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Liu M, Li S. Nitrile biosynthesis in nature: how and why? Nat Prod Rep 2024; 41:649-671. [PMID: 38193577 DOI: 10.1039/d3np00028a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Covering: up to the end of 2023Natural nitriles comprise a small set of secondary metabolites which however show intriguing chemical and functional diversity. Various patterns of nitrile biosynthesis can be seen in animals, plants, and microorganisms with the characteristics of both evolutionary divergence and convergence. These specialized compounds play important roles in nitrogen metabolism, chemical defense against herbivores, predators and pathogens, and inter- and/or intraspecies communications. Here we review the naturally occurring nitrile-forming pathways from a biochemical perspective and discuss the biological and ecological functions conferred by diversified nitrile biosyntheses in different organisms. Elucidation of the mechanisms and evolutionary trajectories of nitrile biosynthesis underpins better understandings of nitrile-related biology, chemistry, and ecology and will ultimately benefit the development of desirable nitrile-forming biocatalysts for practical applications.
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Affiliation(s)
- Mingyu Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
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2
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Yamaguchi T, Asano Y. Nitrile-synthesizing enzymes and biocatalytic synthesis of volatile nitrile compounds: A review. J Biotechnol 2024; 384:20-28. [PMID: 38395363 DOI: 10.1016/j.jbiotec.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/16/2024] [Accepted: 02/17/2024] [Indexed: 02/25/2024]
Abstract
Nitriles (R-CN) comprise a broad group of chemicals industrially produced and used in fine chemicals, pharmaceuticals, and bulk applications, polymer chemistry, solvents, etc. Nitriles are important starting materials for producing carboxylic acids, amides, amines, and several other compounds. In addition, some volatile nitriles have been evaluated for their potential as ingredients in fragrance and flavor formulations. However, many nitrile synthesis methods have drawbacks, such as drastic reaction conditions, limited substrate scope, lack of readily available reagents, poor yields, and long reaction times. In contrast to chemical synthesis, biocatalytic approaches using enzymes can produce nitriles without harsh conditions, such as high temperatures and pressures, or toxic compounds. In this review, we summarize the nitrile-synthesizing enzymes from microorganisms, plants, and animals. Furthermore, we introduce several examples of biocatalytic synthesis of volatile nitrile compounds, particularly those using aldoxime dehydratase.
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Affiliation(s)
- Takuya Yamaguchi
- Biotechnology Research Center and Department of Biotechnology, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan.
| | - Yasuhisa Asano
- Biotechnology Research Center and Department of Biotechnology, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
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3
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Zhang S, Zheng J, Li Z, Ding X, Wang Y. A green catalytic reaction system for the synthesis 5-amino-1-pentanol with furfural and ionic liquid hydroxylamine salt as the initial raw material. MOLECULAR CATALYSIS 2023. [DOI: 10.1016/j.mcat.2023.112995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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4
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Ivshina I, Bazhutin G, Tyumina E. Rhodococcus strains as a good biotool for neutralizing pharmaceutical pollutants and obtaining therapeutically valuable products: Through the past into the future. Front Microbiol 2022; 13:967127. [PMID: 36246215 PMCID: PMC9557007 DOI: 10.3389/fmicb.2022.967127] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 09/12/2022] [Indexed: 11/18/2022] Open
Abstract
Active pharmaceutical ingredients present a substantial risk when they reach the environment and drinking water sources. As a new type of dangerous pollutants with high chemical resistance and pronounced biological effects, they accumulate everywhere, often in significant concentrations (μg/L) in ecological environments, food chains, organs of farm animals and humans, and cause an intense response from the aquatic and soil microbiota. Rhodococcus spp. (Actinomycetia class), which occupy a dominant position in polluted ecosystems, stand out among other microorganisms with the greatest variety of degradable pollutants and participate in natural attenuation, are considered as active agents with high transforming and degrading impacts on pharmaceutical compounds. Many representatives of rhodococci are promising as unique sources of specific transforming enzymes, quorum quenching tools, natural products and novel antimicrobials, biosurfactants and nanostructures. The review presents the latest knowledge and current trends regarding the use of Rhodococcus spp. in the processes of pharmaceutical pollutants’ biodegradation, as well as in the fields of biocatalysis and biotechnology for the production of targeted pharmaceutical products. The current literature sources presented in the review can be helpful in future research programs aimed at promoting Rhodococcus spp. as potential biodegraders and biotransformers to control pharmaceutical pollution in the environment.
