1
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Motter J, Benckendorff CMM, Westarp S, Sunde-Brown P, Neubauer P, Kurreck A, Miller GJ. Purine nucleoside antibiotics: recent synthetic advances harnessing chemistry and biology. Nat Prod Rep 2024; 41:873-884. [PMID: 38197414 PMCID: PMC11188666 DOI: 10.1039/d3np00051f] [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] [Received: 10/12/2023] [Indexed: 01/11/2024]
Abstract
Covering: 2019 to 2023Nucleoside analogues represent one of the most important classes of small molecule pharmaceuticals and their therapeutic development is successfully established within oncology and for the treatment of viral infections. However, there are currently no nucleoside analogues in clinical use for the management of bacterial infections. Despite this, a significant number of clinically recognised nucleoside analogues are known to possess some antibiotic activity, thereby establishing a potential source for new therapeutic discovery in this area. Furthermore, given the rise in antibiotic resistance, the discovery of new clinical candidates remains an urgent global priority and natural product-derived nucleoside analogues may also present a rich source of discovery space for new modalities. This Highlight, covering work published from 2019 to 2023, presents a current perspective surrounding the synthesis of natural purine nucleoside antibiotics. By amalgamating recent efforts from synthetic chemistry with advances in biosynthetic understanding and the use of recombinant enzymes, prospects towards different structural classes of purines are detailed.
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Affiliation(s)
- Jonas Motter
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstraße 76, D-13355, Berlin, Germany
| | - Caecilie M M Benckendorff
- School of Chemical and Physical Sciences and Centre for Glycoscience, Keele University, Keele, Staffordshire, ST5 5BG, UK.
| | - Sarah Westarp
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstraße 76, D-13355, Berlin, Germany
- BioNukleo GmbH, Ackerstraße 76, 13355 Berlin, Germany.
| | - Peter Sunde-Brown
- School of Chemical and Physical Sciences and Centre for Glycoscience, Keele University, Keele, Staffordshire, ST5 5BG, UK.
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstraße 76, D-13355, Berlin, Germany
| | - Anke Kurreck
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstraße 76, D-13355, Berlin, Germany
- BioNukleo GmbH, Ackerstraße 76, 13355 Berlin, Germany.
| | - Gavin J Miller
- School of Chemical and Physical Sciences and Centre for Glycoscience, Keele University, Keele, Staffordshire, ST5 5BG, UK.
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2
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Ni J, Zhuang J, Shi Y, Chiang YC, Cheng GJ. Discovery and substrate specificity engineering of nucleotide halogenases. Nat Commun 2024; 15:5254. [PMID: 38898020 PMCID: PMC11186838 DOI: 10.1038/s41467-024-49147-7] [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: 09/23/2023] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
C2'-halogenation has been recognized as an essential modification to enhance the drug-like properties of nucleotide analogs. The direct C2'-halogenation of the nucleotide 2'-deoxyadenosine-5'-monophosphate (dAMP) has recently been achieved using the Fe(II)/α-ketoglutarate-dependent nucleotide halogenase AdaV. However, the limited substrate scope of this enzyme hampers its broader applications. In this study, we report two halogenases capable of halogenating 2'-deoxyguanosine monophosphate (dGMP), thereby expanding the family of nucleotide halogenases. Computational studies reveal that nucleotide specificity is regulated by the binding pose of the phosphate group. Based on these findings, we successfully engineered the substrate specificity of these halogenases by mutating second-sphere residues. This work expands the toolbox of nucleotide halogenases and provides insights into the regulation mechanism of nucleotide specificity.
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Affiliation(s)
- Jie Ni
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, 518172, Guangdong, China
| | - Jingyuan Zhuang
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, 518172, Guangdong, China
| | - Yiming Shi
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, 518172, Guangdong, China
| | - Ying-Chih Chiang
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, 518172, Guangdong, China
| | - Gui-Juan Cheng
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, 518172, Guangdong, China.
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3
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Kumar R, Ahsan F, Awasthi A, Swart M, Draksharapu A. Generation of Ru(III)-hypochlorite with resemblance to the heme-dependent haloperoxidase enzyme. Dalton Trans 2023; 52:12552-12559. [PMID: 37609762 DOI: 10.1039/d3dt02028b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The reaction of [(Me/BnTPEN)RuII(NCCH3)]2+ (BnTPEN = N1-benzyl-N1,N2,N2-tris(pyridine-2-ylmethyl)ethane-1,2-diamine and MeTPEN = N1-methyl-N1,N2,N2-tris(pyridine-2-ylmethyl)ethane-1,2-diamine) with mCPBA in the presence of chloride ions in CH3CN : H2O generated a novel (Me/BnTPEN)RuIII-OCl species at room temperature. This hypochlorite adduct could also be obtained by the direct reaction of NaOCl and HClO4 with (L)RuII complexes. The current study mimics the synthesis of a metal hypochlorite adduct in a similar fashion as in the heme-dependent haloperoxidase enzyme. As an electrophilic oxidant, the ruthenium hypochlorite adduct catalyzes hydrogen atom abstraction reactions of phenols and their derivatives.
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Affiliation(s)
- Rakesh Kumar
- Southern Laboratories - 208A, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, India.
| | - Faiza Ahsan
- IQCC & Departament de Química, Universitat de Girona, 17003 Girona, Spain
| | - Ayushi Awasthi
- Southern Laboratories - 208A, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, India.
| | - Marcel Swart
- IQCC & Departament de Química, Universitat de Girona, 17003 Girona, Spain
- ICREA, 08010, Barcelona, Spain.
| | - Apparao Draksharapu
- Southern Laboratories - 208A, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, India.
