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Two Novel, Flavin-Dependent Halogenases from the Bacterial Consortia of Botryococcus braunii Catalyze Mono- and Dibromination. Catalysts 2021. [DOI: 10.3390/catal11040485] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Halogen substituents often lead to a profound effect on the biological activity of organic compounds. Flavin-dependent halogenases offer the possibility of regioselective halogenation at non-activated carbon atoms, while employing only halide salts and molecular oxygen. However, low enzyme activity, instability, and narrow substrate scope compromise the use of enzymatic halogenation as an economical and environmentally friendly process. To overcome these drawbacks, it is of tremendous interest to identify novel halogenases with high enzymatic activity and novel substrate scopes. Previously, Neubauer et al. developed a new hidden Markov model (pHMM) based on the PFAM tryptophan halogenase model, and identified 254 complete and partial putative flavin-dependent halogenase genes in eleven metagenomic data sets. In the present study, the pHMM was used to screen the bacterial associates of the Botryococcus braunii consortia (PRJEB21978), leading to the identification of several putative, flavin-dependent halogenase genes. Two of these new halogenase genes were found in one gene cluster of the Botryococcus braunii symbiont Sphingomonas sp. In vitro activity tests revealed that both heterologously expressed enzymes are active flavin-dependent halogenases able to halogenate indole and indole derivatives, as well as phenol derivatives, while preferring bromination over chlorination. Interestingly, SpH1 catalyses only monohalogenation, while SpH2 can catalyse both mono- and dihalogenation for some substrates.
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52
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Paul CE, Eggerichs D, Westphal AH, Tischler D, van Berkel WJH. Flavoprotein monooxygenases: Versatile biocatalysts. Biotechnol Adv 2021; 51:107712. [PMID: 33588053 DOI: 10.1016/j.biotechadv.2021.107712] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/27/2021] [Accepted: 02/06/2021] [Indexed: 12/13/2022]
Abstract
Flavoprotein monooxygenases (FPMOs) are single- or two-component enzymes that catalyze a diverse set of chemo-, regio- and enantioselective oxyfunctionalization reactions. In this review, we describe how FPMOs have evolved from model enzymes in mechanistic flavoprotein research to biotechnologically relevant catalysts that can be applied for the sustainable production of valuable chemicals. After a historical account of the development of the FPMO field, we explain the FPMO classification system, which is primarily based on protein structural properties and electron donor specificities. We then summarize the most appealing reactions catalyzed by each group with a focus on the different types of oxygenation chemistries. Wherever relevant, we report engineering strategies that have been used to improve the robustness and applicability of FPMOs.
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Affiliation(s)
- Caroline E Paul
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Daniel Eggerichs
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Adrie H Westphal
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Dirk Tischler
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Willem J H van Berkel
- Laboratory of Food Chemistry, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands.
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53
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Zallot R, Oberg N, Gerlt JA. Discovery of new enzymatic functions and metabolic pathways using genomic enzymology web tools. Curr Opin Biotechnol 2021; 69:77-90. [PMID: 33418450 DOI: 10.1016/j.copbio.2020.12.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/08/2020] [Accepted: 12/08/2020] [Indexed: 12/11/2022]
Abstract
The continuing expansion of protein and genome sequence databases is an opportunity to identify novel enzymes with biotechnological applications. Whether applied to enzymology, chemical biology, systems biology, and microbiology, database mining must be 'user-friendly' so that experimentalists can devise focused strategies to discover the in vitro activities and in vivo functions of uncharacterized enzymes. We developed a suite of genomic enzymology tools (https://efi.igb.illinois.edu/) to (1) generate sequence similarity networks (SSNs) for exploration of sequence-function space in protein families (EFI-EST) and (2) provide genome context for members of protein families (EFI-GNT). Integrated analysis of this complementary information allows to generate testable hypotheses about new functions. After a brief overview of EFI-EST and EFI-GNT, we describe applications that illustrate their use.
