1
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Skendrović D, Primožič M, Rezić T, Vrsalović Presečki A. Mesocellular Silica Foam as Immobilization Carrier for Production of Statin Precursors. Int J Mol Sci 2024; 25:1971. [PMID: 38396648 PMCID: PMC10887991 DOI: 10.3390/ijms25041971] [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: 01/16/2024] [Revised: 02/01/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
The employment of 2-deoxyribose-5-phosphate aldolase (DERA) stands as a prevalent biocatalytic route for synthesizing statin side chains. The main problem with this pathway is the low stability of the enzyme. In this study, mesocellular silica foam (MCF) with different pore sizes was used as a carrier for the covalent immobilization of DERA. Different functionalizing and activating agents were tested and kinetic modeling was subsequently performed. The use of succinic anhydride as an activating agent resulted in an enzyme hyperactivation of approx. 140%, and the stability almost doubled compared to that of the free enzyme. It was also shown that the pore size of MCF has a decisive influence on the stability of the DERA enzyme.
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Affiliation(s)
- Dino Skendrović
- Faculty of Chemical Engineering and Technology, University of Zagreb, HR-10000 Zagreb, Croatia;
| | - Mateja Primožič
- Faculty of Chemistry and Chemical Engineering, University of Maribor, 2000 Maribor, Slovenia;
| | - Tonči Rezić
- Faculty of Food Technology and Biotechnology, University of Zagreb, HR-10000 Zagreb, Croatia;
| | - Ana Vrsalović Presečki
- Faculty of Chemical Engineering and Technology, University of Zagreb, HR-10000 Zagreb, Croatia;
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2
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Cheon H, Kim JH, Kim JS, Park JB. Valorization of single-carbon chemicals by using carboligases as key enzymes. Curr Opin Biotechnol 2024; 85:103047. [PMID: 38128199 DOI: 10.1016/j.copbio.2023.103047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/23/2023]
Abstract
Single-carbon (C1) biorefinery plays a key role in the consumption of global greenhouse gases and a circular carbon economy. Thereby, we have focused on the valorization of C1 compounds (e.g. methanol, formaldehyde, and formate) into multicarbon products, including bioplastic monomers, glycolate, and ethylene glycol. For instance, methanol, derived from the oxidation of CH4, can be converted into glycolate, ethylene glycol, or erythrulose via formaldehyde and glycolaldehyde, employing C1 and/or C2 carboligases as essential enzymes. Escherichia coli was engineered to convert formate, produced from CO via CO2 or from CO2 directly, into glycolate. Recent progress in the design of biotransformation pathways, enzyme discovery, and engineering, as well as whole-cell biocatalyst engineering for C1 biorefinery, was addressed in this review.
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Affiliation(s)
- Huijin Cheon
- Department of Food Science and Biotechnology, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jun-Hong Kim
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jeong-Sun Kim
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea.
| | - Jin-Byung Park
- Department of Food Science and Biotechnology, Ewha Womans University, Seoul 03760, Republic of Korea.
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3
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Kim JH, Cheon H, Jo HJ, Kim JW, Kim GY, Seo HR, Seo PW, Kim JS, Park JB. Engineering of two thiamine diphosphate-dependent enzymes for the regioselective condensation of C1-formaldehyde into C4-erythrulose. Int J Biol Macromol 2023; 253:127674. [PMID: 37890751 DOI: 10.1016/j.ijbiomac.2023.127674] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/17/2023] [Accepted: 10/24/2023] [Indexed: 10/29/2023]
Abstract
A number of carboligases, which catalyze condensation of C1- and/or C2-aldehydes into multi-carbon products, have been reported. However, their catalytic activities and/or regioselectivities remained rather low. Thereby, this study has focused on engineering of C1 and C2 carboligases for the regioselective condensation of C1-formaldehyde into C4-erythrulose via C2-glycolaldehyde. The crystal structure of the glyoxylate carboligase from Escherichia coli (EcGCL) was elucidated in complex with glycolaldehyde. A structure-guided rationale generated several mutants, one of whose catalytic activity reached 15.6 M-1·s-1, almost 10 times greater than the wild-type enzyme. Another variant (i.e., EcGCL_R484M/N283Q/L478M/M488L/R284K) has shown significantly increased stability to the glycolaldehyde toxicity, enabling production of glycolaldehyde to 31 mM from 75 mM formaldehyde (conversion: 83 %). Besides, the E1 subunit of α-ketoglutarate dehydrogenase complex from Vibrio vulnificus (VvSucA) was engineered as a regiospecific C2 carboligase for condensation of glycolaldehyde into erythrulose. The combination of EcGCL_R484M/N283Q/L478M/M488L/R284K and VvSucA_K228L led to the cascade production of erythrulose to 8 mM from 90 mM formaldehyde via glycolaldehyde without byproduct formation. This study will contribute to valorization of C1 gases into industrially relevant multi-carbon products in an environment-friendly way.
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Affiliation(s)
- Jun-Hong Kim
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Huijin Cheon
- Department of Food Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Hye-Jin Jo
- Department of Food Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Ji-Won Kim
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Ga Young Kim
- Department of Food Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Hye-Rim Seo
- Department of Food Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Pil-Won Seo
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jeong-Sun Kim
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea.
| | - Jin-Byung Park
- Department of Food Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea.
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4
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Biosynthesis of 4-hydroxybenzylideneacetone by Whole-Cell Escherichia coli. Catalysts 2022. [DOI: 10.3390/catal12090997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
4-Hydroxy benzylideneacetone (4-HBA) is an organic synthesis intermediate and can be used as a precursor for the synthesis of raspberry ketone. Herein, 2-deoxy-D-ribose 5-phosphate aldolase (DERA) was overexpressed in E. coli BL21 (DE3) as an attractive catalyst for enzymatic aldol reactions. The aldol reaction between 4-hydroxybenzaldehyde (4-HBD) and acetone to biosynthesize 4-HBA was catalyzed by whole-cell E. coli BL21 (DE3) (pRSF-Deoc). The yield and 4-HBA concentration were 92.8% and 111.35 mM, respectively, when using 120 mM 4-HBD and acetone as substrates. When the concentration of 4-HBD was increased to 480 mM, 376.4 mM 4-HBA was obtained by a fed-batch strategy with a yield of 78.4%, which was about a 28% improvement compared to the one-time addition strategy. E. coli BL21 (DE3) (pRSF-Deoc) cells were further immobilized with K-carrageenan, and the immobilized cells still maintained a residual activity of above 90% after 10 repeated uses. Our study provides a promising method of biosynthesizing 4-HBA.
