Special Issue "Biocatalysis: Chemical Biosynthesis"

A special issue of Catalysts (ISSN 2073-4344). This special issue belongs to the section "Biocatalysis".

Deadline for manuscript submissions: closed (31 July 2019).

Special Issue Editor

Dr. Agatha Bastida Codina
Website
Guest Editor
CSIC, Inst Quim Organ Gen, C Juan de la Cierva 3, E-28006 Madrid, Spain
Interests: Synthetic Biology, Biochemistry, Molecular biology, Biocatalysis, Biotechnology, Medical Chemistry, Molecular docking methodology

Special Issue Information

Dear Colleagues,

Biocatalysis is a topic based on the edge of biology and chemistry, which enroll together scientists from life sciences, engineers and computer field. Biocatalysis, cell free and whole cell systems, play an increasingly role in a broad range of applications, including food processing, materials, fine chemicals, and medicine. Applied biocatalysis is driven by advances in novel protein engineering tools, economic and environmental pollution. Compare to free biocatalyst, the immobilization techniques improve the stability/activity ration, purification, and the ability to recycle the catalyst consequently more efficient process in the industry. Compared to traditional organic synthesis the use of enzymes provide a way of producing enantiomerical pure compounds mainly through high chemoselectivity and streoselective properties and very mild reaction conditions which offers advantages such as minimizing side reactions or not requiring multiple protection/deprotection steps. The advances in directed evolution, molecular cloning, DNA synthesis, bioinformatic tools, high-throughput screening, and process scale-up have opened up a door to a great variety of enzymes as tools in the industry. By other hand, the use of biosynthetic enzymes can introduce structural diversities that are otherwise inaccessible by organic synthesis. Although biocatalysis have expanded in the industry, a lack of structural and mechanistic knowledge about enzymes has limited widespread use of enzymes. Then combination of the in silico methods for engineering physical properties into proteins and structural biology techniques can guide the understanding of biocatalytic mechanisms and the development of new ones in biology and biotechnology.

Dr. Agatha Bastida Codina
Guest Editor

Manuscript Submission Information

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Keywords

  • Biosynthetic enzymes
  • DNA synthesis
  • Protein engineering
  • Microbial enzymes
  • Biocatalysis
  • Organic synthesis
  • Pharmaceutical
  • Green chemistry
  • Synthetic biology
  • Biotransformation

Published Papers (9 papers)

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Editorial

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Open AccessEditorial
Biocatalysis: Chemical Biosynthesis
Catalysts 2020, 10(4), 390; https://doi.org/10.3390/catal10040390 - 02 Apr 2020
Abstract
Biocatalysis is very appealing for industry because it allows the synthesis of products that are not accessible by chemical synthesis, use of alternative raw materials, lower operating costs, low fixed cost infrastructure and improved eco-efficiency [...] Full article
(This article belongs to the Special Issue Biocatalysis: Chemical Biosynthesis)

