1
|
Lewis JC. Identifying and Engineering Flavin Dependent Halogenases for Selective Biocatalysis. Acc Chem Res 2024; 57:2067-2079. [PMID: 39038085 PMCID: PMC11309780 DOI: 10.1021/acs.accounts.4c00172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
ConspectusOrganohalogen compounds are extensively used as building blocks, intermediates, pharmaceuticals, and agrochemicals due to their unique chemical and biological properties. Installing halogen substituents, however, frequently requires functionalized starting materials and multistep functional group interconversion. Several classes of halogenases evolved in nature to enable halogenation of a different classes of substrates; for example, site-selective halogenation of electron rich aromatic compounds is catalyzed by flavin-dependent halogenases (FDHs). Mechanistic studies have shown that these enzymes use FADH2 to reduce O2 to water with concomitant oxidation of X- to HOX (X = Cl, Br, I). This species travels through a tunnel within the enzyme to access the FDH active site. Here, it is believed to interact with an active site lysine proximal to bound substrate, enabling electrophilic halogenation with selectivity imparted via molecular recognition, rather than directing groups or strong electronic activation.The unique selectivity of FDHs led to several early biocatalysis efforts, preparative halogenation was rare, and the hallmark catalyst-controlled selectivity of FDHs did not translate to non-native substrates. FDH engineering was limited to site-directed mutagenesis, which resulted in modest changes in site-selectivity or substrate preference. To address these limitations, we optimized expression conditions for the FDH RebH and its cognate flavin reductase (FRed), RebF. We then showed that RebH could be used for preparative halogenation of non-native substrates with catalyst-controlled selectivity. We reported the first examples in which the stability, substrate scope, and site selectivity of a FDH were improved to synthetically useful levels via directed evolution. X-ray crystal structures of evolved FDHs and reversion mutations showed that random mutations throughout the RebH structure were critical to achieving high levels of activity and selectivity on diverse aromatic substrates, and these data were used in combination with molecular dynamics simulations to develop predictive model for FDH selectivity. Finally, we used family wide genome mining to identify a diverse set of FDHs with novel substrate scope and complementary regioselectivity on large, three-dimensionally complex compounds.The diversity of our evolved and mined FDHs allowed us to pursue synthetic applications beyond simple aromatic halogenation. For example, we established that FDHs catalyze enantioselective reactions involving desymmetrization, atroposelective halogenation, and halocyclization. These results highlight the ability of FDH active sites to tolerate different substrate topologies. This utility was further expanded by our recent studies on the single component FDH/FRed, AetF. While we were initially drawn to AetF because it does not require a separate FRed, we found that it halogenates substrates that are not halogenated efficiently or at all by other FDHs and provides high enantioselectivity for reactions that could only be achieved using RebH variants after extensive mutagenesis. Perhaps most notably, AetF catalyzes site-selective aromatic iodination and enantioselective iodoetherification. Together, these studies highlight the origins of FDH engineering, the utility and limitations of the enzymes developed to date, and the promise of FDHs for an ever-expanding range of biocatalytic halogenation reactions.
Collapse
Affiliation(s)
- Jared C Lewis
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Montua N, Sewald N. Extended Biocatalytic Halogenation Cascades Involving a Single-Polypeptide Regeneration System for Diffusible FADH 2. Chembiochem 2023; 24:e202300478. [PMID: 37549375 DOI: 10.1002/cbic.202300478] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/07/2023] [Accepted: 08/07/2023] [Indexed: 08/09/2023]
Abstract
Flavin-dependent halogenases have attracted increasing interest for aryl halogenation at unactivated C-H positions because they are characterised by high regioselectivity, while requiring only FADH2 , halide salts, and O2 . Their use in combined crosslinked enzyme aggregates (combiCLEAs) together with an NADH-dependent flavin reductase and an NADH-regeneration system for the preparative halogenation of tryptophan and indole derivatives has been previously described. However, multiple cultivations and protein purification steps are necessary for their production. We present a bifunctional regeneration enzyme for two-step catalytic flavin regeneration using phosphite as an inexpensive sacrificial substrate. This fusion protein proved amenable to co-expression with various flavin-dependent Trp-halogenases and enables carrier-free immobilisation as combiCLEAs from a single cultivation for protein production and the preparative synthesis of halotryptophan. The scalability of this system was demonstrated by fed-batch fermentation in bench-top bioreactors on a 2.5 L scale. Furthermore, the inclusion of a 6-halotryptophan-specific dioxygenase into the co-expression strain further converts the halogenation product to the kynurenine derivative. This reaction cascade enables the one-pot synthesis of l-4-Cl-kynurenine and its brominated analogue on a preparative scale.
