1
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Wohlgemuth R. Synthesis of Metabolites and Metabolite-like Compounds Using Biocatalytic Systems. Metabolites 2023; 13:1097. [PMID: 37887422 PMCID: PMC10608848 DOI: 10.3390/metabo13101097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/13/2023] [Accepted: 10/15/2023] [Indexed: 10/28/2023] Open
Abstract
Methodologies for the synthesis and purification of metabolites, which have been developed following their discovery, analysis, and structural identification, have been involved in numerous life science milestones. The renewed focus on the small molecule domain of biological cells has also created an increasing awareness of the rising gap between the metabolites identified and the metabolites which have been prepared as pure compounds. The design and engineering of resource-efficient and straightforward synthetic methodologies for the production of the diverse and numerous metabolites and metabolite-like compounds have attracted much interest. The variety of metabolic pathways in biological cells provides a wonderful blueprint for designing simplified and resource-efficient synthetic routes to desired metabolites. Therefore, biocatalytic systems have become key enabling tools for the synthesis of an increasing number of metabolites, which can then be utilized as standards, enzyme substrates, inhibitors, or other products, or for the discovery of novel biological functions.
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Affiliation(s)
- Roland Wohlgemuth
- MITR, Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego Street 116, 90-924 Lodz, Poland;
- Swiss Coordination Committee Biotechnology (SKB), 8021 Zurich, Switzerland
- European Society of Applied Biocatalysis (ESAB), 1000 Brussels, Belgium
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2
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France SP, Lewis RD, Martinez CA. The Evolving Nature of Biocatalysis in Pharmaceutical Research and Development. JACS AU 2023; 3:715-735. [PMID: 37006753 PMCID: PMC10052283 DOI: 10.1021/jacsau.2c00712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/13/2023] [Accepted: 02/13/2023] [Indexed: 06/19/2023]
Abstract
Biocatalysis is a highly valued enabling technology for pharmaceutical research and development as it can unlock synthetic routes to complex chiral motifs with unparalleled selectivity and efficiency. This perspective aims to review recent advances in the pharmaceutical implementation of biocatalysis across early and late-stage development with a focus on the implementation of processes for preparative-scale syntheses.
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3
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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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4
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Wohlgemuth R, Littlechild J. Complexity reduction and opportunities in the design, integration and intensification of biocatalytic processes for metabolite synthesis. Front Bioeng Biotechnol 2022; 10:958606. [PMID: 35935499 PMCID: PMC9355135 DOI: 10.3389/fbioe.2022.958606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
The biosynthesis of metabolites from available starting materials is becoming an ever important area due to the increasing demands within the life science research area. Access to metabolites is making essential contributions to analytical, diagnostic, therapeutic and different industrial applications. These molecules can be synthesized by the enzymes of biological systems under sustainable process conditions. The facile synthetic access to the metabolite and metabolite-like molecular space is of fundamental importance. The increasing knowledge within molecular biology, enzyme discovery and production together with their biochemical and structural properties offers excellent opportunities for using modular cell-free biocatalytic systems. This reduces the complexity of synthesizing metabolites using biological whole-cell approaches or by classical chemical synthesis. A systems biocatalysis approach can provide a wealth of optimized enzymes for the biosynthesis of already identified and new metabolite molecules.
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Affiliation(s)
- Roland Wohlgemuth
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Lodz, Poland
- Swiss Coordination Committee for Biotechnology, Zurich, Switzerland
| | - Jennifer Littlechild
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
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5
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Wohlgemuth R. Selective Biocatalytic Defunctionalization of Raw Materials. CHEMSUSCHEM 2022; 15:e202200402. [PMID: 35388636 DOI: 10.1002/cssc.202200402] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/05/2022] [Indexed: 06/14/2023]
Abstract
Biobased raw materials, such as carbohydrates, amino acids, nucleotides, or lipids contain valuable functional groups with oxygen and nitrogen atoms. An abundance of many functional groups of the same type, such as primary or secondary hydroxy groups in carbohydrates, however, limits the synthetic usefulness if similar reactivities cannot be differentiated. Therefore, selective defunctionalization of highly functionalized biobased starting materials to differentially functionalized compounds can provide a sustainable access to chiral synthons, even in case of products with fewer functional groups. Selective defunctionalization reactions, without affecting other functional groups of the same type, are of fundamental interest for biocatalytic reactions. Controlled biocatalytic defunctionalizations of biobased raw materials are attractive for obtaining valuable platform chemicals and building blocks. The biocatalytic removal of functional groups, an important feature of natural metabolic pathways, can also be utilized in a systemic strategy for sustainable metabolite synthesis.