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5
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Abstract
The application of biocatalysis in conquering challenging synthesis requires the constant input of new enzymes. Developing novel biocatalysts by absorbing catalysis modes from synthetic chemistry has yielded fruitful new-to-nature enzymes. Organocatalysis was originally bio-inspired and has become the third pillar of asymmetric catalysis. Transferring organocatalytic reactions back to enzyme platforms is a promising approach for biocatalyst creation. Herein, we summarize recent developments in the design of novel biocatalysts that adopt iminium catalysis, a fundamental branch in organocatalysis. By repurposing existing enzymes or constructing artificial enzymes, various biocatalysts for iminium catalysis have been created and optimized via protein engineering to promote valuable abiological transformations. Recent advances in iminium biocatalysis illustrate the power of combining chemomimetic biocatalyst design and directed evolution to generate useful new-to-nature enzymes.
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Affiliation(s)
- Guangcai Xu
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of PharmacyUniversity of GroningenAntonius Deusinglaan 19713AV GroningenThe Netherlands
| | - Gerrit J. Poelarends
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of PharmacyUniversity of GroningenAntonius Deusinglaan 19713AV GroningenThe Netherlands
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6
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Varela RF, Valino AL, Abdelraheem E, Médici R, Sayé M, Pereira CA, Hagedoorn PL, Hanefeld U, Iribarren A, Lewkowicz E. Synthetic Activity of Recombinant Whole Cell Biocatalysts Containing 2-Deoxy-D-ribose-5-phosphate Aldolase from Pectobacterium atrosepticum. Chembiochem 2022; 23:e202200147. [PMID: 35476788 DOI: 10.1002/cbic.202200147] [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: 03/14/2022] [Revised: 04/14/2022] [Indexed: 11/09/2022]
Abstract
In nature 2-deoxy-D-ribose-5-phosphate aldolase (DERA) catalyses the reversible formation of 2-deoxyribose 5-phosphate from D-glyceraldehyde 3-phosphate and acetaldehyde. In addition, this enzyme can use acetaldehyde as the sole substrate, resulting in a tandem aldol reaction, yielding 2,4,6-trideoxy-D-erythro-hexapyranose, which spontaneously cyclizes. This reaction is very useful for the synthesis of the side chain of statin-type drugs used to decrease cholesterol levels in blood. One of the main challenges in the use of DERA in industrial processes, where high substrate loads are needed to achieve the desired productivity, is its inactivation by high acetaldehyde concentration. In this work, the utility of different variants of Pectobacterium atrosepticum DERA (PaDERA) as whole cell biocatalysts to synthesize 2-deoxyribose 5-phosphate and 2,4,6-trideoxy-D-erythro-hexapyranose was analysed. Under optimized conditions, E. coli BL21 (PaDERA C-His AA C49M) whole cells yields 99 % of both products. Furthermore, this enzyme is able to tolerate 500 mM acetaldehyde in a whole-cell experiment which makes it suitable for industrial applications.
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Affiliation(s)
- Romina Fernández Varela
- Laboratorio de Biotransformaciones y Química de, Ácidos Nucléicos, Department of Science and Technology, Universidad Nacional de Quilmes, Roque S. Peña 352, B1876BXD, Bernal and CONICET, Argentina
| | - Ana Laura Valino
- Laboratorio de Biotransformaciones y Química de, Ácidos Nucléicos, Department of Science and Technology, Universidad Nacional de Quilmes, Roque S. Peña 352, B1876BXD, Bernal and CONICET, Argentina
| | - Eman Abdelraheem
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Rosario Médici
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Melisa Sayé
- Instituto de Investigaciones Médicas A. Lanari, Universidad de Buenos Aires, Facultad de Medicina, Buenos Aires, Argentina.,Laboratorio de Parasitología Molecular, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Instituto de Investigaciones Médicas (IDIM), Buenos Aires, Argentina
| | - Claudio A Pereira
- Instituto de Investigaciones Médicas A. Lanari, Universidad de Buenos Aires, Facultad de Medicina, Buenos Aires, Argentina.,Laboratorio de Parasitología Molecular, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Instituto de Investigaciones Médicas (IDIM), Buenos Aires, Argentina
| | - Peter-Leon Hagedoorn
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Ulf Hanefeld
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Adolfo Iribarren
- Laboratorio de Biotransformaciones y Química de, Ácidos Nucléicos, Department of Science and Technology, Universidad Nacional de Quilmes, Roque S. Peña 352, B1876BXD, Bernal and CONICET, Argentina
| | - Elizabeth Lewkowicz
- Laboratorio de Biotransformaciones y Química de, Ácidos Nucléicos, Department of Science and Technology, Universidad Nacional de Quilmes, Roque S. Peña 352, B1876BXD, Bernal and CONICET, Argentina
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7
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Ranjitkar S, Duan JE, Srirattana K, Alqahtani F, Tulman ER, Mandoiu I, Venkitanarayanan K, Tian X. Transcriptomic Responses of Mycoplasma bovis Upon Treatments of trans-Cinnamaldehyde, Carvacrol, and Eugenol. Front Microbiol 2022; 13:888433. [PMID: 35733968 PMCID: PMC9207385 DOI: 10.3389/fmicb.2022.888433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
Mycoplasma bovis (M. bovis) is an insidious, wall-less primary bacterial pathogen that causes bovine pneumonia, mid-ear infection, mastitis, and arthritis. The economic losses caused by M. bovis due to culling, diminished milk production, and feed conversion are underestimated because of poor diagnosis/recognition. Treatment with common antibiotics targeting the cell wall is ineffective. Plant-derived antimicrobials (PDAs) such as food-grade trans-cinnamaldehyde (TC), eugenol (EU), and carvacrol (CAR) are inexpensive and generally regarded as safe for humans and animals yet possess strong anti-bacterial properties. In preliminary studies, we found that all three PDAs inhibited the growth of M. bovis in vitro. Through RNA sequencing, we report here that CAR affected the expression of 153 genes which included the downregulation of energy generation-related proteins, pentose phosphate pathway, and upregulation of ribosomes and translation-related proteins. Few differentially expressed genes were found when M. bovis was treated with TC, EU, or when the three PDAs were double or triple combined. Our results suggest that, as opposed to the effect of CAR, the growth-inhibitory effects of TC and EU at levels tested may be exerted through mechanisms other than gene expression regulations.