Research

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Open AccessArticle
Understanding (R) Specific Carbonyl Reductase from Candida parapsilosis ATCC 7330 [CpCR]: Substrate Scope, Kinetic Studies and the Role of Zinc
Catalysts 2019, 9(9), 702; https://doi.org/10.3390/catal9090702 - 21 Aug 2019
Cited by 1
Abstract
CpCR, an (R) specific carbonyl reductase, so named because it gave (R)-alcohols on asymmetric reduction of ketones and ketoesters, is a recombinantly expressed enzyme from Candida parapsilosis ATCC 7330. It turns out to be a better aldehyde reductase and [...] Read more.
CpCR, an (R) specific carbonyl reductase, so named because it gave (R)-alcohols on asymmetric reduction of ketones and ketoesters, is a recombinantly expressed enzyme from Candida parapsilosis ATCC 7330. It turns out to be a better aldehyde reductase and catalyses cofactor (NADPH) specific reduction of aliphatic and aromatic aldehydes. Kinetics studies against benzaldehyde and 2,4-dichlorobenzaldehyde show that the enzyme affinity and rate of reaction change significantly upon substitution on the benzene ring of benzaldehyde. CpCR, an MDR (medium chain reductase/dehydrogenase) containing both structural and catalytic Zn atoms, exists as a dimer, unlike the (S) specific reductase (SRED) from the same yeast which can exist in both dimeric and tetrameric forms. Divalent metal salts inhibit the enzyme even at nanomolar concentrations. EDTA chelation decreases CpCR activity. However, chelation done after the enzyme is pre-incubated with the NADPH retains most of the activity implying that Zn removal is largely prevented by the formation of the enzyme-cofactor complex. Full article
(This article belongs to the Special Issue Biocatalysis: Chemical Biosynthesis)
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Open AccessArticle
Production and Surfactant Properties of Tert-Butyl α-d-Glucopyranosides Catalyzed by Cyclodextrin Glucanotransferase
Catalysts 2019, 9(7), 575; https://doi.org/10.3390/catal9070575 - 29 Jun 2019
Cited by 2
Abstract
While testing the ability of cyclodextrin glucanotransferases (CGTases) to glucosylate a series of flavonoids in the presence of organic cosolvents, we found out that this enzyme was able to glycosylate a tertiary alcohol (tert-butyl alcohol). In particular, CGTases from Thermoanaerobacter sp. [...] Read more.
While testing the ability of cyclodextrin glucanotransferases (CGTases) to glucosylate a series of flavonoids in the presence of organic cosolvents, we found out that this enzyme was able to glycosylate a tertiary alcohol (tert-butyl alcohol). In particular, CGTases from Thermoanaerobacter sp. and Thermoanaerobacterium thermosulfurigenes EM1 gave rise to the appearance of at least two glycosylation products, which were characterized by mass spectrometry (MS) and nuclear magnetic resonance (NMR) as tert-butyl-α-D-glucoside (major product) and tert-butyl-α-D-maltoside (minor product). Using partially hydrolyzed starch as glucose donor, the yield of transglucosylation was approximately 44% (13 g/L of tert-butyl-α-D-glucoside and 4 g/L of tert-butyl-α-D-maltoside). The synthesized tert-butyl-α-D-glucoside exhibited the typical surfactant behavior (critical micellar concentration, 4.0–4.5 mM) and its properties compared well with those of the related octyl-α-D-glucoside. To the best of our knowledge, this is the first description of an enzymatic α-glucosylation of a tertiary alcohol. Full article
(This article belongs to the Special Issue Biocatalysis: Chemical Biosynthesis)
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Open AccessArticle
Bienzymatic Cascade for the Synthesis of an Optically Active O-benzoyl Cyanohydrin
Catalysts 2019, 9(6), 522; https://doi.org/10.3390/catal9060522 - 12 Jun 2019
Cited by 3
Abstract
A concurrent bienzymatic cascade for the synthesis of optically pure (S)-4-methoxymandelonitrile benzoate ((S)-3) starting from 4-anisaldehyde (1) has been developed. The cascade involves an enantioselective Manihot esculenta hydroxynitrile lyase-catalyzed hydrocyanation of 1, and the [...] Read more.
A concurrent bienzymatic cascade for the synthesis of optically pure (S)-4-methoxymandelonitrile benzoate ((S)-3) starting from 4-anisaldehyde (1) has been developed. The cascade involves an enantioselective Manihot esculenta hydroxynitrile lyase-catalyzed hydrocyanation of 1, and the subsequent benzoylation of the resulting cyanohydrin (S)-2 catalyzed by Candida antarctica lipase A in organic solvent. To accomplish this new direct synthesis of the protected enantiopure cyanohydrin, both enzymes were immobilized and each biocatalytic step was studied separately in search for a window of compatibility. In addition, potential cross-interactions between the two reactions were identified. Optimization of the cascade resulted in 81% conversion of the aldehyde to the corresponding benzoyl cyanohydrin with 98% enantiomeric excess. Full article
(This article belongs to the Special Issue Biocatalysis: Chemical Biosynthesis)
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Open AccessArticle
Accelerated H2 Evolution during Microbial Electrosynthesis with Sporomusa ovata
Catalysts 2019, 9(2), 166; https://doi.org/10.3390/catal9020166 - 08 Feb 2019
Cited by 4
Abstract
Microbial electrosynthesis (MES) is a process where bacteria acquire electrons from a cathode to convert CO2 into multicarbon compounds or methane. In MES with Sporomusa ovata as the microbial catalyst, cathode potential has often been used as a benchmark to determine whether [...] Read more.