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Li N, Zong MH. (Chemo)biocatalytic Upgrading of Biobased Furanic Platforms to Chemicals, Fuels, and Materials: A Comprehensive Review. ACS Catal 2022. [DOI: 10.1021/acscatal.2c02912] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Ning Li
- School of Food Science and Engineering, South China University of Technology, 381 Wushan Road, Guangzhou 510640, China
| | - Min-Hua Zong
- School of Food Science and Engineering, South China University of Technology, 381 Wushan Road, Guangzhou 510640, China
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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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7
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Zhou Y, Wu S, Bornscheuer UT. Recent advances in (chemo)enzymatic cascades for upgrading bio-based resources. Chem Commun (Camb) 2021; 57:10661-10674. [PMID: 34585190 DOI: 10.1039/d1cc04243b] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Developing (chemo)enzymatic cascades is very attractive for green synthesis, because they streamline multistep synthetic processes. In this Feature Article, we have summarized the recent advances in in vitro or whole-cell cascade reactions with a focus on the use of renewable bio-based resources as starting materials. This includes the synthesis of rare sugars (such as ketoses, L-ribulose, D-tagatose, myo-inositol or aminosugars) from readily available carbohydrate sources (cellulose, hemi-cellulose, starch), in vitro enzyme pathways to convert glucose to various biochemicals, cascades to convert 5-hydroxymethylfurfural and furfural obtained from lignin or xylose into novel precursors for polymer synthesis, the syntheses of phenolic compounds, cascade syntheses of aliphatic and highly reduced chemicals from plant oils and fatty acids, upgrading of glycerol or ethanol as well as cascades to transform natural L-amino acids into high-value (chiral) compounds. In several examples these processes have demonstrated their efficiency with respect to high space-time yields and low E-factors enabling mature green chemistry processes. Also, the strengths and limitations are discussed and an outlook is provided for improving the existing and developing new cascades.
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Affiliation(s)
- Yi Zhou
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Street, Wuhan 430070, P. R. China.
| | - Shuke Wu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Street, Wuhan 430070, P. R. China. .,Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany.
| | - Uwe T Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany.
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Chen Z, Mao F, Zheng H, Xiao Q, Ding Z, Wang A, Pei X. Cyanide-free synthesis of aromatic nitriles from aldoximes: Discovery and application of a novel heme-containing aldoxime dehydratase. Enzyme Microb Technol 2021; 150:109883. [PMID: 34489036 DOI: 10.1016/j.enzmictec.2021.109883] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/15/2021] [Accepted: 07/27/2021] [Indexed: 01/03/2023]
Abstract
Aromatic nitriles are important structural motifs that frequently existed in pharmaceutical drugs. Due to the convenient synthesis of aldoximes from aldehydes, the dehydration of aldoximes to corresponding nitriles by aldoxime dehydratases (Oxds) is considered as a safe and robust enzymatic production route. Although the Oxd genes are widely distributed in microbial kingdom, so far less than ten Oxds were expressed and further characterized. In this study, we found 26 predicted putative Oxd genes from the GenBank database using a genome mining strategy. The Oxd gene from Pseudomonas putida F1 was cloned and functionally expressed in Escherichia coli BL21 (DE3). The amino acid sequence of OxdF1 shows high identities of 33∼85 % to other characterized Oxds, and contained a ferrous heme as the catalytic site. The optimum reaction pH and temperature of recombinant OxdF1 were 7.0 and 35 °C, respectively. OxdF1 was stable in pH 7.0 potassium phosphate buffer at 30 °C, and its half-life was approximately 3.8 h. OxdF1 can efficiently dehydrate aromatic and heterocyclic aldoximes to nitriles, such as 2-bromobenzaldoxime, 2-chloro-6-fluorobenzaldoxime, thiophene-2-carboxaldoxime, and pyridine-3-aldoxime. Therefore, the recombinant OxdF1 shows a potential application in the cyanide-free synthesis of aromatic nitriles.
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Affiliation(s)
- Zhiji Chen
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou, 311121, China
| | - Feiying Mao
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou, 311121, China
| | - Haoteng Zheng
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou, 311121, China
| | - Qinjie Xiao
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou, 311121, China
| | - Zhihao Ding
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou, 311121, China
| | - Anming Wang
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou, 311121, China.
| | - Xiaolin Pei
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou, 311121, China.