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Affiliation(s)
- Saurav Ranjitkar
- Department of Animal Science, University of Connecticut, Storrs, CT, United States
| | - Jingyue Ellie Duan
- Department of Animal Science, University of Connecticut, Storrs, CT, United States
| | - Kanokwan Srirattana
- Department of Animal Science, University of Connecticut, Storrs, CT, United States
| | - Fahad Alqahtani
- National Center for Bioinformatics, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Edan R. Tulman
- Department of Pathobiology and Veterinary Science, University of Connecticut, Storrs, CT, United States
| | - Ion Mandoiu
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, United States
| | | | - Xiuchun Tian
- Department of Animal Science, University of Connecticut, Storrs, CT, United States
- *Correspondence: Xiuchun Tian,
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8
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Hindges J, Döbber J, Hayes MR, Classen T, Pohl M, Pietruszka J. Covalently Immobilized 2‐Deoxyribose‐5‐phosphate Aldolase (DERA) for Biocatalysis in Flow: Utilization of the 3‐Hydroxyaldehyde Intermediate in Reaction Cascades. ChemCatChem 2022. [DOI: 10.1002/cctc.202200390] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Julia Hindges
- Heinrich-Heine-Universitat Dusseldorf Institute for bioorganic chemistry GERMANY
| | - Johannes Döbber
- Forschungszentrum Julich Institut fur Bio und Geowissenschaften Biotechnologie GERMANY
| | - Marc Richard Hayes
- Heinrich-Heine-Universitat Dusseldorf Institute for bioorganic chemistry GERMANY
| | - Thomas Classen
- Forschungszentrum Julich Institut fur Bio und Geowissenschaften Biotechnologie GERMANY
| | - Martina Pohl
- Forschungszentrum Julich Institut fur Bio und Geowissenschaften Biotechnologie GERMANY
| | - Joerg Pietruszka
- Heinrich-Heine-Universitat Dusseldorf Institut für Bioorganische Chemie Im Forschungszentrum JülichGeb. 15.8 52426 Jülich GERMANY
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9
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Xu G, Poelarends GJ. Unlocking New Reactivities in Enzymes by Iminium Catalysis. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Guangcai Xu
- University of Groningen: Rijksuniversiteit Groningen Chemical and Pharmaceutical Biology NETHERLANDS
| | - Gerrit J. Poelarends
- University of Groningen Chemical and Pharmaceutical Biology Antonius Deusinglaan 1 9713 AV Groningen NETHERLANDS
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10
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Hélaine V, Gastaldi C, Lemaire M, Clapés P, Guérard-Hélaine C. Recent Advances in the Substrate Selectivity of Aldolases. ACS Catal 2021. [DOI: 10.1021/acscatal.1c04273] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Virgil Hélaine
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
| | - Cédric Gastaldi
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
| | - Marielle Lemaire
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
| | - Pere Clapés
- Biological Chemistry Department, Institute for Advanced Chemistry of Catalonia, IQAC−CSIC, 08034 Barcelona, Spain
| | - Christine Guérard-Hélaine
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
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11
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Abstract
Biocatalysis has an enormous impact on chemical synthesis. The waves in which biocatalysis has developed, and in doing so changed our perception of what organic chemistry is, were reviewed 20 and 10 years ago. Here we review the consequences of these waves of development. Nowadays, hydrolases are widely used on an industrial scale for the benign synthesis of commodity and bulk chemicals and are fully developed. In addition, further enzyme classes are gaining ever increasing interest. Particularly, enzymes catalysing selective C-C-bond formation reactions and enzymes catalysing selective oxidation and reduction reactions are solving long-standing synthetic challenges in organic chemistry. Combined efforts from molecular biology, systems biology, organic chemistry and chemical engineering will establish a whole new toolbox for chemistry. Recent developments are critically reviewed.
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Affiliation(s)
- Ulf Hanefeld
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, The Netherlands.
| | - Frank Hollmann
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, The Netherlands.
| | - Caroline E Paul
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, The Netherlands.
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12
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Simić S, Zukić E, Schmermund L, Faber K, Winkler CK, Kroutil W. Shortening Synthetic Routes to Small Molecule Active Pharmaceutical Ingredients Employing Biocatalytic Methods. Chem Rev 2021; 122:1052-1126. [PMID: 34846124 DOI: 10.1021/acs.chemrev.1c00574] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Biocatalysis, using enzymes for organic synthesis, has emerged as powerful tool for the synthesis of active pharmaceutical ingredients (APIs). The first industrial biocatalytic processes launched in the first half of the last century exploited whole-cell microorganisms where the specific enzyme at work was not known. In the meantime, novel molecular biology methods, such as efficient gene sequencing and synthesis, triggered breakthroughs in directed evolution for the rapid development of process-stable enzymes with broad substrate scope and good selectivities tailored for specific substrates. To date, enzymes are employed to enable shorter, more efficient, and more sustainable alternative routes toward (established) small molecule APIs, and are additionally used to perform standard reactions in API synthesis more efficiently. Herein, large-scale synthetic routes containing biocatalytic key steps toward >130 APIs of approved drugs and drug candidates are compared with the corresponding chemical protocols (if available) regarding the steps, reaction conditions, and scale. The review is structured according to the functional group formed in the reaction.
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Affiliation(s)
- Stefan Simić
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Erna Zukić
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Luca Schmermund
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Kurt Faber
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Christoph K Winkler
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Wolfgang Kroutil
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria.,Field of Excellence BioHealth─University of Graz, 8010 Graz, Austria.,BioTechMed Graz, 8010 Graz, Austria
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13
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Kunzendorf A, Xu G, van der Velde JJH, Rozeboom H, Thunnissen AMWH, Poelarends GJ. Unlocking Asymmetric Michael Additions in an Archetypical Class I Aldolase by Directed Evolution. ACS Catal 2021; 11:13236-13243. [PMID: 34765282 PMCID: PMC8576802 DOI: 10.1021/acscatal.1c03911] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/02/2021] [Indexed: 01/06/2023]
Abstract
Class I aldolases catalyze asymmetric aldol addition reactions and have found extensive application in the biocatalytic synthesis of chiral β-hydroxy-carbonyl compounds. However, the usefulness of these powerful enzymes for application in other C-C bond-forming reactions remains thus far unexplored. The redesign of class I aldolases to expand their catalytic repertoire to include non-native carboligation reactions therefore continues to be a major challenge. Here, we report the successful redesign of 2-deoxy-d-ribose-5-phosphate aldolase (DERA) from Escherichia coli, an archetypical class I aldolase, to proficiently catalyze enantioselective Michael additions of nitromethane to α,β-unsaturated aldehydes to yield various pharmaceutically relevant chiral synthons. After 11 rounds of directed evolution, the redesigned DERA enzyme (DERA-MA) carried 12 amino-acid substitutions and had an impressive 190-fold enhancement in catalytic activity compared to the wildtype enzyme. The high catalytic efficiency of DERA-MA for this abiological reaction makes it a proficient "Michaelase" with potential for biocatalytic application. Crystallographic analysis provides a structural context for the evolved activity. Whereas an aldolase acts naturally by activating the enzyme-bound substrate as a nucleophile (enamine-based mechanism), DERA-MA instead acts by activating the enzyme-bound substrate as an electrophile (iminium-based mechanism). This work demonstrates the power of directed evolution to expand the reaction scope of natural aldolases to include asymmetric Michael addition reactions and presents opportunities to explore iminium catalysis with DERA-derived catalysts inspired by developments in the organocatalysis field.