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4
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Nanjo T, Matsumoto A, Oshita T, Takemoto Y. Synthesis of Chlorinated Oligopeptides via γ- and δ-Selective Hydrogen Atom Transfer Enabled by the N-Chloropeptide Strategy. J Am Chem Soc 2023; 145:19067-19075. [PMID: 37594470 DOI: 10.1021/jacs.3c06931] [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: 08/19/2023]
Abstract
The introduction of a chlorine atom could potentially endow peptide derivatives with notable bioactivity and applicability. However, despite considerable recent progress in C(sp3)-H functionalization chemistry, a general method for the site-selective chlorination of inert aliphatic C-H bonds in peptides still remains elusive. Herein, we report a site-selective C(sp3)-H chlorination of oligopeptides based on an N-chloropeptide strategy. N-chloropeptides, which are easily prepared from the corresponding native oligopeptides, are smoothly degraded in the presence of an appropriate copper catalyst, and a subsequent 1,5-hydrogen atom transfer affords γ- or δ-chlorinated peptides in excellent yield. A wide variety of amino acid residues can thus be site-selectively chlorinated in a predictable manner. This method hence enables the efficient synthesis of otherwise less accessible, chlorine-containing peptide fragments of natural peptides. We moreover demonstrate here the successful estimation of the stereochemistry of the chlorinated carbon atom in aquimarin A. Furthermore, we reveal that side-chain-chlorinated peptides can serve as highly useful substructures with a fine balance between stability and reactivity, which renders them promising targets for synthetic and medicinal applications.
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Affiliation(s)
- Takeshi Nanjo
- Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - Ayaka Matsumoto
- Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takuma Oshita
- Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yoshiji Takemoto
- Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
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5
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Mao Y, Zhang W, Fu Z, Liu Y, Chen L, Lian X, Zhuo D, Wu J, Zheng M, Liao C. Versatile Biocatalytic C(sp 3 )-H Oxyfunctionalization for the Site- Selective and Stereodivergent Synthesis of α- and β-Hydroxy Acids. Angew Chem Int Ed Engl 2023; 62:e202305250. [PMID: 37340543 DOI: 10.1002/anie.202305250] [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: 04/14/2023] [Revised: 06/03/2023] [Accepted: 06/20/2023] [Indexed: 06/22/2023]
Abstract
C(sp3 )-H oxyfunctionalization, the insertion of an O-atom into C(sp3 )-H bonds, streamlines the synthesis of complex molecules from easily accessible precursors and represents one of the most challenging tasks in organic chemistry with regard to site and stereoselectivity. Biocatalytic C(sp3 )-H oxyfunctionalization has the potential to overcome limitations inherent to small-molecule-mediated approaches by delivering catalyst-controlled selectivity. Through enzyme repurposing and activity profiling of natural variants, we have developed a subfamily of α-ketoglutarate-dependent iron dioxygenases that catalyze the site- and stereodivergent oxyfunctionalization of secondary and tertiary C(sp3 )-H bonds, providing concise synthetic routes towards four types of 92 α- and β-hydroxy acids with high efficiency and selectivity. This method provides a biocatalytic approach for the production of valuable but synthetically challenging chiral hydroxy acid building blocks.
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Affiliation(s)
- Yingle Mao
- Chemical Biology Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Science, 201203, Shanghai, China
| | - Weijie Zhang
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, 510006, Guangzhou, China
| | - Zunyun Fu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
| | - Yanqiong Liu
- Chemical Biology Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Science, 201203, Shanghai, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 210023, Nanjing, China
| | - Lin Chen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
| | - Xin Lian
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, 510006, Guangzhou, China
| | - Dan Zhuo
- Chemical Biology Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Science, 201203, Shanghai, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 210023, Nanjing, China
| | - Jiewei Wu
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, 510006, Guangzhou, China
| | - Mingyue Zheng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 210023, Nanjing, China
| | - Cangsong Liao
- Chemical Biology Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Science, 201203, Shanghai, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 210023, Nanjing, China
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6
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Gomez CA, Mondal D, Du Q, Chan N, Lewis JC. Directed Evolution of an Iron(II)- and α-Ketoglutarate-Dependent Dioxygenase for Site-Selective Azidation of Unactivated Aliphatic C-H Bonds. Angew Chem Int Ed Engl 2023; 62:e202301370. [PMID: 36757808 PMCID: PMC10050089 DOI: 10.1002/anie.202301370] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/10/2023]
Abstract
FeII - and α-ketoglutarate-dependent halogenases and oxygenases can catalyze site-selective functionalization of C-H bonds via a variety of C-X bond forming reactions, but achieving high chemoselectivity for functionalization using non-native functional groups remains rare. The current study shows that directed evolution can be used to engineer variants of the dioxygenase SadX that address this challenge. Site-selective azidation of succinylated amino acids and a succinylated amine was achieved as a result of mutations throughout the SadX structure. The installed azide group was reduced to a primary amine, and the succinyl group required for azidation was enzymatically cleaved to provide the corresponding amine. These results provide a promising starting point for evolving additional SadX variants with activity on structurally distinct substrates and for enabling enzymatic C-H functionalization with other non-native functional groups.
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Affiliation(s)
- Christian A Gomez
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Dibyendu Mondal
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
- Kalsec Inc., 3713W. Main St., Kalamazoo, MI 49006, USA
| | - Qian Du
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Natalie Chan
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Jared C Lewis
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
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7
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Zwick CR, Renata H. Overview of Amino Acid Modifications by Iron- and α-Ketoglutarate-Dependent Enzymes. ACS Catal 2023. [DOI: 10.1021/acscatal.3c00424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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8
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Kastner DW, Nandy A, Mehmood R, Kulik HJ. Mechanistic Insights into Substrate Positioning That Distinguish Non-heme Fe(II)/α-Ketoglutarate-Dependent Halogenases and Hydroxylases. ACS Catal 2023. [DOI: 10.1021/acscatal.2c06241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- David W. Kastner
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Aditya Nandy
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Rimsha Mehmood
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J. Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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9
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Papadopoulou A, Meyer F, Buller RM. Engineering Fe(II)/α-Ketoglutarate-Dependent Halogenases and Desaturases. Biochemistry 2023; 62:229-240. [PMID: 35446547 DOI: 10.1021/acs.biochem.2c00115] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Fe(II)/α-ketoglutarate-dependent dioxygenases (α-KGDs) are widespread enzymes in aerobic biology and serve a remarkable array of biological functions, including roles in collagen biosynthesis, plant and animal development, transcriptional regulation, nucleic acid modification, and secondary metabolite biosynthesis. This functional diversity is reflected in the enzymes' catalytic flexibility as α-KGDs can catalyze an intriguing set of synthetically valuable reactions, such as hydroxylations, halogenations, and desaturations, capturing the interest of scientists across disciplines. Mechanistically, all α-KGDs are understood to follow a similar activation pathway to generate a substrate radical, yet how individual members of the enzyme family direct this key intermediate toward the different reaction outcomes remains elusive, triggering structural, computational, spectroscopic, kinetic, and enzyme engineering studies. In this Perspective, we will highlight how first enzyme and substrate engineering examples suggest that the chemical reaction pathway within α-KGDs can be intentionally tailored using rational design principles. We will delineate the structural and mechanistic investigations of the reprogrammed enzymes and how they begin to inform about the enzymes' structure-function relationships that determine chemoselectivity. Application of this knowledge in future enzyme and substrate engineering campaigns will lead to the development of powerful C-H activation catalysts for chemical synthesis.