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Affiliation(s)
- Remi Zallot
- Carl. R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801, United States; Institute of Life Sciences, Swansea University Medical School, Swansea SA2 8PP, Wales, United Kingdom
| | - Nils Oberg
- Carl. R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801, United States
| | - John A Gerlt
- Carl. R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801, United States; Departments of Biochemistry and Chemistry, University of Illinois, Urbana, Illinois 61801, United States.
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54
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Slagman S, Fessner WD. Biocatalytic routes to anti-viral agents and their synthetic intermediates. Chem Soc Rev 2021; 50:1968-2009. [DOI: 10.1039/d0cs00763c] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
An assessment of biocatalytic strategies for the synthesis of anti-viral agents, offering guidelines for the development of sustainable production methods for a future COVID-19 remedy.
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Affiliation(s)
- Sjoerd Slagman
- Institut für Organische Chemie und Biochemie
- Technische Universität Darmstadt
- Germany
| | - Wolf-Dieter Fessner
- Institut für Organische Chemie und Biochemie
- Technische Universität Darmstadt
- Germany
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55
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Walter A, Storch G. Synthetic C6-Functionalized Aminoflavin Catalysts Enable Aerobic Bromination of Oxidation-Prone Substrates. Angew Chem Int Ed Engl 2020; 59:22505-22509. [PMID: 32790228 PMCID: PMC7756793 DOI: 10.1002/anie.202009657] [Citation(s) in RCA: 4] [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: 07/13/2020] [Revised: 08/08/2020] [Indexed: 12/19/2022]
Abstract
Flavoenzymes catalyze oxidations via hydroperoxide intermediates that result from activation of molecular O2. These reactions—such as hydroxylation and halogenation—depend on the additional catalytic activity of functional groups in the peptide environment of the flavin cofactor. We report synthetic flavin catalysts that contain C6 amino modifications at the isoalloxazine core and are consequently capable of mediating halogenations outside the peptide surrounding. The catalysts are competent in the selective, biomimetic bromination of oxidation‐prone phenols, flavones, and flavanones using a halide salt in combination with 2,6‐lutidinium oxalate as a flavin reductant under visible‐light irradiation. Our studies show the beneficial effect of stacked bisflavins as well as the catalytic activity of the flavin modifications. The designed flavin catalysts outperform isolated natural (−)‐riboflavin and contribute to the continuing search for tailored flavins in oxidation reactions.
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Affiliation(s)
- Alexandra Walter
- Department ChemieTechnische Universität MünchenLichtenbergstr. 485747GarchingGermany
| | - Golo Storch
- Department ChemieTechnische Universität MünchenLichtenbergstr. 485747GarchingGermany
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56
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Walter A, Storch G. Synthetische, C6‐funktionalisierte Aminoflavinkatalysatoren ermöglichen die aerobe Bromierung oxidationsanfälliger Substrate. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Alexandra Walter
- Department Chemie Technische Universität München Lichtenbergstr. 4 85747 Garching Deutschland
| | - Golo Storch
- Department Chemie Technische Universität München Lichtenbergstr. 4 85747 Garching Deutschland
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57
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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]
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58
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Neubauer PR, Pienkny S, Wessjohann L, Brandt W, Sewald N. Predicting the Substrate Scope of the Flavin-Dependent Halogenase BrvH. Chembiochem 2020; 21:3282-3288. [PMID: 32645255 PMCID: PMC7754283 DOI: 10.1002/cbic.202000444] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Indexed: 01/16/2023]
Abstract
The recently described flavin-dependent halogenase BrvH is able to catalyse both the bromination and chlorination of indole, but shows significantly higher bromination activity. BrvH was annotated as a tryptophan halogenase, but does not accept tryptophan as a substrate. Its native substrate remains unknown. A predictive model with the data available for BrvH was analysed. A training set of compounds tested in vitro was docked into the active site of a complete protein model based on the X-ray structure of BrvH. The atoms not resolved experimentally were modelled by using molecular mechanics force fields to obtain this protein model. Furthermore, docking poses for the substrates and known non-substrates have been calculated. Parameters like distance, partial charge and hybridization state were analysed to derive rules for predicting activity. With this model for activity of the BrvH, a virtual screening suggested several structures for potential substrates. Some of the compounds preselected in this way were tested in vitro, and several could be verified as convertible substrates. Based on information on halogenated natural products, a new dataset was created to specifically search for natural products as substrates/products, and virtual screening in this database yielded further hits.