Collapse
Affiliation(s)
- Nicolai Montua
- 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
| |
Collapse
|
4
|
Ashaduzzaman M, Lingkon K, De Silva AJ, Bellizzi JJ. Crystallographic and thermodynamic evidence of negative cooperativity of flavin and tryptophan binding in the flavin-dependent halogenases AbeH and BorH. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.22.554356. [PMID: 37662313 PMCID: PMC10473636 DOI: 10.1101/2023.08.22.554356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The flavin-dependent halogenase AbeH produces 5-chlorotryptophan in the biosynthetic pathway of the chlorinated bisindole alkaloid BE-54017. We report that in vitro, AbeH (assisted by the flavin reductase AbeF) can chlorinate and brominate tryptophan as well as other indole derivatives and substrates with phenyl and quinoline groups. We solved the X-ray crystal structures of AbeH alone and complexed with FAD, as well as crystal structures of the tryptophan-6-halogenase BorH alone, in complex with 6-chlorotryptophan, and in complex with FAD and tryptophan. Partitioning of FAD and tryptophan into different chains of BorH and failure to incorporate tryptophan into AbeH/FAD crystals suggested that flavin and tryptophan binding are negatively coupled in both proteins. ITC and fluorescence quenching experiments confirmed the ability of both AbeH and BorH to form binary complexes with FAD or tryptophan and the inability of tryptophan to bind to AbeH/FAD or BorH/FAD complexes. FAD could not bind to BorH/tryptophan complexes, but FAD appears to displace tryptophan from AbeH/tryptophan complexes in an endothermic entropically-driven process.
Collapse
Affiliation(s)
- Md Ashaduzzaman
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo OH 43606
| | - Kazi Lingkon
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo OH 43606
| | - Aravinda J De Silva
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo OH 43606
| | - John J Bellizzi
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo OH 43606
| |
Collapse
|
5
|
Andorfer MC, Evans D, Yang S, He CQ, Girlich AM, Vergara-Coll J, Sukumar N, Houk KN, Lewis JC. Analysis of Laboratory-Evolved Flavin-Dependent Halogenases Affords a Computational Model for Predicting Halogenase Site Selectivity. CHEM CATALYSIS 2022; 2:2658-2674. [PMID: 36569427 PMCID: PMC9784200 DOI: 10.1016/j.checat.2022.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Flavin-dependent halogenases (FDHs) catalyze selective halogenation of electron-rich aromatic compounds without the need for harsh oxidants required by conventional oxidative halogenation reactions. Predictive models for halogenase site selectivity could greatly improve their utility for chemical synthesis. Toward this end, we analyzed the structures and selectivity of three halogenase variants evolved to halogenate tryptamine with orthogonal selectivity. Crystal structures and reversion mutations revealed key residues involved in altering halogenase selectivity. Density functional theory calculations and molecular dynamics simulations are both consistent with hypohalous acid as the active halogenating species in FDH catalysis. This model was used to accurately predict the site selectivity of halogenase variants toward different synthetic substrates, providing a valuable tool for implementing halogenases in biocatalysis efforts.