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Affiliation(s)
- Athena Papadopoulou
- Competence Center for Biocatalysis, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
| | - Fabian Meyer
- Competence Center for Biocatalysis, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
| | - Rebecca M Buller
- Competence Center for Biocatalysis, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
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10
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Büchler J, Hegarty E, Schroer K, Snajdrova R, Turner NJ, Loiseleur O, Buller R, Le Chapelain C. A Collaborative Journey towards the Late‐Stage Functionalization of Added‐Value Chemicals Using Engineered Halogenases. Helv Chim Acta 2022. [DOI: 10.1002/hlca.202200128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Affiliation(s)
- Johannes Büchler
- Zurich University of Applied Sciences School of Life Sciences and Facility Management Institute of Chemistry and Biotechnology, CH- 8820 Wädenswil Switzerland
- Department of Chemistry The University of Manchester Manchester Institute of Biotechnology, UK- Manchester M1 7DN United Kingdom
| | - Eimear Hegarty
- Zurich University of Applied Sciences School of Life Sciences and Facility Management Institute of Chemistry and Biotechnology, CH- 8820 Wädenswil Switzerland
| | - Kirsten Schroer
- Novartis Institutes for BioMedical Research Global Discovery Chemistry, CH- 4056 Basel Switzerland
| | - Radka Snajdrova
- Novartis Institutes for BioMedical Research Global Discovery Chemistry, CH- 4056 Basel Switzerland
| | - Nicholas J. Turner
- Department of Chemistry The University of Manchester Manchester Institute of Biotechnology, UK- Manchester M1 7DN United Kingdom
| | - Olivier Loiseleur
- Syngenta Crop Protection AG Schaffhauserstr. 101 CH-4332 Stein Switzerland
| | - Rebecca Buller
- Zurich University of Applied Sciences School of Life Sciences and Facility Management Institute of Chemistry and Biotechnology, CH- 8820 Wädenswil Switzerland
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11
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Chan NH, Gomez CA, Vennelakanti V, Du Q, Kulik HJ, Lewis JC. Non-Native Anionic Ligand Binding and Reactivity in Engineered Variants of the Fe(II)- and α-Ketoglutarate-Dependent Oxygenase, SadA. Inorg Chem 2022; 61:14477-14485. [PMID: 36044713 PMCID: PMC9789792 DOI: 10.1021/acs.inorgchem.2c02872] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Mononuclear non-heme Fe(II)- and α-ketoglutarate-dependent oxygenases (FeDOs) catalyze a site-selective C-H hydroxylation. Variants of these enzymes in which a conserved Asp/Glu residue in the Fe(II)-binding facial triad is replaced by Ala/Gly can, in some cases, bind various anionic ligands and catalyze non-native chlorination and bromination reactions. In this study, we explore the binding of different anions to an FeDO facial triad variant, SadX, and the effects of that binding on HO• vs X• rebound. We establish not only that chloride and bromide enable non-native halogenation reactions but also that all anions investigated, including azide, cyanate, formate, and fluoride, significantly accelerate and influence the site selectivity of SadX hydroxylation catalysis. Azide and cyanate also lead to the formation of products resulting from N3•, NCO•, and OCN• rebound. While fluoride rebound is not observed, the rate acceleration provided by this ligand leads us to calculate barriers for HO• and F• rebound from a putative Fe(III)(OH)(F) intermediate. These calculations suggest that the lack of fluorination is due to the relative barriers of the HO• and F• rebound transition states rather than an inaccessible barrier for F• rebound. Together, these results improve our understanding of the FeDO facial triad variant tolerance of different anionic ligands, their ability to promote rebound involving these ligands, and inherent rebound preferences relative to HO• that will aid efforts to develop non-native catalysis using these enzymes.
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Affiliation(s)
- Natalie H. Chan
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Christian A. Gomez
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Vyshnavi Vennelakanti
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Qian Du
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Heather J. Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jared C. Lewis
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
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12
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Kumar R, Awasthi A, Gupta S, Eerlapally R, Draksharapu A. Spectroscopic characterization of a Ru(III)-OCl intermediate: a structural mimic of haloperoxidase enzymes. Dalton Trans 2022; 51:12848-12854. [PMID: 35968730 DOI: 10.1039/d2dt01947g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Haloperoxidase enzymes utilize metal hypohalite species to halogenate aliphatic and aromatic C-H bonds to C-X (X = Cl, Br, I) in nature. In this work, we report the synthesis and spectroscopic characterization of a unique RuIII-OCl species as a structural mimic of haloperoxidase enzymes. The reaction of [(BnTPEN)RuII(NCCH3)]2+ (BnTPEN = N1-benzyl-N1,N2,N2-tris(pyridine-2-ylmethyl)ethane-1,2-diamine) with hypochlorite in the presence of an acid in CH3CN : H2O mixtures generated a novel [(BnTPEN)RuIII-OCl]2+ species that persists for 4.5 h at room temperature. This new species was characterized by UV-vis absorption, EPR, and resonance Raman spectroscopic techniques, and ESI-MS. The RuIII-OCl species is capable of performing oxygen atom transfer and hydrogen atom abstraction to various organic substrates.