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Affiliation(s)
- Pia R. Neubauer
- Organic and Bioorganic ChemistryDepartment of ChemistryBielefeld UniversityUniversitätsstrasse 2533501BielefeldGermany
| | - Silke Pienkny
- Leibniz Institute for Plant Biochemistry (IPB)Weinberg 306120HalleGermany
| | - Ludger Wessjohann
- Leibniz Institute for Plant Biochemistry (IPB)Weinberg 306120HalleGermany
| | - Wolfgang Brandt
- Leibniz Institute for Plant Biochemistry (IPB)Weinberg 306120HalleGermany
| | - Norbert Sewald
- Organic and Bioorganic ChemistryDepartment of ChemistryBielefeld UniversityUniversitätsstrasse 2533501BielefeldGermany
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59
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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
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60
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Minges H, Sewald N. Recent Advances in Synthetic Application and Engineering of Halogenases. ChemCatChem 2020. [DOI: 10.1002/cctc.202000531] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Hannah Minges
- Organic and Bioorganic Chemistry Department of Chemistry Bielefeld University Universitätsstraße 25 33501 Bielefeld Germany
| | - Norbert Sewald
- Organic and Bioorganic Chemistry Department of Chemistry Bielefeld University Universitätsstraße 25 33501 Bielefeld Germany
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61
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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.
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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
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62
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Santos R, Pinto D, Magalhães C, Silva A. Halogenated Flavones and Isoflavones: A State-of-Art on their Synthesis. Curr Org Synth 2020; 17:415-425. [PMID: 32473000 DOI: 10.2174/1570179417666200530213737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/04/2020] [Accepted: 05/04/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Flavonoid is a family of compounds present in the everyday consumption plants and fruits, contributing to a balanced diet and beneficial health effects. Being a scaffold for new drugs and presenting a wide range of applicability in the treatment of illnesses give them also an impact in medicine. Among the several types of flavonoids, flavone and isoflavone derivatives can be highlighted due to their prevalence in nature and biological activities already established. The standard synthetic route to obtain both halogenated flavones and isoflavones is through the use of already halogenated starting materials. Halogenation of the flavone and isoflavone core is less common because it is more complicated and involves some selectivity issues. OBJECTIVE Considering the importance of these flavonoids, we aim to present the main and more recent synthetic approaches towards their halogenation. METHODS The most prominent methodologies for the synthesis of halogenated flavones and isoflavones were reviewed. A careful survey of the reported data, using mainly the Scopus database and halogenation, flavones and isoflavones as keywords, was conducted. RESULTS Herein, a review is provided on the latest and more efficient halogenation protocols of flavones and isoflavones. Selective halogenation and the greener methodologies, including enzymatic and microbial halogenations, were reported. Nevertheless, some interesting protocols that allowed the synthesis of halogenated flavone and isoflavone derivatives in specific positions using halogenated reagents are also summarized. CONCLUSION Halogenated flavones and isoflavones have risen as noticeable structures; however, most of the time, the synthetic procedures involve toxic reagents and harsh reaction conditions. Therefore, the development of new synthetic routes with low environmental impact is desirable.
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Affiliation(s)
- Ricardo Santos
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Diana Pinto
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Clara Magalhães
- Department of Chemistry and CICECO, Universidade de Aveiro, Aveiro, Portugal
| | - Artur Silva
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, Aveiro, Portugal
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63
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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.
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Rodríguez Benítez A, Narayan ARH. Frontiers in Biocatalysis: Profiling Function across Sequence Space. ACS CENTRAL SCIENCE 2019; 5:1747-1749. [PMID: 31807675 PMCID: PMC6891852 DOI: 10.1021/acscentsci.9b01112] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
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