Collapse
Affiliation(s)
- Mary C. Andorfer
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
- Present address: Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- These authors contributed equally
| | - Declan Evans
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- These authors contributed equally
| | - Song Yang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Present address: Merck Research Laboratories, South San Francisco, CA, USA
| | - Cyndi Qixin He
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Present address: Merck Research Laboratories, Kenilworth, NJ, USA
| | - Anna M. Girlich
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | | | - Narayanasami Sukumar
- NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Building 436E, Argonne, IL 60439, USA
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jared C. Lewis
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
- Lead contact
| |
Collapse
|
6
|
Mechanism-guided tunnel engineering to increase the efficiency of a flavin-dependent halogenase. Nat Catal 2022. [DOI: 10.1038/s41929-022-00800-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
7
|
Crowe C, Molyneux S, Sharma SV, Zhang Y, Gkotsi DS, Connaris H, Goss RJM. Halogenases: a palette of emerging opportunities for synthetic biology-synthetic chemistry and C-H functionalisation. Chem Soc Rev 2021; 50:9443-9481. [PMID: 34368824 PMCID: PMC8407142 DOI: 10.1039/d0cs01551b] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Indexed: 12/14/2022]
Abstract
The enzymatic generation of carbon-halogen bonds is a powerful strategy used by both nature and synthetic chemists to tune the bioactivity, bioavailability and reactivity of compounds, opening up the opportunity for selective C-H functionalisation. Genes encoding halogenase enzymes have recently been shown to transcend all kingdoms of life. These enzymes install halogen atoms into aromatic and less activated aliphatic substrates, achieving selectivities that are often challenging to accomplish using synthetic methodologies. Significant advances in both halogenase discovery and engineering have provided a toolbox of enzymes, enabling the ready use of these catalysts in biotransformations, synthetic biology, and in combination with chemical catalysis to enable late stage C-H functionalisation. With a focus on substrate scope, this review outlines the mechanisms employed by the major classes of halogenases, while in parallel, it highlights key advances in the utilisation of the combination of enzymatic halogenation and chemical catalysis for C-H activation and diversification.
Collapse
Affiliation(s)
- Charlotte Crowe
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Samuel Molyneux
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Sunil V. Sharma
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Ying Zhang
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Danai S. Gkotsi
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Helen Connaris
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Rebecca J. M. Goss
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
De Silva AJ, Sehgal R, Kim J, Bellizzi JJ. Steady-state kinetic analysis of halogenase-supporting flavin reductases BorF and AbeF reveals different kinetic mechanisms. Arch Biochem Biophys 2021; 704:108874. [PMID: 33862020 DOI: 10.1016/j.abb.2021.108874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/03/2021] [Accepted: 04/05/2021] [Indexed: 11/28/2022]
Abstract
The short-chain flavin reductases BorF and AbeF reduce FAD to FADH2, which is then used by flavin-dependent halogenases (BorH and AbeH respectively) to regioselectively chlorinate tryptophan in the biosynthesis of indolotryptoline natural products. Recombinant AbeF and BorF were overexpressed and purified as homodimers from E. coli, and copurified with substoichiometric amounts of FAD, which could be easily removed. AbeF and BorF can reduce FAD, FMN, and riboflavin in vitro and are selective for NADH over NADPH. Initial velocity studies in the presence and absence of inhibitors showed that BorF proceeds by a sequential ordered kinetic mechanism in which FAD binds first, while AbeF follows a random-ordered sequence of substrate binding. Fluorescence quenching experiments verified that NADH does not bind BorF in the absence of FAD, and that both AbeF and BorF bind FAD with higher affinity than FADH2. pH-rate profiles of BorF and AbeF were bell-shaped with maximum kcat at pH 7.5, and site-directed mutagenesis of BorF implicated His160 and Arg38 as contributing to the catalytic activity and the pH dependence.
Collapse
Affiliation(s)
- Aravinda J De Silva
- Department of Chemistry and Biochemistry, College of Natural Sciences and Mathematics, The University of Toledo Toledo, OH, 43606, USA
| | - Rippa Sehgal
- Department of Chemistry and Biochemistry, College of Natural Sciences and Mathematics, The University of Toledo Toledo, OH, 43606, USA
| | - Jennifer Kim
- Department of Chemistry and Biochemistry, College of Natural Sciences and Mathematics, The University of Toledo Toledo, OH, 43606, USA
| | - John J Bellizzi
- Department of Chemistry and Biochemistry, College of Natural Sciences and Mathematics, The University of Toledo Toledo, OH, 43606, USA.