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Affiliation(s)
- Roland Wohlgemuth
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology Łódź, 90-537, Lodz, Poland
- Swiss Coordination Committee Biotechnology (SKB), 8002, Zurich, Switzerland
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6
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Alcántara AR, Domínguez de María P, Littlechild JA, Schürmann M, Sheldon RA, Wohlgemuth R. Biocatalysis as Key to Sustainable Industrial Chemistry. CHEMSUSCHEM 2022; 15:e202102709. [PMID: 35238475 DOI: 10.1002/cssc.202102709] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/10/2022] [Indexed: 06/14/2023]
Abstract
The role and power of biocatalysis in sustainable chemistry has been continuously brought forward step by step to its present outstanding position. The problem-solving capabilities of biocatalysis have been realized by numerous substantial achievements in biology, chemistry and engineering. Advances and breakthroughs in the life sciences and interdisciplinary cooperation with chemistry have clearly accelerated the implementation of biocatalytic synthesis in modern chemistry. Resource-efficient biocatalytic manufacturing processes have already provided numerous benefits to sustainable chemistry as well as customer-centric value creation in the pharmaceutical, food, flavor, fragrance, vitamin, agrochemical, polymer, specialty, and fine chemical industries. Biocatalysis can make significant contributions not only to manufacturing processes, but also to the design of completely new value-creation chains. Biocatalysis can now be considered as a key enabling technology to implement sustainable chemistry.
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Affiliation(s)
- Andrés R Alcántara
- Department of Chemistry in Pharmaceutical Sciences (QUICIFARM), Complutense University of Madrid (UCM), 28040-, Madrid, Spain
| | - Pablo Domínguez de María
- Sustainable Momentum, SL, Av. Ansite 3, 4-6, 35011, Las Palmas de Gran Canaria, Canary Is., Spain
| | - Jennifer A Littlechild
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, United Kingdom
| | | | - Roger A Sheldon
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Braamfontein, Johannesburg, South Africa
| | - Roland Wohlgemuth
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, 90-537, Lodz, Poland
- Swiss Coordination Committee for Biotechnology, 8021, Zurich, Switzerland
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7
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Höfmann S, Dziwornu PA, Klaus T, Knura T, Wohlgemuth R, Bräsen C, Siebers B. Simplified Enzymatic Synthesis of 2-Keto-3-Deoxy-D-Gluconate from D-Gluconate Using the Gluconate Dehydratase from Thermoproteus tenax. Methods Mol Biol 2022; 2522:351-362. [PMID: 36125762 DOI: 10.1007/978-1-0716-2445-6_23] [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
Many research areas, e.g., basic research but also applied fields of biotechnology, biomedicine, and diagnostics often suffer from the unavailability of metabolic compounds. This is mostly due to missing easy and efficient synthesis procedures. We herein describe the biocatalytic/enzymatic production of 2-keto-3-deoxy-D-gluconate, an intermediate of central metabolic pathways in all three domains of life and also of bacterial polysaccharides, lipopolysaccharides, and cell wall components. The method is based on the gluconate dehydratase from the hyperthermophilic crenarchaeon Thermoproteus tenax, which can be easily recombinantly overproduced in Escherichia coli and-due to its intrinsic thermostability-rapidly be purified by two precipitation steps. The enzyme completely converts D-gluconate to solely stereochemically pure KDG, taking benefits from the enol-keto-tautomerism of the primary reaction product. The final product can then easily be separated from the protein by ultrafiltration. The simple one-step procedure, which is suitable at least for the lab-scale/gram-scale production of KDG, replaces lengthy multi-step reactions and is easily scalable. This approach also illustrates the great application potential of Archaea with their unusual metabolic pathways and enzymes for the synthesis of added value products.