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Affiliation(s)
- Andreas Kunzendorf
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Guangcai Xu
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Jesse J. H. van der Velde
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Henriëtte
J. Rozeboom
- Molecular
Enzymology Group, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Andy-Mark W. H. Thunnissen
- Molecular
Enzymology Group, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Gerrit J. Poelarends
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
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14
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Coloma J, Guiavarc'h Y, Hagedoorn PL, Hanefeld U. Immobilisation and flow chemistry: tools for implementing biocatalysis. Chem Commun (Camb) 2021; 57:11416-11428. [PMID: 34636371 DOI: 10.1039/d1cc04315c] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The merger of enzyme immobilisation and flow chemistry has attracted the attention of the scientific community during recent years. Immobilisation enhances enzyme stability and enables recycling, flow chemistry allows process intensification. Their combination is desirable for the development of more efficient and environmentally friendly biocatalytic processes. In this feature article, we aim to point out important metrics for successful enzyme immobilisation and for reporting flow biocatalytic processes. Relevant examples of immobilised enzymes used in flow systems in organic, biphasic and aqueous systems are discussed. Finally, we describe recent developments to address the cofactor recycling hurdle.
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Affiliation(s)
- José Coloma
- Biokatalyse, Afdeling Biotechnologie, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ Delft, The Netherlands. .,Universidad Laica Eloy Alfaro de Manabí, Avenida Circunvalación s/n, P. O. Box 13-05-2732, Manta, Ecuador
| | - Yann Guiavarc'h
- Biokatalyse, Afdeling Biotechnologie, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ Delft, The Netherlands. .,Laboratory Reactions and Process Engineering, University of Lorraine, CNRS, LRGP, F-54000 Nancy, France
| | - Peter-Leon Hagedoorn
- Biokatalyse, Afdeling Biotechnologie, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Ulf Hanefeld
- Biokatalyse, Afdeling Biotechnologie, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
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15
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Catalytic and structural insights into a stereospecific and thermostable Class II aldolase HpaI from Acinetobacter baumannii. J Biol Chem 2021; 297:101280. [PMID: 34624314 PMCID: PMC8560999 DOI: 10.1016/j.jbc.2021.101280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 10/01/2021] [Accepted: 10/01/2021] [Indexed: 11/21/2022] Open
Abstract
Aldolases catalyze the reversible reactions of aldol condensation and cleavage and have strong potential for the synthesis of chiral compounds, widely used in pharmaceuticals. Here, we investigated a new Class II metal aldolase from the p-hydroxyphenylacetate degradation pathway in Acinetobacter baumannii, 4-hydroxy-2-keto-heptane-1,7-dioate aldolase (AbHpaI), which has various properties suitable for biocatalysis, including stereoselectivity/stereospecificity, broad aldehyde utilization, thermostability, and solvent tolerance. Notably, the use of Zn2+ by AbHpaI as a native cofactor is distinct from other enzymes in this class. AbHpaI can also use other metal ion (M2+) cofactors, except Ca2+, for catalysis. We found that Zn2+ yielded the highest enzyme complex thermostability (Tm of 87 °C) and solvent tolerance. All AbHpaI•M2+ complexes demonstrated preferential cleavage of (4R)-2-keto-3-deoxy-D-galactonate ((4R)-KDGal) over (4S)-2-keto-3-deoxy-D-gluconate ((4S)-KDGlu), with AbHpaI•Zn2+ displaying the highest R/S stereoselectivity ratio (sixfold higher than other M2+ cofactors). For the aldol condensation reaction, AbHpaI•M2+ only specifically forms (4R)-KDGal and not (4S)-KDGlu and preferentially catalyzes condensation rather than cleavage by ∼40-fold. Based on 11 X-ray structures of AbHpaI complexed with M2+ and ligands at 1.85 to 2.0 Å resolution, the data clearly indicate that the M2+ cofactors form an octahedral geometry with Glu151 and Asp177, pyruvate, and water molecules. Moreover, Arg72 in the Zn2+-bound form governs the stereoselectivity/stereospecificity of AbHpaI. X-ray structures also show that Ca2+ binds at the trimer interface via interaction with Asp51. Hence, we conclude that AbHpaI•Zn2+ is distinctive from its homologues in substrate stereospecificity, preference for aldol formation over cleavage, and protein robustness, and is attractive for biocatalytic applications.
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Lee SH, Yeom SJ, Kim SE, Oh DK. Development of aldolase-based catalysts for the synthesis of organic chemicals. Trends Biotechnol 2021; 40:306-319. [PMID: 34462144 DOI: 10.1016/j.tibtech.2021.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/01/2021] [Accepted: 08/02/2021] [Indexed: 11/28/2022]
Abstract
Aldol chemicals are synthesized by condensation reactions between the carbon units of ketones and aldehydes using aldolases. The efficient synthesis of diverse organic chemicals requires intrinsic modification of aldolases via engineering and design, as well as extrinsic modification through immobilization or combination with other catalysts. This review describes the development of aldolases, including their engineering and design, and the selection of desired aldolases using high-throughput screening, to enhance their catalytic properties and perform novel reactions. Aldolase-containing catalysts, which catalyze the aldol reaction combined with other enzymatic and/or chemical reactions, can efficiently synthesize diverse complex organic chemicals using inexpensive and simple materials as substrates. We also discuss the current challenges and emerging solutions for aldolase-based catalysts.
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Affiliation(s)
- Seon-Hwa Lee
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Soo-Jin Yeom
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Seong-Eun Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Deok-Kun Oh
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea.