| |
Collapse
|
11
|
Halogenases: structures and functions. Curr Opin Struct Biol 2020; 65:51-60. [DOI: 10.1016/j.sbi.2020.05.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/13/2020] [Accepted: 05/17/2020] [Indexed: 11/23/2022]
|
12
|
Bradley SA, Zhang J, Jensen MK. Deploying Microbial Synthesis for Halogenating and Diversifying Medicinal Alkaloid Scaffolds. Front Bioeng Biotechnol 2020; 8:594126. [PMID: 33195162 PMCID: PMC7644825 DOI: 10.3389/fbioe.2020.594126] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 10/02/2020] [Indexed: 11/13/2022] Open
Abstract
Plants produce some of the most potent therapeutics and have been used for thousands of years to treat human diseases. Today, many medicinal natural products are still extracted from source plants at scale as their complexity precludes total synthesis from bulk chemicals. However, extraction from plants can be an unreliable and low-yielding source for human therapeutics, making the supply chain for some of these life-saving medicines expensive and unstable. There has therefore been significant interest in refactoring these plant pathways in genetically tractable microbes, which grow more reliably and where the plant pathways can be more easily engineered to improve the titer, rate and yield of medicinal natural products. In addition, refactoring plant biosynthetic pathways in microbes also offers the possibility to explore new-to-nature chemistry more systematically, and thereby help expand the chemical space that can be probed for drugs as well as enable the study of pharmacological properties of such new-to-nature chemistry. This perspective will review the recent progress toward heterologous production of plant medicinal alkaloids in microbial systems. In particular, we focus on the refactoring of halogenated alkaloids in yeast, which has created an unprecedented opportunity for biosynthesis of previously inaccessible new-to-nature variants of the natural alkaloid scaffolds.
Collapse
Affiliation(s)
| | | | - Michael K. Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| |
Collapse
|
13
|
Menon BRK, Richmond D, Menon N. Halogenases for biosynthetic pathway engineering: Toward new routes to naturals and non-naturals. CATALYSIS REVIEWS-SCIENCE AND ENGINEERING 2020. [DOI: 10.1080/01614940.2020.1823788] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Binuraj R. K. Menon
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Coventry, UK
| | - Daniel Richmond
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Coventry, UK
| | - Navya Menon
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Coventry, UK
| |
Collapse
|
14
|
Abstract
Overall, this review highlights the structures, mechanisms and applications of flavin-dependent halogenases (FDHs) for future development of FDHs as potential biocatalysts. FDHs catalyze incorporation of halogen atoms into a broad range of substrates. The reactions involved in the production of various halogenated natural products which are important drugs. Typical substrates for FDHs include indole, pyrrole, phenolic and aliphatic compounds. In addition to organic substrates, all FDHs utilize reduced FAD (FADH-), oxygen and halides as co-substrates. Structural studies reveal that FDHs all have similar FAD binding sites. However, FDHs have variations between the different isotypes including different recognition residues for substrate binding and some unique loop structures and conformations. These different structural differences suggest that variations in reaction catalysis exist. However, limited knowledge of the reaction mechanisms of FDHs is currently available. Various biocatalytic applications of FDHs have been explored. Further investigation of the catalytic reactions of FDHs is essential for improving enzyme engineering work to enable FDHs catalysis of challenging reactions.
Collapse
Affiliation(s)
- Aisaraphon Phintha
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Kridsadakorn Prakinee
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong, Thailand.
| |
Collapse
|
15
|
Widmann C, Ismail M, Sewald N, Niemann HH. Structure of apo flavin-dependent halogenase Xcc4156 hints at a reason for cofactor-soaking difficulties. Acta Crystallogr D Struct Biol 2020; 76:687-697. [PMID: 32627741 PMCID: PMC7336383 DOI: 10.1107/s2059798320007731] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 06/05/2020] [Indexed: 01/18/2023] Open
Abstract
Flavin-dependent halogenases regioselectively introduce halide substituents into electron-rich substrates under mild reaction conditions. For the enzyme Xcc4156 from Xanthomonas campestris, the structure of a complex with the cofactor flavin adenine dinucleotide (FAD) and a bromide ion would be of particular interest as this enzyme exclusively brominates model substrates in vitro. Apo Xcc4156 crystals diffracted to 1.6 Å resolution. The structure revealed an open substrate-binding site lacking the loop regions that close off the active site and contribute to substrate binding in tryptophan halogenases. Therefore, Xcc4156 might accept larger substrates, possibly even peptides. Soaking of apo Xcc4156 crystals with FAD led to crumbling of the intergrown crystals. Around half of the crystals soaked with FAD did not diffract, while in the others there was no electron density for FAD. The FAD-binding loop, which changes its conformation between the apo and the FAD-bound form in related enzymes, is involved in a crystal contact in the apo Xcc4156 crystals. The conformational change that is predicted to occur upon FAD binding would disrupt this crystal contact, providing a likely explanation for the destruction of the apo crystals in the presence of FAD. Soaking with only bromide did not result in bromide bound to the catalytic halide-binding site. Simultaneous soaking with FAD and bromide damaged the crystals more severely than soaking with only FAD. Together, these latter two observations suggest that FAD and bromide bind to Xcc4156 with positive cooperativity. Thus, apo Xcc4156 crystals provide functional insight into FAD and bromide binding, even though neither the cofactor nor the halide is visible in the structure.