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Affiliation(s)
- Svenja Höfmann
- Department of Chemistry, Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Essen, Germany
| | - Promise Akua Dziwornu
- Department of Chemistry, Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Essen, Germany
| | - Thomas Klaus
- Department of Chemistry, Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Essen, Germany
| | - Thomas Knura
- Department of Chemistry, Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Essen, Germany
| | - Roland Wohlgemuth
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Lodz, Poland
| | - Christopher Bräsen
- Department of Chemistry, Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Essen, Germany
| | - Bettina Siebers
- Department of Chemistry, Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Essen, Germany.
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8
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Wohlgemuth R. Key advances in biocatalytic phosphorylations in the last two decades: Biocatalytic syntheses in vitro and biotransformations in vivo (in humans). Biotechnol J 2020; 16:e2000090. [PMID: 33283467 DOI: 10.1002/biot.202000090] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/06/2020] [Indexed: 01/05/2023]
Abstract
Biocatalytic phosphorylation reactions provide several benefits, such as more direct, milder, more selective, and shorter access routes to phosphorylated products. Favorable characteristics of biocatalytic methodologies represent advantages for in vitro as well as for in vivo phosphorylation reactions, leading to important advances in the science of synthesis towards bioactive phosphorylated compounds in various areas. The scope of this review covers key advances of biocatalytic phosphorylation reactions over the last two decades, for biocatalytic syntheses in vitro and for biotransformations in vivo (in humans). From the origins of probiotic life to in vitro synthetic applications and in vivo formation of bioactive pharmaceuticals, the common purpose is to outline the importance, relevance, and underlying connections of biocatalytic phosphorylations of small molecules. Asymmetric phosphorylations attracting increased attention are highlighted. Phosphohydrolases, phosphotransferases, phosphorylases, phosphomutases, and other enzymes involved in phosphorus chemistry provide powerful toolboxes for resource-efficient and selective in vitro biocatalytic syntheses of phosphorylated metabolites, chiral building blocks, pharmaceuticals as well as in vivo enzymatic formation of biologically active forms of pharmaceuticals. Nature's large diversity of phosphoryl-group-transferring enzymes, advanced enzyme and reaction engineering toolboxes make biocatalytic asymmetric phosphorylations using enzymes a powerful and privileged phosphorylation methodology.
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Affiliation(s)
- Roland Wohlgemuth
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Lodz, Poland.,Swiss Coordination Committee Biotechnology, Zurich, Switzerland
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9
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Abstract
Biocatalysis has undergone a remarkable transition in the last two decades, from being considered a niche technology to playing a much more relevant role in organic synthesis today. Advances in molecular biology and bioinformatics, and the decreasing costs for gene synthesis and sequencing contribute to the growing success of engineered biocatalysts in industrial applications. However, the incorporation of biocatalytic process steps in new or established manufacturing routes is not always straightforward. To realize the full synthetic potential of biocatalysis for the sustainable manufacture of chemical building blocks, it is therefore important to regularly analyze the success factors and existing hurdles for the implementation of enzymes in large scale small molecule synthesis. Building on our previous analysis of biocatalysis in the Swiss manufacturing environment, we present a follow-up study on how the industrial biocatalysis situation in Switzerland has evolved in the last four years. Considering the current industrial landscape, we record recent advances in biocatalysis in Switzerland as well as give suggestions where enzymatic transformations may be valuably employed to address some of the societal challenges we face today, particularly in the context of the current Coronavirus disease 2019 (COVID-19) pandemic.