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17
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Engineering of Yeast Old Yellow Enzyme OYE3 Enables Its Capability Discriminating of ( E)-Citral and ( Z)-Citral. Molecules 2021; 26:molecules26165040. [PMID: 34443627 PMCID: PMC8399149 DOI: 10.3390/molecules26165040] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/11/2021] [Accepted: 08/17/2021] [Indexed: 11/17/2022] Open
Abstract
The importance of yeast old yellow enzymes is increasingly recognized for direct asymmetric reduction of (E/Z)-citral to (R)-citronellal. As one of the most performing old yellow enzymes, the enzyme OYE3 from Saccharomyces cerevisiae S288C exhibited complementary enantioselectivity for the reduction of (E)-citral and (Z)-citral, resulting in lower e.e. value of (R)-citronellal in the reduction of (E/Z)-citral. To develop a novel approach for the direct synthesis of enantio-pure (R)-citronellal from the reduction of (E/Z)-citral, the enzyme OYE3 was firstly modified by semi-rational design to improve its (R)-enantioselectivity. The OYE3 variants W116A and S296F showed strict (R)-enantioselectivity in the reduction of (E)-citral, and significantly reversed the (S)-enantioselectivity in the reduction of (Z)-citral. Next, the double substitution of OYE3 led to the unique variant S296F/W116G, which exhibited strict (R)-enantioselectivity in the reduction of (E)-citral and (E/Z)-citral, but was not active on (Z)-citral. Relying on its capability discriminating (E)-citral and (Z)-citral, a new cascade reaction catalyzed by the OYE3 variant S296F/W116G and glucose dehydrogenase was developed, providing the enantio-pure (R)-citronellal and the retained (Z)-citral after complete reduction of (E)-citral.
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18
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Current state of and need for enzyme engineering of 2-deoxy-D-ribose 5-phosphate aldolases and its impact. Appl Microbiol Biotechnol 2021; 105:6215-6228. [PMID: 34410440 PMCID: PMC8403123 DOI: 10.1007/s00253-021-11462-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/13/2021] [Accepted: 07/19/2021] [Indexed: 01/28/2023]
Abstract
Abstract Deoxyribose-5-phosphate aldolases (DERAs, EC 4.1.2.4) are acetaldehyde-dependent, Class I aldolases catalyzing in nature a reversible aldol reaction between an acetaldehyde donor (C2 compound) and glyceraldehyde-3-phosphate acceptor (C3 compound, C3P) to generate deoxyribose-5-phosphate (C5 compound, DR5P). DERA enzymes have been found to accept also other types of aldehydes as their donor, and in particular as acceptor molecules. Consequently, DERA enzymes can be applied in C–C bond formation reactions to produce novel compounds, thus offering a versatile biocatalytic alternative for synthesis. DERA enzymes, found in all kingdoms of life, share a common TIM barrel fold despite the low overall sequence identity. The catalytic mechanism is well-studied and involves formation of a covalent enzyme-substrate intermediate. A number of protein engineering studies to optimize substrate specificity, enzyme efficiency, and stability of DERA aldolases have been published. These have employed various engineering strategies including structure-based design, directed evolution, and recently also machine learning–guided protein engineering. For application purposes, enzyme immobilization and usage of whole cell catalysis are preferred methods as they improve the overall performance of the biocatalytic processes, including often also the stability of the enzyme. Besides single-step enzymatic reactions, DERA aldolases have also been applied in multi-enzyme cascade reactions both in vitro and in vivo. The DERA-based applications range from synthesis of commodity chemicals and flavours to more complicated and high-value pharmaceutical compounds. Key points • DERA aldolases are versatile biocatalysts able to make new C–C bonds. • Synthetic utility of DERAs has been improved by protein engineering approaches. • Computational methods are expected to speed up the future DERA engineering efforts. Graphical abstract ![]()
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19
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Liu M, Wei D, Wen Z, Wang JB. Progress in Stereoselective Construction of C-C Bonds Enabled by Aldolases and Hydroxynitrile Lyases. Front Bioeng Biotechnol 2021; 9:653682. [PMID: 33968915 PMCID: PMC8097096 DOI: 10.3389/fbioe.2021.653682] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/25/2021] [Indexed: 11/13/2022] Open
Abstract
The creation of C-C bonds is an effective strategy for constructing complex compounds from simple synthetic blocks. Although many methods have been developed for C-C bond construction, the stereoselective creation of new C-C bonds remains a challenge. The selectivities (enantioselectivity, regioselectivity, and chemoselectivity) of biocatalysts are higher than those of chemical catalysts, therefore biocatalysts are excellent candidates for use in stereoselective C-C bond formation. Here, we summarize progress made in the past 10 years in stereoselective C-C bond formation enabled by two classic types of enzyme, aldolases and hydroxynitrile lyases. The information in this review will enable the development of new routes to the stereoselective construction of C-C bonds.
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Affiliation(s)
- Mi Liu
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, China.,Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, China
| | - Dan Wei
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, China.,Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, China
| | - Zexing Wen
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, China.,Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, China
| | - Jian-Bo Wang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, China.,Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, China
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20
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Liu H, Bowie JU. Cell-free synthetic biochemistry upgrading of ethanol to 1,3 butanediol. Sci Rep 2021; 11:9449. [PMID: 33941811 PMCID: PMC8093283 DOI: 10.1038/s41598-021-88899-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/19/2021] [Indexed: 11/30/2022] Open
Abstract
It is now possible to efficiently fix flue gas CO/CO2 into ethanol using acetogens, thereby making carbon negative ethanol. While the ethanol could be burned as a fuel, returning the CO2 to the atmosphere, it might also be possible to use the fixed carbon in more diverse chemicals, thereby keeping it fixed. Here we describe a simple synthetic biochemistry approach for converting carbon negative ethanol into the synthetic building block chemical 1,3 butanediol (1,3-BDO). The pathway completely conserves carbon from ethanol and can ultimately be powered electrochemically via formate oxidation. Our proof-of-principle system reached a maximum productivity of 0.16 g/L/h and, with replenishment of feedstock and enzymes, achieved a titer of 7.7 g/L. We identify a number of elements that can be addressed in future work to improve both cell-free and cell-based production of 1,3-BDO.
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Affiliation(s)
- Hongjiang Liu
- Department of Chemistry and Biochemistry, Molecular Biology Institute, UCLA-DOE Institute, University of California, 611 Charles E. Young Dr. E, Los Angeles, CA, 90095-1570, USA
| | - James U Bowie
- Department of Chemistry and Biochemistry, Molecular Biology Institute, UCLA-DOE Institute, University of California, 611 Charles E. Young Dr. E, Los Angeles, CA, 90095-1570, USA.