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Affiliation(s)
- Rakesh Kumar
- Southern Laboratories-208A, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, India.
| | - Ayushi Awasthi
- Southern Laboratories-208A, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, India.
| | - Sikha Gupta
- Southern Laboratories-208A, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, India.
| | - Raju Eerlapally
- Southern Laboratories-208A, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, India.
| | - Apparao Draksharapu
- Southern Laboratories-208A, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, India.
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13
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Zhu G, Yan W, Wang X, Cheng R, Naowarojna N, Wang K, Wang J, Song H, Wang Y, Liu H, Xia X, Costello CE, Liu X, Zhang L, Liu P. Dissecting the Mechanism of the Nonheme Iron Endoperoxidase FtmOx1 Using Substrate Analogues. JACS AU 2022; 2:1686-1698. [PMID: 35911443 PMCID: PMC9326825 DOI: 10.1021/jacsau.2c00248] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
FtmOx1 is a nonheme iron (NHFe) endoperoxidase, catalyzing three disparate reactions, endoperoxidation, alcohol dehydrogenation, and dealkylation, under in vitro conditions; the diversity complicates its mechanistic studies. In this study, we use two substrate analogues to simplify the FtmOx1-catalyzed reaction to either a dealkylation or an alcohol dehydrogenation reaction for structure-function relationship analysis to address two key FtmOx1 mechanistic questions: (1) Y224 flipping in the proposed COX-like model vs α-ketoglutarate (αKG) rotation proposed in the CarC-like mechanistic model and (2) the involvement of a Y224 radical (COX-like model) or a Y68 radical (CarC-like model) in FtmOx1-catalysis. When 13-oxo-fumitremorgin B (7) is used as the substrate, FtmOx1-catalysis changes from the endoperoxidation to a hydroxylation reaction and leads to dealkylation. In addition, consistent with the dealkylation side-reaction in the COX-like model prediction, the X-ray structure of the FtmOx1•CoII•αKG•7 ternary complex reveals a flip of Y224 to an alternative conformation relative to the FtmOx1•FeII•αKG binary complex. Verruculogen (2) was used as a second substrate analogue to study the alcohol dehydrogenation reaction to examine the involvement of the Y224 radical or Y68 radical in FtmOx1-catalysis, and again, the results from the verruculogen reaction are more consistent with the COX-like model.
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Affiliation(s)
- Guoliang Zhu
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Wupeng Yan
- School
of Life Sciences and Biotechnology, Shanghai
Jiao Tong University, Shanghai 200237, China
| | - Xinye Wang
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Ronghai Cheng
- Department
of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Nathchar Naowarojna
- Department
of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Kun Wang
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Jun Wang
- School
of Life Sciences and Biotechnology, Shanghai
Jiao Tong University, Shanghai 200237, China
| | - Heng Song
- College
of Chemistry and Molecular Sciences, Wuhan
University, Wuhan, Hubei Province 430072, China
| | - Yuyang Wang
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Hairong Liu
- Key
Biosensor Laboratory of Shandong Province, Biology Institute, Qilu University of Technology (Shandong Academy
of Sciences), Jinan, Shandong Province 250013, China
| | - Xuekui Xia
- Key
Biosensor Laboratory of Shandong Province, Biology Institute, Qilu University of Technology (Shandong Academy
of Sciences), Jinan, Shandong Province 250013, China
| | - Catherine E. Costello
- Department
of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Xueting Liu
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Lixin Zhang
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Pinghua Liu
- Department
of Chemistry, Boston University, Boston, Massachusetts 02215, United States
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14
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Gérard EF, Yadav V, Goldberg DP, de Visser SP. What Drives Radical Halogenation versus Hydroxylation in Mononuclear Nonheme Iron Complexes? A Combined Experimental and Computational Study. J Am Chem Soc 2022; 144:10752-10767. [PMID: 35537044 PMCID: PMC9228086 DOI: 10.1021/jacs.2c01375] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
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Nonheme iron halogenases
are unique enzymes in nature that selectively
activate an aliphatic C–H bond of a substrate to convert it
into C–X (X = Cl/Br, but not F/I). It is proposed that they
generate an FeIII(OH)(X) intermediate in their catalytic
cycle. The analogous FeIII(OH) intermediate in nonheme
iron hydroxylases transfers OH• to give alcohol
product, whereas the halogenases transfer X• to
the carbon radical substrate. There remains significant debate regarding
what factors control their remarkable selectivity of the halogenases.
The reactivity of the complexes FeIII(BNPAPh2O)(OH)(X) (X = Cl, Br) with a secondary carbon radical (R•) is described. It is found that X• transfer occurs
with a secondary carbon radical, as opposed to OH• transfer with tertiary radicals. Comprehensive computational studies
involving density functional theory were carried out to examine the
possible origins of this selectivity. The calculations reproduce the
experimental findings, which indicate that halogen transfer is not
observed for the tertiary radicals because of a nonproductive equilibrium
that results from the endergonic nature of these reactions, despite
a potentially lower reaction barrier for the halogenation pathway.
In contrast, halogen transfer is favored for secondary carbon radicals,
for which the halogenated product complex is thermodynamically more
stable than the reactant complex. These results are rationalized by
considering the relative strengths of the C–X bonds that are
formed for tertiary versus secondary carbon centers. The computational
analysis also shows that the reaction barrier for halogen transfer
is significantly dependent on secondary coordination sphere effects,
including steric and H-bonding interactions.