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10
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Wohlgemuth R. Biocatalysis - Key enabling tools from biocatalytic one-step and multi-step reactions to biocatalytic total synthesis. N Biotechnol 2020; 60:113-123. [PMID: 33045418 DOI: 10.1016/j.nbt.2020.08.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 07/07/2020] [Accepted: 08/31/2020] [Indexed: 12/20/2022]
Abstract
In the area of human-made innovations to improve the quality of life, biocatalysis has already had a great impact and contributed enormously to a growing number of catalytic transformations aimed at the detection and analysis of compounds, the bioconversion of starting materials and the preparation of target compounds at any scale, from laboratory small scale to industrial large scale. The key enabling tools which have been developed in biocatalysis over the last decades also provide great opportunities for further development and numerous applications in various sectors of the global bioeconomy. Systems biocatalysis is a modular, bottom-up approach to designing the architecture of enzyme-catalyzed reaction steps in a synthetic route from starting materials to target molecules. The integration of biocatalysis and sustainable chemistry in vitro aims at ideal conversions with high molecular economy and their intensification. Retrosynthetic analysis in the chemical and biological domain has been a valuable tool for target-oriented synthesis while, on the other hand, diversity-oriented synthesis builds on forward-looking analysis. Bioinformatic tools for rapid identification of the required enzyme functions, efficient enzyme production systems, as well as generalized bioprocess design tools, are important for rapid prototyping of the biocatalytic reactions. The tools for enzyme engineering and the reaction engineering of each enzyme-catalyzed one-step reaction are also valuable for coupling reactions. The tools to overcome interaction issues with other components or enzymes are of great interest in designing multi-step reactions as well as in biocatalytic total synthesis.
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Affiliation(s)
- Roland Wohlgemuth
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Lodz, Poland; Swiss Coordination Committee on Biotechnology (SKB), Nordstrasse 15, 8021 Zürich, Switzerland.
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11
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Löwe J, Dietz K, Gröger H. From a Biosynthetic Pathway toward a Biocatalytic Process and Chemocatalytic Modifications: Three-Step Enzymatic Cascade to the Plant Metabolite cis-(+)-12-OPDA and Metathesis-Derived Products. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1902973. [PMID: 32670743 PMCID: PMC7341106 DOI: 10.1002/advs.201902973] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 01/11/2020] [Indexed: 05/05/2023]
Abstract
A biotechnological approach toward the plant metabolite and regulator cis-(+)-12-oxophytodienoic acid (cis-(+)-12-OPDA) in a one-pot process with >99% conversion, at least 90% selectivity and ≤10% of side products as well as a high diastereoselectivity (leading to d.r. of at least 90:10) is reported. The optimized organic-synthetic enzyme cascade for preparing this bioactive and commercial molecule with pharmaceutical relevance on a gram per L scale is designed based on its biosynthetic pathway starting from cheap and readily accessible linolenic acid. Toward this end, a recombinant biocatalyst system has been prepared for carrying out the most critical two key steps in a tailored manner, thus avoiding sensitive intermediate decomposition. Furthermore, cis-(+)-12-OPDA is successfully modified via a cross-alkene metathesis reaction with conversions of up to >99%, leading to a compound library of new cis-(+)-12-OPDA derivatives with different substitution pattern of the side chain at the 2-position. By means of such a combined biotechnological and chemocatalytic route, a straightforward approach to a structurally unique oxylipin library is realized, which would be highly difficult or not accessible by pure chemical and biotechnological methods, respectively.