Microbial electrosynthesis (MES) is a process where bacteria acquire electrons from a cathode to convert CO2 into multicarbon compounds or methane. In MES with Sporomusa ovata as the microbial catalyst, cathode potential has often been used as a benchmark to determine whether electron uptake is hydrogen-dependent. In this study, H2 was detected by a microsensor in proximity to the cathode. With a sterile fresh medium, H2 was produced at a potential of −700 mV versus Ag/AgCl, whereas H2 was detected at −500 mV versus Ag/AgCl with cell-free spent medium from a S. ovata culture. Furthermore, H2 evolution rates were increased with potentials lower than −500 mV in the presence of cell-free spent medium in the cathode chamber. Nickel and cobalt were detected at the cathode surface after exposure to the spent medium, suggesting a possible participation of these catalytic metals in the observed faster hydrogen evolution. The results presented here show that S. ovata-induced alterations of the cathodic electrolytes of a MES reactor reduced the electrical energy required for hydrogen evolution. These observations also indicated that, even at higher cathode potentials, at least a part of the electrons coming from the electrode are transferred to S. ovata via H2 during MES. Full article
(This article belongs to the Special Issue Biocatalysis: Chemical Biosynthesis)
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Open AccessArticle
Production of New Isoflavone Glucosides from Glycosylation of 8-Hydroxydaidzein by Glycosyltransferase from Bacillus subtilis ATCC 6633
Catalysts 2018, 8(9), 387; https://doi.org/10.3390/catal8090387 - 10 Sep 2018
Cited by 10
Abstract
8-Hydroxydaidzein (8-OHDe) has been proven to possess some important bioactivities; however, the low aqueous solubility and stability of 8-OHDe limit its pharmaceutical and cosmeceutical applications. The present study focuses on glycosylation of 8-OHDe to improve its drawbacks in solubility and stability. According to [...] Read more.
8-Hydroxydaidzein (8-OHDe) has been proven to possess some important bioactivities; however, the low aqueous solubility and stability of 8-OHDe limit its pharmaceutical and cosmeceutical applications. The present study focuses on glycosylation of 8-OHDe to improve its drawbacks in solubility and stability. According to the results of phylogenetic analysis with several identified flavonoid-catalyzing glycosyltransferases (GTs), three glycosyltransferase genes (BsGT110, BsGT292 and BsGT296) from the genome of the Bacillus subtilis ATCC 6633 strain were cloned and expressed in Escherichia coli. The three BsGTs were then purified and the glycosylation activity determined toward 8-OHDe. The results showed that only BsGT110 possesses glycosylation activity. The glycosylated metabolites were then isolated with preparative high-performance liquid chromatography and identified as two new isoflavone glucosides, 8-OHDe-7-O-β-glucoside and8-OHDe-8-O-β-glucoside, whose identity was confirmed by mass spectrometry and nuclear magnetic resonance spectroscopy. The aqueous solubility of 8-OHDe-7-O-β-glucoside and 8-OHDe-8-O-β-glucoside is 9.0- and 4.9-fold, respectively, higher than that of 8-OHDe. Moreover, more than 90% of the initial concentration of the two 8-OHDe glucoside derivatives remained after 96 h of incubation in 50 mM of Tris buffer at pH 8.0. In contrast, the concentration of 8-OHDe decreased to 0.8% of the initial concentration after 96 h of incubation. The two new isoflavone glucosides might have potential in pharmaceutical and cosmeceutical applications. Full article
(This article belongs to the Special Issue Biocatalysis: Chemical Biosynthesis)
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Open AccessArticle
Developing a High-Temperature Solvent-Free System for Efficient Biocatalysis of Octyl Ferulate
Catalysts 2018, 8(8), 338; https://doi.org/10.3390/catal8080338 - 20 Aug 2018
Cited by 5
Abstract
Ferulic acid esters have been suggested as a group of natural chemicals that have the function of sunscreen. The study aimed to utilize an environmentally-friendly enzymatic method through the esterification of ferulic acid with octanol, producing octyl ferulate. The Box-Behnken experimental design for [...] Read more.
Ferulic acid esters have been suggested as a group of natural chemicals that have the function of sunscreen. The study aimed to utilize an environmentally-friendly enzymatic method through the esterification of ferulic acid with octanol, producing octyl ferulate. The Box-Behnken experimental design for response surface methodology (RSM) was performed to determine the synthesis effects of variables, including enzyme amount (1000–2000 propyl laurate units (PLU)), reaction temperature (70–90 °C), and stir speed (50–150 rpm) on the molar conversion of octyl ferulate. According to the joint test, both the enzyme amount and reaction temperature had great impacts on the molar conversion. An RSM-developed second-order polynomial equation further showed a data-fitting ability. Using ridge max analysis, the optimal parameters of the biocatalyzed reaction were: 72 h reaction time, 92.2 °C reaction temperature, 1831 PLU enzyme amount, and 92.4 rpm stir speed, respectively. Finally, the molar conversion of octyl ferulate under optimum conditions was verified to be 93.2 ± 1.5%. In conclusion, it has been suggested that a high yield of octyl ferulate should be synthesized under elevated temperature conditions with a commercial immobilized lipase. Our findings could broaden the utilization of the lipase and provide a biocatalytic approach, instead of the chemical method, for ferulic acid ester synthesis. Full article
(This article belongs to the Special Issue Biocatalysis: Chemical Biosynthesis)
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Review