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Affiliation(s)
- Emilie F Gérard
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.,Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Vishal Yadav
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - David P Goldberg
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Sam P de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.,Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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15
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Wojdyla Z, Borowski T. Properties of the Reactants and Their Interactions within and with the Enzyme Binding Cavity Determine Reaction Selectivities. The Case of Fe(II)/2-Oxoglutarate Dependent Enzymes. Chemistry 2022; 28:e202104106. [PMID: 34986268 DOI: 10.1002/chem.202104106] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Indexed: 12/12/2022]
Abstract
Fe(II)/2-oxoglutarate dependent dioxygenases (ODDs) share a double stranded beta helix (DSBH) fold and utilise a common reactive intermediate, ferryl species, to catalyse oxidative transformations of substrates. Despite the structural similarities, ODDs accept a variety of substrates and facilitate a wide range of reactions, that is hydroxylations, desaturations, (oxa)cyclisations and ring rearrangements. In this review we present and discuss the factors contributing to the observed (regio)selectivities of ODDs. They span from inherent properties of the reactants, that is, substrate molecule and iron cofactor, to the interactions between the substrate and the enzyme's binding cavity; the latter can counterbalance the effect of the former. Based on results of both experimental and computational studies dedicated to ODDs, we also line out the properties of the reactants which promote reaction outcomes other than the "default" hydroxylation. It turns out that the reaction selectivity depends on a delicate balance of interactions between the components of the investigated system.
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Affiliation(s)
- Zuzanna Wojdyla
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Kraków, Niezapominajek 8, 30239 Krakow, Poland
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Kraków, Niezapominajek 8, 30239 Krakow, Poland
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16
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Biosynthesizing structurally diverse diols via a general route combining oxidative and reductive formations of OH-groups. Nat Commun 2022; 13:1595. [PMID: 35332143 PMCID: PMC8948231 DOI: 10.1038/s41467-022-29216-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 03/02/2022] [Indexed: 11/09/2022] Open
Abstract
Diols encompass important bulk and fine chemicals for the chemical, pharmaceutical and cosmetic industries. During the past decades, biological production of C3-C5 diols from renewable feedstocks has received great interest. Here, we elaborate a general principle for effectively synthesizing structurally diverse diols by expanding amino acid metabolism. Specifically, we propose to combine oxidative and reductive formations of hydroxyl groups from amino acids in a thermodynamically favorable order of four reactions catalyzed by amino acid hydroxylase, L-amino acid deaminase, α-keto acid decarboxylase and aldehyde reductase consecutively. The oxidative formation of hydroxyl group from an alkyl group is energetically more attractive than the reductive pathway, which is exclusively used in the synthetic pathways of diols reported so far. We demonstrate this general route for microbial production of branched-chain diols in E. coli. Ten C3-C5 diols are synthesized. Six of them, namely isopentyldiol (IPDO), 2-methyl-1,3-butanediol (2-M-1,3-BDO), 2-methyl-1,4-butanediol (2-M-1,4-BDO), 2-methyl-1,3-propanediol (MPO), 2-ethyl-1,3-propanediol (2-E-1,3-PDO), 1,4-pentanediol (1,4-PTD), have not been biologically synthesized before. This work opens up opportunities for synthesizing structurally diverse diols and triols, especially by genome mining, rational design or directed evolution of proper enzymes. Diols are important bulk and fine chemicals, but bioproduciton of branch-chain diols is hampered by the unknown biological route. Here, the authors report the expanding of amino acid metabolism for biosynthesis of branch-chain diols via a general route of combined oxidative and reductive formations of hydroxyl groups.
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17
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Büchler J, Malca SH, Patsch D, Voss M, Turner NJ, Bornscheuer UT, Allemann O, Le Chapelain C, Lumbroso A, Loiseleur O, Buller R. Algorithm-aided engineering of aliphatic halogenase WelO5* for the asymmetric late-stage functionalization of soraphens. Nat Commun 2022; 13:371. [PMID: 35042883 PMCID: PMC8766452 DOI: 10.1038/s41467-022-27999-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/17/2021] [Indexed: 02/08/2023] Open
Abstract
Late-stage functionalization of natural products offers an elegant route to create novel entities in a relevant biological target space. In this context, enzymes capable of halogenating sp3 carbons with high stereo- and regiocontrol under benign conditions have attracted particular attention. Enabled by a combination of smart library design and machine learning, we engineer the iron/α-ketoglutarate dependent halogenase WelO5* for the late-stage functionalization of the complex and chemically difficult to derivatize macrolides soraphen A and C, potent anti-fungal agents. While the wild type enzyme WelO5* does not accept the macrolide substrates, our engineering strategy leads to active halogenase variants and improves upon their apparent kcat and total turnover number by more than 90-fold and 300-fold, respectively. Notably, our machine-learning guided engineering approach is capable of predicting more active variants and allows us to switch the regio-selectivity of the halogenases facilitating the targeted analysis of the derivatized macrolides’ structure-function activity in biological assays. The late-stage functionalization of unactivated carbon–hydrogen bonds is a difficult but important task, which has been met with promising but limited success through synthetic organic chemistry. Here the authors use machine learning to engineer WelO5* halogenase variants, which led to regioselective chlorination of inert C–H bonds on a representative polyketide that is a non-natural substrate for the enzyme.
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Affiliation(s)
- Johannes Büchler
- Competence Center for Biocatalysis, Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland.,School of Chemistry, The University of Manchester, Manchester Institute of Biotechnology, Manchester, M1 7DN, United Kingdom
| | - Sumire Honda Malca
- Competence Center for Biocatalysis, Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
| | - David Patsch
- Competence Center for Biocatalysis, Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland.,Institute of Biochemistry, Dept. of Biotechnology & Enzyme Catalysis, Greifswald University, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Moritz Voss
- Competence Center for Biocatalysis, Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
| | - Nicholas J Turner
- School of Chemistry, The University of Manchester, Manchester Institute of Biotechnology, Manchester, M1 7DN, United Kingdom
| | - Uwe T Bornscheuer
- Institute of Biochemistry, Dept. of Biotechnology & Enzyme Catalysis, Greifswald University, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Oliver Allemann
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, 4332, Stein, Switzerland.,Idorsia Pharmaceuticals Ltd, Hegenheimermattweg 91, 4123, Allschwil, Switzerland
| | | | - Alexandre Lumbroso
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, 4332, Stein, Switzerland
| | - Olivier Loiseleur
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, 4332, Stein, Switzerland.
| | - Rebecca Buller
- Competence Center for Biocatalysis, Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland.