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Affiliation(s)
- Jana Löwe
- Chair of Industrial Organic Chemistry and BiotechnologyFaculty of ChemistryBielefeld UniversityUniversitätsstr. 2533615BielefeldGermany
| | - Karl‐Josef Dietz
- Chair of Plant Biochemistry and PhysiologyFaculty of BiologyBielefeld UniversityUniversitätsstr. 2533615BielefeldGermany
| | - Harald Gröger
- Chair of Industrial Organic Chemistry and BiotechnologyFaculty of ChemistryBielefeld UniversityUniversitätsstr. 2533615BielefeldGermany
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12
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Krevet S, Shen L, Bohnen T, Schoenenberger B, Meier R, Obkircher M, Bangert K, Koehling R, Allenspach E, Wohlgemuth R, Siebers B, Bräsen C. Enzymatic Synthesis of 2-Keto-3-Deoxy-6-Phosphogluconate by the 6-Phosphogluconate-Dehydratase From Caulobacter crescentus. Front Bioeng Biotechnol 2020; 8:185. [PMID: 32266226 PMCID: PMC7099567 DOI: 10.3389/fbioe.2020.00185] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 02/25/2020] [Indexed: 11/25/2022] Open
Abstract
The availability of metabolic intermediates is a prerequisite in many fields ranging from basic research, to biotechnological and biomedical applications as well as diagnostics. 2-keto-3-deoxy-6-phosphogluconate (KDPG) is the key intermediate of the Entner-Doudoroff (ED) pathway for sugar degradation and of sugar acid and sugar polymer breakdown in many organisms including human and plant pathogens. However, so far KDPG is hardly available due to missing efficient synthesis routes. We here report the efficient biocatalytic KDPG production through enzymatic dehydration of 6-phosphogluconate (6PG) up to gram scale using the 6PG dehydratase/Entner-Doudoroff dehydratase (EDD) from Caulobacter crescentus (CcEDD). The enzyme was recombinantly produced in Escherichia coli, purified to apparent homogeneity in a simple one-step procedure using nickel ion affinity chromatography, and characterized with respect to molecular and kinetic properties. The homodimeric CcEDD catalyzed the irreversible 6PG dehydration to KDPG with a Vmax of 61.6 U mg–1 and a KM of 0.3 mM for 6PG. Most importantly, the CcEDD showed sufficient long-term stability and activity to provide the enzyme in amounts and purity required for the efficient downstream synthesis of KDPG. CcEDD completely converted 1 g 6PG and a straight forward purification method yielded 0.81 g of stereochemically pure KDPG corresponding to a final yield of 90% as shown by HPLC-MS and NMR analyses.
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Affiliation(s)
- Sabine Krevet
- Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Lu Shen
- Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Timon Bohnen
- Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | | | - Roland Meier
- Member of Merck Group, Sigma-Aldrich Production GmbH, Buchs, Switzerland
| | - Markus Obkircher
- Member of Merck Group, Sigma-Aldrich Production GmbH, Buchs, Switzerland
| | - Klara Bangert
- Member of Merck Group, Sigma-Aldrich Production GmbH, Buchs, Switzerland
| | - Rudolf Koehling
- Member of Merck Group, Sigma-Aldrich Production GmbH, Buchs, Switzerland
| | - Eric Allenspach
- Member of Merck Group, Sigma-Aldrich Production GmbH, Buchs, Switzerland
| | - Roland Wohlgemuth
- Member of Merck Group, Sigma-Aldrich Production GmbH, Buchs, Switzerland.,Institute of Molecular and Industrial Biotechnology, Technical University Lodz, Lodz, Poland
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Christopher Bräsen
- Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
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13
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Tian Y, Wu L, Yuan L, Ding S, Chen F, Zhang T, Ren A, Zhang D, Tu W, Chen J, Hu QN. BCSExplorer: a customized biosynthetic chemical space explorer with multifunctional objective function analysis. Bioinformatics 2020; 36:1642-1643. [PMID: 31593245 DOI: 10.1093/bioinformatics/btz755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 09/11/2019] [Accepted: 10/01/2019] [Indexed: 11/14/2022] Open
Abstract
SUMMARY The biosynthetic ability of living organisms has important applications in producing bulk chemicals, biofuels and natural products. Based on the most comprehensive biosynthesis knowledgebase, a computational system, BCSExplorer, is proposed to discover the unexplored chemical space using nature's biosynthetic potential. BCSExplorer first integrates the most comprehensive biosynthetic reaction database with 280 000 biochemical reactions and 60 000 chemicals biosynthesized globally over the past 130 years. Second, in this study, a biosynthesis tree is computed for a starting chemical molecule based on a comprehensive biotransformation rule library covering almost all biosynthetic possibilities, in which redundant rules are removed using a new algorithm. Moreover, biosynthesis feasibility, drug-likeness and toxicity analysis of a new generation of compounds will be pursued in further studies to meet various needs. BCSExplorer represents a novel method to explore biosynthetically available chemical space. AVAILABILITY AND IMPLEMENTATION BCSExplorer is available at: http://www.rxnfinder.org/bcsexplorer/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yu Tian