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21
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Xue F, Li C, Xu Q. Biocatalytic approaches for the synthesis of optically pure vic-halohydrins. Appl Microbiol Biotechnol 2021; 105:3411-3421. [PMID: 33851239 DOI: 10.1007/s00253-021-11266-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 03/28/2021] [Accepted: 04/04/2021] [Indexed: 11/30/2022]
Abstract
Enantiopure vicinal halohydrins (vic-halohydrins) are highly valuable building blocks for the synthesis of many different natural products and pharmaceuticals, and biocatalytic methods for their synthesis have received considerable interest. This review emphasizes the application of biocatalytic approaches as an efficient alternative or complement to conventional chemical reactions, with a special focus on the asymmetric reductions catalyzed by ketoreductases, kinetic resolution catalyzed using lipases or esterases, stereoselective biotransformation catalyzed by halohydrin dehalogenases, asymmetric hydroxylation catalyzed by cytochrome P450 monooxygenases, asymmetric dehalogenation catalyzed by haloalkane dehalogenases, and aldehyde condensation catalyzed by aldolases. Although many chiral vic-halohydrins have been successfully synthesized using wild-type biocatalysts, their enantioselectivity is often too low for enantiopure synthesis. To overcome these limitations, catalytic properties of wild-type enzymes have been improved by rational and semi-rational protein design or directed evolution. This review briefly introduces the research status in this field, highlighting aspects of basic academic research in the biocatalytic synthesis of optically active vic-halohydrins by employing such unconventional approaches. KEY POINTS: • Outlines the enzymatic strategies for the production of enantiopure vic-halohydrins • Highlights recent advances in biocatalytic production of enantiopure vic-halohydrins • Provide guidance for efficient preparation of enantiopure vic-halohydrins.
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Affiliation(s)
- Feng Xue
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, NO 1, Wenyuan Road, Nanjing, 210023, People's Republic of China
| | - Changfan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, NO 1, Wenyuan Road, Nanjing, 210023, People's Republic of China
| | - Qing Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, NO 1, Wenyuan Road, Nanjing, 210023, People's Republic of China.
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22
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Švarc A, Fekete M, Hernandez K, Clapés P, Findrik Blažević Z, Szekrenyi A, Skendrović D, Vasić-Rački Đ, Charnock SJ, Presečki AV. An innovative route for the production of atorvastatin side-chain precursor by DERA-catalysed double aldol addition. Chem Eng Sci 2021. [DOI: 10.1016/j.ces.2020.116312] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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23
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Voutilainen S, Heinonen M, Andberg M, Jokinen E, Maaheimo H, Pääkkönen J, Hakulinen N, Rouvinen J, Lähdesmäki H, Kaski S, Rousu J, Penttilä M, Koivula A. Substrate specificity of 2-deoxy-D-ribose 5-phosphate aldolase (DERA) assessed by different protein engineering and machine learning methods. Appl Microbiol Biotechnol 2020; 104:10515-10529. [PMID: 33147349 PMCID: PMC7671976 DOI: 10.1007/s00253-020-10960-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 10/01/2020] [Accepted: 10/12/2020] [Indexed: 11/29/2022]
Abstract
In this work, deoxyribose-5-phosphate aldolase (Ec DERA, EC 4.1.2.4) from Escherichia coli was chosen as the protein engineering target for improving the substrate preference towards smaller, non-phosphorylated aldehyde donor substrates, in particular towards acetaldehyde. The initial broad set of mutations was directed to 24 amino acid positions in the active site or in the close vicinity, based on the 3D complex structure of the E. coli DERA wild-type aldolase. The specific activity of the DERA variants containing one to three amino acid mutations was characterised using three different substrates. A novel machine learning (ML) model utilising Gaussian processes and feature learning was applied for the 3rd mutagenesis round to predict new beneficial mutant combinations. This led to the most clear-cut (two- to threefold) improvement in acetaldehyde (C2) addition capability with the concomitant abolishment of the activity towards the natural donor molecule glyceraldehyde-3-phosphate (C3P) as well as the non-phosphorylated equivalent (C3). The Ec DERA variants were also tested on aldol reaction utilising formaldehyde (C1) as the donor. Ec DERA wild-type was shown to be able to carry out this reaction, and furthermore, some of the improved variants on acetaldehyde addition reaction turned out to have also improved activity on formaldehyde. KEY POINTS: • DERA aldolases are promiscuous enzymes. • Synthetic utility of DERA aldolase was improved by protein engineering approaches. • Machine learning methods aid the protein engineering of DERA.
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Affiliation(s)
- Sanni Voutilainen
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, FI-02044 VTT, Espoo, Finland.
| | - Markus Heinonen
- Department of Computer Science, Aalto University, Espoo, Finland
- Helsinki Institute for Information Technology, Espoo, Finland
| | - Martina Andberg
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Emmi Jokinen
- Department of Computer Science, Aalto University, Espoo, Finland
| | - Hannu Maaheimo
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Johan Pääkkönen
- Department of Chemistry, University of Eastern Finland, PO Box 111, FI-80101, Joensuu, Finland
| | - Nina Hakulinen
- Department of Chemistry, University of Eastern Finland, PO Box 111, FI-80101, Joensuu, Finland
| | - Juha Rouvinen
- Department of Chemistry, University of Eastern Finland, PO Box 111, FI-80101, Joensuu, Finland
| | - Harri Lähdesmäki
- Department of Computer Science, Aalto University, Espoo, Finland
| | - Samuel Kaski
- Department of Computer Science, Aalto University, Espoo, Finland
- Helsinki Institute for Information Technology, Espoo, Finland
| | - Juho Rousu
- Department of Computer Science, Aalto University, Espoo, Finland
- Helsinki Institute for Information Technology, Espoo, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Anu Koivula
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
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24
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Discovery and Engineering of an Aldehyde Tolerant 2-deoxy-D-ribose 5-phosphate Aldolase (DERA) from Pectobacterium atrosepticum. Catalysts 2020. [DOI: 10.3390/catal10080883] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
DERA (2-Deoxy-D-ribose 5-phosphate aldolase) is the only known aldolase that accepts two aldehyde substrates, which makes it an attractive catalyst for the synthesis of a chiral polyol motif that is present in several pharmaceuticals, such as atorvastatin and pravastatin. However, inactivation of the enzyme in the presence of aldehydes hinders its practical application. Whole cells of Pectobacterium atrosepticum were reported to exhibit good tolerance toward acetaldehyde and to afford 2-deoxyribose 5-phosphate with good yields. The DERA gene (PaDERA) was identified, and both the wild-type and a C49M mutant were heterologously expressed in Escherichia coli. The purification protocol was optimized and an initial biochemical characterization was conducted. Unlike other DERAs, which show a maximal activity between pH 4.0 and 7.5, PaDERA presented an optimum pH in the alkaline range between 8.0 and 9.0. This could warrant its use for specific syntheses in the future. PaDERA also displayed fourfold higher specific activity than DERA from E. coli (EcDERA) and displayed a promising acetaldehyde resistance outside the whole-cell environment. The C49M mutation, which was previously identified to increase acetaldehyde tolerance in EcDERA, also led to significant improvements in the acetaldehyde tolerance of PaDERA.
