiliation(s)
- Allwin D McDonald
- Department of Chemistry, University of Wisconsin, Madison, Madison, WI, 53705, USA
| | - Lydia J Perkins
- Department of Chemistry, University of Wisconsin, Madison, Madison, WI, 53705, USA
| | - Andrew R Buller
- Department of Chemistry, University of Wisconsin, Madison, Madison, WI, 53705, USA
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Boville CE, Scheele RA, Koch P, Brinkmann-Chen S, Buller AR, Arnold FH. Engineered Biosynthesis of β-Alkyl Tryptophan Analogues. Angew Chem Int Ed Engl 2018; 57:14764-14768. [PMID: 30215880 DOI: 10.1002/anie.201807998] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Indexed: 11/12/2022]
Abstract
Noncanonical amino acids (ncAAs) with dual stereocenters at the α and β positions are valuable precursors to natural products and therapeutics. Despite the potential applications of such bioactive β-branched ncAAs, their availability is limited due to the inefficiency of the multistep methods used to prepare them. Herein we report a stereoselective biocatalytic synthesis of β-branched tryptophan analogues using an engineered variant of Pyrococcus furiosus tryptophan synthase (PfTrpB), PfTrpB7E6 . PfTrpB7E6 is the first biocatalyst to synthesize bulky β-branched tryptophan analogues in a single step, with demonstrated access to 27 ncAAs. The molecular basis for the efficient catalysis and broad substrate tolerance of PfTrpB7E6 was explored through X-ray crystallography and UV/Vis spectroscopy, which revealed that a combination of active-site and remote mutations increase the abundance and persistence of a key reactive intermediate. PfTrpB7E6 provides an operationally simple and environmentally benign platform for the preparation of β-branched tryptophan building blocks.
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Affiliation(s)
- Christina E Boville
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, 1200 East California Boulevard, Pasadena, California, 91125, USA
| | - Remkes A Scheele
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, 1200 East California Boulevard, Pasadena, California, 91125, USA
| | - Philipp Koch
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, 1200 East California Boulevard, Pasadena, California, 91125, USA
| | - Sabine Brinkmann-Chen
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, 1200 East California Boulevard, Pasadena, California, 91125, USA
| | - Andrew R Buller
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI, 53706, USA
| | - Frances H Arnold
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, 1200 East California Boulevard, Pasadena, California, 91125, USA
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Boville CE, Scheele RA, Koch P, Brinkmann-Chen S, Buller AR, Arnold FH. Engineered Biosynthesis of β-Alkyl Tryptophan Analogues. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807998] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Christina E. Boville
- Division of Chemistry and Chemical Engineering 210-41; California Institute of Technology; 1200 East California Boulevard Pasadena California 91125 USA
| | - Remkes A. Scheele
- Division of Chemistry and Chemical Engineering 210-41; California Institute of Technology; 1200 East California Boulevard Pasadena California 91125 USA
| | - Philipp Koch
- Division of Chemistry and Chemical Engineering 210-41; California Institute of Technology; 1200 East California Boulevard Pasadena California 91125 USA
| | - Sabine Brinkmann-Chen
- Division of Chemistry and Chemical Engineering 210-41; California Institute of Technology; 1200 East California Boulevard Pasadena California 91125 USA
| | - Andrew R. Buller
- Department of Chemistry; University of Wisconsin; 1101 University Avenue Madison WI 53706 USA
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering 210-41; California Institute of Technology; 1200 East California Boulevard Pasadena California 91125 USA
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Malcolm McIntosh Prize: R. J. Payne / Heinrich Wieland Prize: P. G. Schultz / FCI Dozentenpreis: T. Magauer / Bohlmann Lectureship: F. H. Arnold. Angew Chem Int Ed Engl 2016; 55:15469. [DOI: 10.1002/anie.201610316] [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]
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Malcolm-McIntosh-Preis: R. J. Payne / Heinrich-Wieland-Preis: P. G. Schultz / FCI-Dozentenpreis: T. Magauer / Bohlmann-Vorlesung: F. H. Arnold. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201610316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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