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Domínguez de María P. Nitrile Synthesis with Aldoxime Dehydratases: A Biocatalytic Platform with Applications in Asymmetric Synthesis, Bulk Chemicals, and Biorefineries. Molecules 2021; 26:molecules26154466. [PMID: 34361620 PMCID: PMC8347273 DOI: 10.3390/molecules26154466] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/17/2021] [Accepted: 07/22/2021] [Indexed: 12/05/2022] Open
Abstract
Nitriles comprise a broad group of chemicals that are currently being industrially produced and used in fine chemicals and pharmaceuticals, as well as in bulk applications, polymer chemistry, solvents, etc. Aldoxime dehydratases catalyze the cyanide-free synthesis of nitriles starting from aldoximes under mild conditions, holding potential to become sustainable alternatives for industrial processes. Different aldoxime dehydratases accept a broad range of aldoximes with impressive high substrate loadings of up to >1 Kg L−1 and can efficiently catalyze the reaction in aqueous media as well as in non-aqueous systems, such as organic solvents and solvent-free (neat substrates). This paper provides an overview of the recent developments in this field with emphasis on strategies that may be of relevance for industry and sustainability. When possible, potential links to biorefineries and to the use of biogenic raw materials are discussed.
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Affiliation(s)
- Pablo Domínguez de María
- Sustainable Momentum, SL, Av. Ansite 3, 4-6, 35011 Las Palmas de Gran Canaria, Canary Islands, Spain
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Protein engineering of the aldoxime dehydratase from Bacillus sp. OxB-1 based on a rational sequence alignment approach. Sci Rep 2021; 11:14316. [PMID: 34253740 PMCID: PMC8275659 DOI: 10.1038/s41598-021-92749-0] [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: 09/26/2020] [Accepted: 06/08/2021] [Indexed: 12/31/2022] Open
Abstract
Recently, the program INTMSAlign_HiSol for identifying aggregation hotspots in proteins only requiring secondary structure data was introduced. We explored the utility of this program further and applied it for engineering of the aldoxime dehydratase from Bacillus sp. OxB-1. Towards this end, the effect of inverting the hydropathy at selected positions of the amino acid sequence on the enzymatic activity was studied leading to 60% of our constructed variants, which showed improved activity. In part, this activity increase can be rationalised by an improved heme incorporation of the variants. For example, a single mutation gave a 1.8 fold increased enzymatic activity and 30% improved absolute heme incorporation.
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Hinzmann A, Betke T, Asano Y, Gröger H. Synthetic Processes toward Nitriles without the Use of Cyanide: A Biocatalytic Concept Based on Dehydration of Aldoximes in Water. Chemistry 2021; 27:5313-5321. [PMID: 33112445 PMCID: PMC8049032 DOI: 10.1002/chem.202001647] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 10/22/2020] [Indexed: 11/29/2022]
Abstract
While belonging to the most fundamental functional groups, nitriles represent a class of compound that still raises challenges in terms of an efficient, cost‐effective, general and, at the same time, sustainable way for their synthesis. Complementing existing chemical routes, recently a cyanide‐free enzymatic process technology based on the use of an aldoxime dehydratase (Oxd) as a biocatalyst component has been developed and successfully applied for the synthesis of a range of nitrile products. In these biotransformations, the Oxd enzymes catalyze the dehydration of aldoximes as readily available substrates to the nitrile products. Herein, these developments with such enzymes are summarized, with a strong focus on synthetic applications. It is demonstrated that this biocatalytic technology has the potential to “cross the bridge” between the production of fine chemicals and pharmaceuticals, on one hand, and bulk and commodity chemicals, on the other.
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Affiliation(s)
- Alessa Hinzmann
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Tobias Betke
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Yasuhisa Asano
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Harald Gröger
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
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Aldoxime Dehydratase Mutants as Improved Biocatalysts for a Sustainable Synthesis of Biorenewables-Based 2-Furonitrile. Catalysts 2020. [DOI: 10.3390/catal10040362] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
2-Furonitrile is an interesting nitrile product for the chemical industry due to its use as intermediate in the field of fine chemicals and pharmaceuticals or as a potential sweetener, as well as due to its access from biorenewables. As an alternative to current processes based on, e.g., the ammoxidation of furfural with ammonia as a gas phase reaction running at > 400 °C, we recently reported an enzymatic dehydration of 2-furfuryl aldoxime being obtained easily from furfural and hydroxylamine. However, improving the catalytic properties of the aldoxime dehydratase biocatalyst from Rhodococcus sp. YH3-3 (OxdYH3-3) in terms of activity and stability remained a challenge. In this contribution, the successful development of aldoxime dehydratase OxdYH3-3 mutants that were generated by directed evolution and its enhanced activity toward 2-furfuryl aldoxime is reported. The mutant OxdYH3-3 N266S showed an improved activity of up to six times higher than the wild type when utilizing a substrate concentration of 50–100 mM of 2-furfuryl aldoxime.
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