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25
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Xuan K, Yang G, Wu Z, Xu Y, Zhang R. Efficient synthesis of (3R,5S)-6-chloro-2,4,6-trideoxyhexapyranose by using new 2-deoxy-d-ribose-5-phosphate aldolase from Streptococcus suis with moderate activity and aldehyde tolerance. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Sheldon RA, Brady D, Bode ML. The Hitchhiker's guide to biocatalysis: recent advances in the use of enzymes in organic synthesis. Chem Sci 2020; 11:2587-2605. [PMID: 32206264 PMCID: PMC7069372 DOI: 10.1039/c9sc05746c] [Citation(s) in RCA: 146] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/12/2020] [Indexed: 12/12/2022] Open
Abstract
Enzymes are excellent catalysts that are increasingly being used in industry and academia. This perspective is primarily aimed at synthetic organic chemists with limited experience using enzymes and provides a general and practical guide to enzymes and their synthetic potential, with particular focus on recent applications.
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Affiliation(s)
- Roger A Sheldon
- Molecular Sciences Institute , School of Chemistry , University of the Witwatersrand , Johannesburg , South Africa .
- Department of Biotechnology , Delft University of Technology , Delft , The Netherlands
| | - Dean Brady
- Molecular Sciences Institute , School of Chemistry , University of the Witwatersrand , Johannesburg , South Africa .
| | - Moira L Bode
- Molecular Sciences Institute , School of Chemistry , University of the Witwatersrand , Johannesburg , South Africa .
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27
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Biewenga L, Crotti M, Saifuddin M, Poelarends GJ. Selective Colorimetric "Turn-On" Probe for Efficient Engineering of Iminium Biocatalysis. ACS OMEGA 2020; 5:2397-2405. [PMID: 32064400 PMCID: PMC7017405 DOI: 10.1021/acsomega.9b03849] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 01/16/2020] [Indexed: 06/10/2023]
Abstract
The efficient engineering of iminium biocatalysis has drawn considerable attention, with many applications in pharmaceutical synthesis. Here, we report a tailor-made iminium-activated colorimetric "turn-on" probe, specifically designed as a prescreening tool to facilitate engineering of iminium biocatalysis. Upon complexation of the probe with the catalytic Pro-1 residue of the model enzyme 4-oxalocrotonate tautomerase (4-OT), a brightly colored merocyanine-dye-type structure is formed. 4-OT mutants that formed this brightly colored species upon incubation with the probe proved to have a substantial activity for the iminium-based Michael-type addition of nitromethane to cinnamaldehyde, whereas mutants that showed no staining by the probe exhibited no or very low-level "Michaelase" activity. This system was exploited in a solid-phase prescreening assay termed as activated iminium colony staining (AICS) to enrich libraries for active mutants. AICS prescreening reduced the screening effort up to 20-fold. After two rounds of directed evolution, two artificial Michaelases were identified with up to 39-fold improvement in the activity for the addition of nitromethane to cinnamaldehyde, yielding the target γ-nitroaldehyde product with excellent isolated yield (up to 95%) and enantiopurity (up to >99% ee). The colorimetric activation of the turn-on probe could be extended to the class I aldolase 2-deoxy-d-ribose 5-phosphate aldolase, implicating a broader application of AICS in engineering iminium biocatalysis.
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28
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Kim T, Stogios PJ, Khusnutdinova AN, Nemr K, Skarina T, Flick R, Joo JC, Mahadevan R, Savchenko A, Yakunin AF. Rational engineering of 2-deoxyribose-5-phosphate aldolases for the biosynthesis of ( R)-1,3-butanediol. J Biol Chem 2019; 295:597-609. [PMID: 31806708 DOI: 10.1074/jbc.ra119.011363] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 12/04/2019] [Indexed: 12/14/2022] Open
Abstract
Carbon-carbon bond formation is one of the most important reactions in biocatalysis and organic chemistry. In nature, aldolases catalyze the reversible stereoselective aldol addition between two carbonyl compounds, making them attractive catalysts for the synthesis of various chemicals. In this work, we identified several 2-deoxyribose-5-phosphate aldolases (DERAs) having acetaldehyde condensation activity, which can be used for the biosynthesis of (R)-1,3-butanediol (1,3BDO) in combination with aldo-keto reductases (AKRs). Enzymatic screening of 20 purified DERAs revealed the presence of significant acetaldehyde condensation activity in 12 of the enzymes, with the highest activities in BH1352 from Bacillus halodurans, TM1559 from Thermotoga maritima, and DeoC from Escherichia coli The crystal structures of BH1352 and TM1559 at 1.40-2.50 Å resolution are the first full-length DERA structures revealing the presence of the C-terminal Tyr (Tyr224 in BH1352). The results from structure-based site-directed mutagenesis of BH1352 indicated a key role for the catalytic Lys155 and other active-site residues in the 2-deoxyribose-5-phosphate cleavage and acetaldehyde condensation reactions. These experiments also revealed a 2.5-fold increase in acetaldehyde transformation to 1,3BDO (in combination with AKR) in the BH1352 F160Y and F160Y/M173I variants. The replacement of the WT BH1352 by the F160Y or F160Y/M173I variants in E. coli cells expressing the DERA + AKR pathway increased the production of 1,3BDO from glucose five and six times, respectively. Thus, our work provides detailed insights into the molecular mechanisms of substrate selectivity and activity of DERAs and identifies two DERA variants with enhanced activity for in vitro and in vivo 1,3BDO biosynthesis.
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Affiliation(s)
- Taeho Kim
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada; Future Technology Center, LG Chem, Gangseo-gu, Seoul 150-721, Korea
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Anna N Khusnutdinova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Kayla Nemr
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Tatiana Skarina
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Robert Flick
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Jeong Chan Joo
- Center for Bio-Based Chemistry, Division of Convergence Chemistry, Korea Research Institute of Chemical Technology, Yuseong-gu, Daejeon 34114, Korea
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada; Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada; Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor LL57 2UW, United Kingdom.