Collapse
Affiliation(s)
- Christiane Widmann
- Structural Biochemistry (BCIV), Department of Chemistry, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
| | - Mohamed Ismail
- Organic and Bioorganic Chemistry (OC III), Department of Chemistry, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
| | - Norbert Sewald
- Organic and Bioorganic Chemistry (OC III), Department of Chemistry, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
| | - Hartmut H. Niemann
- Structural Biochemistry (BCIV), Department of Chemistry, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
| |
Collapse
|
16
|
Lee J, Kim J, Kim H, Kim EJ, Jeong HJ, Choi KY, Kim BG. Characterization of a Tryptophan 6-Halogenase from Streptomyces albus and Its Regioselectivity Determinants. Chembiochem 2020; 21:1446-1452. [PMID: 31916339 DOI: 10.1002/cbic.201900723] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Indexed: 11/08/2022]
Abstract
Tryptophan halogenases are found in diverse organisms and catalyze regiospecific halogenation. They play an important role in the biosynthesis of halogenated indole alkaloids, which are biologically active and of therapeutic importance. Here, a tryptophan 6-halogenase (SatH) from Streptomyces albus was characterized by using a whole-cell reaction system in Escherichia coli. SatH showed substrate specificity for chloride and bromide ions, leading to regiospecific halogenation at the C6-position of l-tryptophan. In addition, SatH exhibited higher performance in bromination than that of previously reported tryptophan halogenases in the whole-cell reaction system. Through structure-based protein mutagenesis, it has been revealed that two consecutive residues, A78/V79 in SatH and G77/I78 in PyrH, are key determinants in the regioselectivity difference between tryptophan 6- and 5-halogenases. Substituting the AV with GI residues switched the regioselectivity of SatH by moving the orientation of tryptophan. These data contribute to an understanding of the key residues that determine the regioselectivity of tryptophan halogenases.
Collapse
Affiliation(s)
- Jeongchan Lee
- School of Chemical and Biological Engineering, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea.,Institute of Molecular Biology and Genetics, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Joonwon Kim
- Institute of Molecular Biology and Genetics, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea.,Institute of Engineering Research, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Hyun Kim
- School of Chemical and Biological Engineering, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea.,Institute of Molecular Biology and Genetics, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Eun-Jung Kim
- Institute of Molecular Biology and Genetics, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Hee-Jin Jeong
- Department of Biological and Chemical Engineering, Hongik University, Sejong-ro 2639, Jochiwon-eup, Sejong, 30016, Republic of Korea
| | - Kwon-Young Choi
- Department of Environmental Engineering, Ajou University, World cup-ro 206, Yeongtong-gu, Suwon, 16499, Republic of Korea
| | - Byung-Gee Kim
- School of Chemical and Biological Engineering, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea.,Institute of Molecular Biology and Genetics, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea.,Institute of Engineering Research, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea.,Institute of Bioengineering in Bio-Max, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea.,Interdisciplinary Program of Bioengineering, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea
| |
Collapse
|
17
|
Recent Advances in Flavin-Dependent Halogenase Biocatalysis: Sourcing, Engineering, and Application. Catalysts 2019. [DOI: 10.3390/catal9121030] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The introduction of a halogen atom into a small molecule can effectively modulate its properties, yielding bioactive substances of agrochemical and pharmaceutical interest. Consequently, the development of selective halogenation strategies is of high technological value. Besides chemical methodologies, enzymatic halogenations have received increased interest as they allow the selective installation of halogen atoms in molecular scaffolds of varying complexity under mild reaction conditions. Today, a comprehensive library of aromatic halogenases exists, and enzyme as well as reaction engineering approaches are being explored to broaden this enzyme family’s biocatalytic application range. In this review, we highlight recent developments in the sourcing, engineering, and application of flavin-dependent halogenases with a special focus on chemoenzymatic and coupled biosynthetic approaches.
Collapse
|