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Open AccessReview
Biocatalysis as Useful Tool in Asymmetric Synthesis: An Assessment of Recently Granted Patents (2014–2019)
Catalysts 2019, 9(10), 802; https://doi.org/10.3390/catal9100802 - 25 Sep 2019
Cited by 6
Abstract
The broad interdisciplinary nature of biocatalysis fosters innovation, as different technical fields are interconnected and synergized. A way to depict that innovation is by conducting a survey on patent activities. This paper analyses the intellectual property activities of the last five years (2014–2019) [...] Read more.
The broad interdisciplinary nature of biocatalysis fosters innovation, as different technical fields are interconnected and synergized. A way to depict that innovation is by conducting a survey on patent activities. This paper analyses the intellectual property activities of the last five years (2014–2019) with a specific focus on biocatalysis applied to asymmetric synthesis. Furthermore, to reflect the inventive and innovative steps, only patents that were granted during that period are considered. Patent searches using several keywords (e.g., enzyme names) have been conducted by using several patent engine servers (e.g., Espacenet, SciFinder, Google Patents), with focus on granted patents during the period 2014–2019. Around 200 granted patents have been identified, covering all enzyme types. The inventive pattern focuses on the protection of novel protein sequences, as well as on new substrates. In some other cases, combined processes, multi-step enzymatic reactions, as well as process conditions are the innovative basis. Both industries and academic groups are active in patenting. As a conclusion of this survey, we can assert that biocatalysis is increasingly recognized as a useful tool for asymmetric synthesis and being considered as an innovative option to build IP and protect synthetic routes. Full article
(This article belongs to the Special Issue Biocatalysis: Chemical Biosynthesis)
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Open AccessReview
Pseudokinases: From Allosteric Regulation of Catalytic Domains and the Formation of Macromolecular Assemblies to Emerging Drug Targets
Catalysts 2019, 9(9), 778; https://doi.org/10.3390/catal9090778 - 19 Sep 2019
Cited by 3
Abstract
Pseudokinases are a member of the kinase superfamily that lack one or more of the canonical residues required for catalysis. Protein pseudokinases are widely distributed across species and are present in proteins that perform a great diversity of roles in the cell. They [...] Read more.
Pseudokinases are a member of the kinase superfamily that lack one or more of the canonical residues required for catalysis. Protein pseudokinases are widely distributed across species and are present in proteins that perform a great diversity of roles in the cell. They represent approximately 10% to 40% of the kinome of a multicellular organism. In the human, the pseudokinase subfamily consists of approximately 60 unique proteins. Despite their lack of one or more of the amino acid residues typically required for the productive interaction with ATP and metal ions, which is essential for the phosphorylation of specific substrates, pseudokinases are important functional molecules that can act as dynamic scaffolds, competitors, or modulators of protein–protein interactions. Indeed, pseudokinase misfunctions occur in diverse diseases and represent a new therapeutic window for the development of innovative therapeutic approaches. In this contribution, we describe the structural features of pseudokinases that are used as the basis of their classification; analyse the interactome space of human pseudokinases and discuss their potential as suitable drug targets for the treatment of various diseases, including metabolic, neurological, autoimmune, and cell proliferation disorders. Full article
(This article belongs to the Special Issue Biocatalysis: Chemical Biosynthesis)
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