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P.R. China.,University of Chinese Academy of Sciences, Beijing 100864, P.R. China
| | - Ling Wu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P.R. China
| | - Le Yuan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P.R. China.,University of Chinese Academy of Sciences, Beijing 100864, P.R. China
| | - Shaozhen Ding
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200333, P.R. China
| | - Fu Chen
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P.R. China.,College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P.R. China
| | - Tong Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P.R. China.,College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P.R. China
| | - Ailin Ren
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P.R. China.,University of Chinese Academy of Sciences, Beijing 100864, P.R. China
| | - Dachuan Zhang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200333, P.R. China
| | - Weizhong Tu
- Wuhan LifeSynther Science and Technology Co. Limited, Wuhan 430070, P.R. China
| | - Junni Chen
- Wuhan LifeSynther Science and Technology Co. Limited, Wuhan 430070, P.R. China
| | - Qian-Nan Hu
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200333, P.R. China
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14
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Aguilar A, Twardowski T, Wohlgemuth R. Bioeconomy for Sustainable Development. Biotechnol J 2019; 14:e1800638. [PMID: 31106982 DOI: 10.1002/biot.201800638] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 04/04/2019] [Indexed: 01/12/2023]
Abstract
Bioeconomy is an emerging paradigm under which the creation, development, and revitalization of economic systems based on a sustainable use of renewable biological resources in a balanced way is rapidly spreading globally. Bioeconomy is building bridges between biotechnology and economy as well as between science, industry, and society. Biotechnology, from its ancient origins up to the present is at the core of the scientific and innovative foundation of bioeconomy policies developed in numerous countries. The challenges and perspectives of bioeconomies are immense, from resource-efficient large-scale manufacturing of products such as chemicals, materials, food, pharmaceuticals, polymers, flavors, and fragrances to the production of new biomaterials and bioenergy in a sustainable and economic way for a growing world population. Key success factors for different countries working on the bioeconomy vary widely from high-tech bioeconomies, emerging diversified or diversified bioeconomies to advanced and basic primary sector bioeconomies. Despite the large variety of bioeconomies, several common elements are identified, which are simultaneously needed altogether.
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Affiliation(s)
- Alfredo Aguilar
- Task Force Bioeconomy, European Federation of Biotechnology, Parc Científic Barcelona Torres R+D+I, Baldiri Reixac 4-8, 08028, Barcelona, Spain
| | - Tomasz Twardowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61704, Poland
| | - Roland Wohlgemuth
- Institute of Technical Biochemistry, Lodz University of Technology, Lodz, 90-924, Poland.,Swiss Coordination Committee for Biotechnology, Zürich, 8021, Switzerland.,ESAB (EFB Section on Applied Biocatalysis), Frankfurt, 60486, Germany
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Gandomkar S, Żądło‐Dobrowolska A, Kroutil W. Extending Designed Linear Biocatalytic Cascades for Organic Synthesis. ChemCatChem 2019; 11:225-243. [PMID: 33520008 PMCID: PMC7814890 DOI: 10.1002/cctc.201801063] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Indexed: 02/05/2023]
Abstract
Artificial cascade reactions involving biocatalysts have demonstrated a tremendous potential during the recent years. This review just focuses on selected examples of the last year and putting them into context to a previously published suggestion for classification. Subdividing the cascades according to the number of catalysts in the linear sequence, and classifying whether the steps are performed simultaneous or in a sequential fashion as well as whether the reaction sequence is performed in vitro or in vivo allows to organise the concepts. The last year showed, that combinations of in vivo as well as in vitro are possible. Incompatible reaction steps may be run in a sequential fashion or by compartmentalisation of the incompatible steps either by using special reactors (membrane), polymersomes or flow techniques.
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Affiliation(s)
- Somayyeh Gandomkar
- Institute of ChemistryUniversity of GrazHeinrichstrasse 28Graz8010Austria
| | | | - Wolfgang Kroutil
- Institute of ChemistryUniversity of GrazHeinrichstrasse 28Graz8010Austria
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