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18
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Tang Q, Aslan-Üzel AS, Schuiten ED, Badenhorst CPS, Pavlidis IV, Bornscheuer UT. Enzymatic Photometric Assays for the Selective Detection of Halides. Methods Mol Biol 2022; 2487:361-375. [PMID: 35687247 DOI: 10.1007/978-1-0716-2269-8_22] [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] [Indexed: 06/15/2023]
Abstract
Halides are substrates and products of a number of biotechnologically important enzymes like dehalogenases, halide methyltransferases, and halogenases. Therefore, the determination of halide concentrations in samples is important. The classical methods based on mercuric thiocyanate are very dangerous, produce hazardous waste, and do not discriminate between chloride, bromide, and iodide. In this chapter, we describe a detailed protocol for the determination of halide concentrations based on the haloperoxidase-catalyzed oxidation of halides. The resulting hypohalous acids are detected using commercially available colorimetric or fluorimetric probes. The biocatalytic nature of the assays allows them to be implemented in one-pot cascade reactions with halide-generating enzymes. Since chloride is ubiquitous in biological systems, we also describe convenient photometric assays for the selective detection of bromide and iodide in the presence of chloride, obviating the need for laborious dialyses to obtain halide-free enzymes and reagents.
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Affiliation(s)
- Qingyun Tang
- Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Askin S Aslan-Üzel
- Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Eva D Schuiten
- Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | | | | | - Uwe T Bornscheuer
- Institute of Biochemistry, University of Greifswald, Greifswald, Germany.
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19
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Dieterich CL, Probst SI, Ueoka R, Sandu I, Schäfle D, Molin MD, Minas HA, Costa R, Oxenius A, Sander P, Piel J. Aquimarins, Peptide Antibiotics with Amino‐Modified C‐Termini from a Sponge‐Derived
Aquimarina
sp. Bacterium. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202115802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Cora L. Dieterich
- Institute of Microbiology Eidgenössische Technische Hochschule (ETH) Zürich Vladimir-Prelog-Weg 4 CH-8093 Zurich Switzerland
| | - Silke I. Probst
- Institute of Microbiology Eidgenössische Technische Hochschule (ETH) Zürich Vladimir-Prelog-Weg 4 CH-8093 Zurich Switzerland
| | - Reiko Ueoka
- Institute of Microbiology Eidgenössische Technische Hochschule (ETH) Zürich Vladimir-Prelog-Weg 4 CH-8093 Zurich Switzerland
- School of Marine Biosciences Kitasato University 1-15-1 Kitasato, Minami-ku Sagamihara Kanagawa 252-0373 Japan
| | - Ioana Sandu
- Institute of Microbiology Eidgenössische Technische Hochschule (ETH) Zürich Vladimir-Prelog-Weg 4 CH-8093 Zurich Switzerland
| | - Daniel Schäfle
- Institut für Medizinische Mikrobiologie University of Zurich Gloriastrasse 28/30 CH-8006 Zurich Switzerland
| | - Michael Dal Molin
- Institut für Medizinische Mikrobiologie University of Zurich Gloriastrasse 28/30 CH-8006 Zurich Switzerland
- Center for Molecular Medicine Cologne University of Cologne Robert-Koch-Str. 21 D-50931 Cologne Germany
| | - Hannah A. Minas
- Institute of Microbiology Eidgenössische Technische Hochschule (ETH) Zürich Vladimir-Prelog-Weg 4 CH-8093 Zurich Switzerland
| | - Rodrigo Costa
- Institute for Bioengineering and Biosciences (iBB) Instituto Superior Técnico Universidade de Lisboa Av. Rovisco Pais 1049-001 Lisboa Portugal
| | - Annette Oxenius
- Institute of Microbiology Eidgenössische Technische Hochschule (ETH) Zürich Vladimir-Prelog-Weg 4 CH-8093 Zurich Switzerland
| | - Peter Sander
- Institut für Medizinische Mikrobiologie University of Zurich Gloriastrasse 28/30 CH-8006 Zurich Switzerland
- Nationales Zentrum für Mykobakterien Gloriastrasse 28/30 CH-8006 Zurich Switzerland
| | - Jörn Piel
- Institute of Microbiology Eidgenössische Technische Hochschule (ETH) Zürich Vladimir-Prelog-Weg 4 CH-8093 Zurich Switzerland
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20
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Dieterich CL, Probst SI, Ueoka R, Sandu I, Schäfle D, Molin MD, Minas HA, Costa R, Oxenius A, Sander P, Piel J. Aquimarins, Peptide Antibiotics with Amino-Modified C-Termini from a Sponge-Derived Aquimarina sp. Bacterium. Angew Chem Int Ed Engl 2021; 61:e202115802. [PMID: 34918870 DOI: 10.1002/anie.202115802] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Indexed: 11/11/2022]
Abstract
Genome mining and bioactivity studies suggested the sponge-derived bacterium Aquimarina sp. Aq135 as a producer of new antibiotics. Activity-guided isolation identified antibacterial peptides, named aquimarins, featuring a new scaffold with an unusual C-terminal amino group and chlorine moieties. Responsible for the halogenation is the FeII /α-ketoglutarate-dependent chlorinase AqmA that halogenates up to two isoleucine residues in a carrier protein-dependent fashion. Total syntheses of two natural aquimarins and eight non-natural variants were developed. Structure-activity relationship (SAR) studies with these compounds showed that the synthetically more laborious chlorinations are not required for antibacterial activity but enhance cytotoxicity. In contrast, variants lacking the C-terminal amine were virtually inactive, suggesting diamines similar to the terminal aquimarin residue as candidate building blocks for new peptidomimetic antibiotics.