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Zhang S, Bramski J, Tutus M, Pietruszka J, Böker A, Reinicke S. A Biocatalytically Active Membrane Obtained from Immobilization of 2-Deoxy-d-ribose-5-phosphate Aldolase on a Porous Support. ACS APPLIED MATERIALS & INTERFACES 2019; 11:34441-34453. [PMID: 31448894 DOI: 10.1021/acsami.9b12029] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Aldol reactions play an important role in organic synthesis, as they belong to the class of highly beneficial C-C-linking reactions. Aldol-type reactions can be efficiently and stereoselectively catalyzed by the enzyme 2-deoxy-d-ribose-5-phosphate aldolase (DERA) to gain key intermediates for pharmaceuticals such as atorvastatin. The immobilization of DERA would open the opportunity for a continuous operation mode which gives access to an efficient, large-scale production of respective organic intermediates. In this contribution, we synthesize and utilize DERA/polymer conjugates for the generation and fixation of a DERA bearing thin film on a polymeric membrane support. The conjugation strongly increases the tolerance of the enzyme toward the industrial relevant substrate acetaldehyde while UV-cross-linkable groups along the conjugated polymer chains provide the opportunity for covalent binding to the support. First, we provide a thorough characterization of the conjugates followed by immobilization tests on representative, nonporous cycloolefinic copolymer supports. Finally, immobilization on the target supports constituted of polyacrylonitrile (PAN) membranes is performed, and the resulting enzymatically active membranes are implemented in a simple membrane module setup for the first assessment of biocatalytic performance in the continuous operation mode using the combination hexanal/acetaldehyde as the substrate.
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Affiliation(s)
- Shuhao Zhang
- Chair of Polymer Materials and Polymer Technologies , University of Potsdam, Institute of Chemistry , Karl-Liebknecht-Straße 24-25 , 14476 Potsdam , Germany
| | - Julia Bramski
- Institute of Bioorganic Chemistry , Heinrich Heine University of Düsseldorf at Forschungszentrum Jülich , Stetternicher Forst , 52426 Jülich , Germany
| | | | - Jörg Pietruszka
- Institute of Bioorganic Chemistry , Heinrich Heine University of Düsseldorf at Forschungszentrum Jülich , Stetternicher Forst , 52426 Jülich , Germany
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH , 52425 Jülich , Germany
| | - Alexander Böker
- Chair of Polymer Materials and Polymer Technologies , University of Potsdam, Institute of Chemistry , Karl-Liebknecht-Straße 24-25 , 14476 Potsdam , Germany
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Laurent V, Hélaine V, Vergne-Vaxelaire C, Nauton L, Traikia M, Petit JL, Salanoubat M, de Berardinis V, Lemaire M, Guérard-Hélaine C. Achiral Hydroxypyruvaldehyde Phosphate as a Platform for Multi-Aldolases Cascade Synthesis of Diuloses and for a Quadruple Acetaldehyde Addition Catalyzed by 2-Deoxyribose-5-Phosphate Aldolases. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02668] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Victor Laurent
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
| | - Virgil Hélaine
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
| | - Carine Vergne-Vaxelaire
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Univ Paris-Saclay, 91000 Evry, France
| | - Lionel Nauton
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
| | - Mounir Traikia
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
| | - Jean-Louis Petit
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Univ Paris-Saclay, 91000 Evry, France
| | - Marcel Salanoubat
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Univ Paris-Saclay, 91000 Evry, France
| | - Véronique de Berardinis
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Univ Paris-Saclay, 91000 Evry, France
| | - Marielle Lemaire
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
| | - Christine Guérard-Hélaine
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
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Chambre D, Guérard-Hélaine C, Darii E, Mariage A, Petit JL, Salanoubat M, de Berardinis V, Lemaire M, Hélaine V. 2-Deoxyribose-5-phosphate aldolase, a remarkably tolerant aldolase towards nucleophile substrates. Chem Commun (Camb) 2019; 55:7498-7501. [PMID: 31187106 DOI: 10.1039/c9cc03361k] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We explored a collection of 2-deoxyribose-5-phosphate aldolases (DERAs) from biodiversity for their nucleophile substrate promiscuity. The DERAs were screened using as nucleophiles propanone, propanal, cyclobutanone, cyclopentanone, dihydroxyacetone, and glycolaldehyde with l-glyceraldehyde-3-phosphate as an electrophile in aldol addition. A DERA from Arthrobacter chlorophenolicus (DERAArthro) efficiently allowed the synthesis of the corresponding aldol adducts in good yields, displaying complementarity in terms of configuration and substrate specificity with fructose-6-phosphate aldolase, the only previously known aldolase with a large nucleophile tolerance.
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Affiliation(s)
- Domitille Chambre
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France.
| | - Christine Guérard-Hélaine
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France.
| | - Ekaterina Darii
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Aline Mariage
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Jean-Louis Petit
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Marcel Salanoubat
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Véronique de Berardinis
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Marielle Lemaire
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France.
| | - Virgil Hélaine
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France.
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Heterologous expression and characterization of novel 2-Deoxy-d-ribose-5-phosphate aldolase (DERA) from Pyrobaculum calidifontis and Meiothermus ruber. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.02.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Biocatalyzed Synthesis of Statins: A Sustainable Strategy for the Preparation of Valuable Drugs. Catalysts 2019. [DOI: 10.3390/catal9030260] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Statins, inhibitors of 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase, are the largest selling class of drugs prescribed for the pharmacological treatment of hypercholesterolemia and dyslipidaemia. Statins also possess other therapeutic effects, called pleiotropic, because the blockade of the conversion of HMG-CoA to (R)-mevalonate produces a concomitant inhibition of the biosynthesis of numerous isoprenoid metabolites (e.g., geranylgeranyl pyrophosphate (GGPP) or farnesyl pyrophosphate (FPP)). Thus, the prenylation of several cell signalling proteins (small GTPase family members: Ras, Rac, and Rho) is hampered, so that these molecular switches, controlling multiple pathways and cell functions (maintenance of cell shape, motility, factor secretion, differentiation, and proliferation) are regulated, leading to beneficial effects in cardiovascular health, regulation of the immune system, anti-inflammatory and immunosuppressive properties, prevention and treatment of sepsis, treatment of autoimmune diseases, osteoporosis, kidney and neurological disorders, or even in cancer therapy. Thus, there is a growing interest in developing more sustainable protocols for preparation of statins, and the introduction of biocatalyzed steps into the synthetic pathways is highly advantageous—synthetic routes are conducted under mild reaction conditions, at ambient temperature, and can use water as a reaction medium in many cases. Furthermore, their high selectivity avoids the need for functional group activation and protection/deprotection steps usually required in traditional organic synthesis. Therefore, biocatalysis provides shorter processes, produces less waste, and reduces manufacturing costs and environmental impact. In this review, we will comment on the pleiotropic effects of statins and will illustrate some biotransformations nowadays implemented for statin synthesis.
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