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Affiliation(s)
- Cora L Dieterich
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, CH-8093, Zurich, Switzerland
| | - Silke I Probst
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, CH-8093, Zurich, Switzerland
| | - Reiko Ueoka
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, CH-8093, Zurich, Switzerland.,School of Marine Biosciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Ioana Sandu
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, CH-8093, Zurich, Switzerland
| | - Daniel Schäfle
- Institut für Medizinische Mikrobiologie, University of Zurich, Gloriastrasse 28/30, CH-8006, Zurich, Switzerland
| | - Michael Dal Molin
- Institut für Medizinische Mikrobiologie, University of Zurich, Gloriastrasse 28/30, CH-8006, Zurich, Switzerland.,Center for Molecular Medicine Cologne, University of Cologne, Robert-Koch-Str. 21, D-50931, Cologne, Germany
| | - Hannah A Minas
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, CH-8093, Zurich, Switzerland
| | - Rodrigo Costa
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisboa, Portugal
| | - Annette Oxenius
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, CH-8093, Zurich, Switzerland
| | - Peter Sander
- Institut für Medizinische Mikrobiologie, University of Zurich, Gloriastrasse 28/30, CH-8006, Zurich, Switzerland.,Nationales Zentrum für Mykobakterien, Gloriastrasse 28/30, CH-8006, Zurich, Switzerland
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, CH-8093, Zurich, Switzerland
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21
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Tang Q, Pavlidis IV, Badenhorst CPS, Bornscheuer UT. From Natural Methylation to Versatile Alkylations Using Halide Methyltransferases. Chembiochem 2021; 22:2584-2590. [PMID: 33890381 PMCID: PMC8453949 DOI: 10.1002/cbic.202100153] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/22/2021] [Indexed: 11/06/2022]
Abstract
Halide methyltransferases (HMTs) enable the enzymatic synthesis of S-adenosyl-l-methionine (SAM) from S-adenosyl-l-homocysteine (SAH) and methyl iodide. Characterisation of a range of naturally occurring HMTs and subsequent protein engineering led to HMT variants capable of synthesising ethyl, propyl, and allyl analogues of SAM. Notably, HMTs do not depend on chemical synthesis of methionine analogues, as required by methionine adenosyltransferases (MATs). However, at the moment MATs have a much broader substrate scope than the HMTs. Herein we provide an overview of the discovery and engineering of promiscuous HMTs and how these strategies will pave the way towards a toolbox of HMT variants for versatile chemo- and regioselective biocatalytic alkylations.
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Affiliation(s)
- Qingyun Tang
- Institute of BiochemistryUniversity of GreifswaldFelix-Hausdorff-Str. 417489GreifswaldGermany
| | - Ioannis V. Pavlidis
- Dept. of ChemistryUniversity of CreteVoutes University Campus70013HeraklionGreece
| | | | - Uwe T. Bornscheuer
- Institute of BiochemistryUniversity of GreifswaldFelix-Hausdorff-Str. 417489GreifswaldGermany
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22
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García‐Ramos M, Cuetos A, Kroutil W, Grogan G, Lavandera I. The Reactivity of α‐Fluoroketones with PLP Dependent Enzymes: Transaminases as Hydrodefluorinases. ChemCatChem 2021. [DOI: 10.1002/cctc.202100901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Marina García‐Ramos
- Organic and Inorganic Chemistry Department University of Oviedo Avenida Julián Clavería 8 33006 Oviedo Spain
| | - Aníbal Cuetos
- York Structural Biology Laboratory Department of Chemistry University of York Heslington York YO10 5DD UK
- ENANTIA C/ Baldiri Reixac, 10 08028 Barcelona Spain
| | - Wolfgang Kroutil
- Institute of Chemistry NAWI Graz Field of Excellence BioHealth University of Graz Heinrichstrasse 28 8010 Graz Austria
| | - Gideon Grogan
- York Structural Biology Laboratory Department of Chemistry University of York Heslington York YO10 5DD UK
| | - Iván Lavandera
- Organic and Inorganic Chemistry Department University of Oviedo Avenida Julián Clavería 8 33006 Oviedo Spain
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23
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Hall M. Enzymatic strategies for asymmetric synthesis. RSC Chem Biol 2021; 2:958-989. [PMID: 34458820 PMCID: PMC8341948 DOI: 10.1039/d1cb00080b] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 05/28/2021] [Indexed: 12/13/2022] Open
Abstract
Enzymes, at the turn of the 21st century, are gaining a momentum. Especially in the field of synthetic organic chemistry, a broad variety of biocatalysts are being applied in an increasing number of processes running at up to industrial scale. In addition to the advantages of employing enzymes under environmentally friendly reaction conditions, synthetic chemists are recognizing the value of enzymes connected to the exquisite selectivity of these natural (or engineered) catalysts. The use of hydrolases in enantioselective protocols paved the way to the application of enzymes in asymmetric synthesis, in particular in the context of biocatalytic (dynamic) kinetic resolutions. After two decades of impressive development, the field is now mature to propose a panel of catalytically diverse enzymes for (i) stereoselective reactions with prochiral compounds, such as double bond reduction and bond forming reactions, (ii) formal enantioselective replacement of one of two enantiotopic groups of prochiral substrates, as well as (iii) atroposelective reactions with noncentrally chiral compounds. In this review, the major enzymatic strategies broadly applicable in the asymmetric synthesis of optically pure chiral compounds are presented, with a focus on the reactions developed within the past decade.
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Affiliation(s)
- Mélanie Hall
- Institute of Chemistry, University of Graz Heinrichstrasse 28 8010 Graz Austria
- Field of Excellence BioHealth - University of Graz Austria
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24
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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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25
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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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26
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Yi D, Bayer T, Badenhorst CPS, Wu S, Doerr M, Höhne M, Bornscheuer UT. Recent trends in biocatalysis. Chem Soc Rev 2021; 50:8003-8049. [PMID: 34142684 PMCID: PMC8288269 DOI: 10.1039/d0cs01575j] [Citation(s) in RCA: 122] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Indexed: 12/13/2022]
Abstract
Biocatalysis has undergone revolutionary progress in the past century. Benefited by the integration of multidisciplinary technologies, natural enzymatic reactions are constantly being explored. Protein engineering gives birth to robust biocatalysts that are widely used in industrial production. These research achievements have gradually constructed a network containing natural enzymatic synthesis pathways and artificially designed enzymatic cascades. Nowadays, the development of artificial intelligence, automation, and ultra-high-throughput technology provides infinite possibilities for the discovery of novel enzymes, enzymatic mechanisms and enzymatic cascades, and gradually complements the lack of remaining key steps in the pathway design of enzymatic total synthesis. Therefore, the research of biocatalysis is gradually moving towards the era of novel technology integration, intelligent manufacturing and enzymatic total synthesis.
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Affiliation(s)
- Dong Yi
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Thomas Bayer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Christoffel P. S. Badenhorst
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Shuke Wu
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Mark Doerr
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Matthias Höhne
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Uwe T. Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
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27
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Papadopoulou A, Meierhofer J, Meyer F, Hayashi T, Schneider S, Sager E, Buller R. Re‐Programming and Optimization of a
L
‐Proline
cis
‐4‐Hydroxylase for the
cis
‐3‐Halogenation of its Native Substrate. ChemCatChem 2021. [DOI: 10.1002/cctc.202100591] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Athena Papadopoulou
- Competence Center for Biocatalysis Institute of Chemistry and Biotechnology Zurich University of Applied Sciences 8820 Wädenswil Switzerland
| | - Jasmin Meierhofer
- Competence Center for Biocatalysis Institute of Chemistry and Biotechnology Zurich University of Applied Sciences 8820 Wädenswil Switzerland
| | - Fabian Meyer
- Competence Center for Biocatalysis Institute of Chemistry and Biotechnology Zurich University of Applied Sciences 8820 Wädenswil Switzerland
| | - Takahiro Hayashi
- Competence Center for Biocatalysis Institute of Chemistry and Biotechnology Zurich University of Applied Sciences 8820 Wädenswil Switzerland
- Current address: Science & Innovation Center Mitsubishi Chemical Corporation Yokohama Kanagawa 227-8502 Japan
| | - Samuel Schneider
- Competence Center for Biocatalysis Institute of Chemistry and Biotechnology Zurich University of Applied Sciences 8820 Wädenswil Switzerland
| | - Emine Sager
- Novartis Institutes for BioMedical Research Global Discovery Chemistry 4056 Basel Switzerland
| | - Rebecca Buller
- Competence Center for Biocatalysis Institute of Chemistry and Biotechnology Zurich University of Applied Sciences 8820 Wädenswil Switzerland
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28
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Meyer F, Frey R, Ligibel M, Sager E, Schroer K, Snajdrova R, Buller R. Modulating Chemoselectivity in a Fe(II)/α-Ketoglutarate-Dependent Dioxygenase for the Oxidative Modification of a Nonproteinogenic Amino Acid. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00678] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Fabian Meyer
- Competence Center for Biocatalysis, Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
| | - Raphael Frey
- Competence Center for Biocatalysis, Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
| | - Mathieu Ligibel
- Novartis Institutes for BioMedical Research, Global Discovery Chemistry, 4056 Basel, Switzerland
| | - Emine Sager
- Novartis Institutes for BioMedical Research, Global Discovery Chemistry, 4056 Basel, Switzerland
| | - Kirsten Schroer
- Novartis Institutes for BioMedical Research, Global Discovery Chemistry, 4056 Basel, Switzerland
| | - Radka Snajdrova
- Novartis Institutes for BioMedical Research, Global Discovery Chemistry, 4056 Basel, Switzerland
| | - Rebecca Buller
- Competence Center for Biocatalysis, Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
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29
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Wu S, Snajdrova R, Moore JC, Baldenius K, Bornscheuer UT. Biocatalysis: Enzymatic Synthesis for Industrial Applications. Angew Chem Int Ed Engl 2021; 60:88-119. [PMID: 32558088 PMCID: PMC7818486 DOI: 10.1002/anie.202006648] [Citation(s) in RCA: 522] [Impact Index Per Article: 174.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Indexed: 12/12/2022]
Abstract
Biocatalysis has found numerous applications in various fields as an alternative to chemical catalysis. The use of enzymes in organic synthesis, especially to make chiral compounds for pharmaceuticals as well for the flavors and fragrance industry, are the most prominent examples. In addition, biocatalysts are used on a large scale to make specialty and even bulk chemicals. This review intends to give illustrative examples in this field with a special focus on scalable chemical production using enzymes. It also discusses the opportunities and limitations of enzymatic syntheses using distinct examples and provides an outlook on emerging enzyme classes.
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Affiliation(s)
- Shuke Wu
- Institute of BiochemistryDept. of Biotechnology & Enzyme CatalysisGreifswald UniversityFelix-Hausdorff-Strasse 417487GreifswaldGermany
| | - Radka Snajdrova
- Novartis Institutes for BioMedical ResearchGlobal Discovery Chemistry4056BaselSwitzerland
| | - Jeffrey C. Moore
- Process Research and DevelopmentMerck & Co., Inc.126 E. Lincoln AveRahwayNJ07065USA
| | - Kai Baldenius
- Baldenius Biotech ConsultingHafenstr. 3168159MannheimGermany
| | - Uwe T. Bornscheuer
- Institute of BiochemistryDept. of Biotechnology & Enzyme CatalysisGreifswald UniversityFelix-Hausdorff-Strasse 417487GreifswaldGermany
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30
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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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31
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Wu S, Snajdrova R, Moore JC, Baldenius K, Bornscheuer UT. Biokatalyse: Enzymatische Synthese für industrielle Anwendungen. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006648] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Shuke Wu
- Institut für Biochemie Abt. Biotechnologie & Enzymkatalyse Universität Greifswald Felix-Hausdorff-Straße 4 17487 Greifswald Deutschland
| | - Radka Snajdrova
- Novartis Institutes for BioMedical Research Global Discovery Chemistry 4056 Basel Schweiz
| | - Jeffrey C. Moore
- Process Research and Development Merck & Co., Inc. 126 E. Lincoln Ave Rahway NJ 07065 USA
| | - Kai Baldenius
- Baldenius Biotech Consulting Hafenstraße 31 68159 Mannheim Deutschland
| | - Uwe T. Bornscheuer
- Institut für Biochemie Abt. Biotechnologie & Enzymkatalyse Universität Greifswald Felix-Hausdorff-Straße 4 17487 Greifswald Deutschland
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32
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Affiliation(s)
- Bernhard Hauer
- Institute of Biochemistry and Technical Biochemistry, Department of Technical Biochemistry, Universitaet Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
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