Special Issue "Applied Biocatalysis in Europe: A Sustainable Tool for Improving Life Quality"

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

Deadline for manuscript submissions: closed (31 August 2020).

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A printed edition of this Special Issue is available here.

Special Issue Editors

Prof. Dr. Andres R. Alcantara
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Guest Editor
Department of Chemistry in Pharmaceutical Sciences, Faculty of Pharmacy, Complutense University, Plaza De Ramon y Cajal, S/N University City, Madrid, Spain
Interests: enzymatic synthesis of drugs and bioactive compounds; sustainable processes; biocatalyst upgrading; pharmaceutical industry; organic chemistry; pharmaceutical chemistry
Special Issues and Collections in MDPI journals
Prof. Dr. Francisco Plou
E-Mail Website
Guest Editor
Institute of Catalysis and Petrochemistry, CSIC, Marie Curie 2, 28049 Madrid, Spain
Interests: enzymatic transformation of carbohydrates; immobilization of enzymes; enzymatic glycosylation of polyphenols; enzymatic acylation with lipases

Special Issue Information

Dear Colleagues,

Applied Biocatalysis and Biotransformation, that is, the use of enzymes and whole-cell systems in manufacturing processes for synthetic purposes, has been experiencing a clear boom in recent years, which has led to the start of the so-called “fourth wave”. In fact, the latest advances in bioinformatics, system biology, process intensification, and, in particular, enzyme-directed evolution (encouraged by the 2018 Nobel Prize awarded to F. Arnold) are widening the range of the efficacy of biocatalysts and accelerating the rate at which new enzymes are becoming available, even for activities not previously known. Moreover, xenobiology, the insertion of non-canonical amino acids into protein sequences, is creating fascinating new possibilities for the preparation of biocatalysts with improved properties.

Traditionally, European scientists have been very actively involved in different aspects of Applied Biocatalysis. This Special Issue aims to gather contributions from European research groups, in the form of either original research articles or up-to-date reviews, to exemplify recent advances in this area. This includes, but is not restricted to, the discovery of new enzymatic activities, the chemical or genetic modification of known biocatalysts for further application in the development of commodities and fine chemicals, and the implementation of biocatalyzed protocols using enzymes (in any stage) and cells to increase the sustainability of synthetic procedures.

Prof. Andres R Alcantara
Prof. Francisco J. Plou
Guest Editors

Manuscript Submission Information

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Keywords

  • Biocatalysis
  • Biotransformations
  • Sustainable processes
  • Enzyme engineering
  • Metagenomics
  • White biotechnology

Published Papers (11 papers)

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Editorial

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Editorial
Special Issue on “Applied Biocatalysis in Europe: A Sustainable Tool for Improving Life Quality”
Catalysts 2021, 11(3), 339; https://doi.org/10.3390/catal11030339 - 06 Mar 2021
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Abstract
Applied biocatalysis, i [...] Full article
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Research

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Article
An Alternative Enzymatic Route to the Ergogenic Ketone Body Ester (R)-3-Hydroxybutyl (R)-3-Hydroxybutyrate
Catalysts 2021, 11(1), 140; https://doi.org/10.3390/catal11010140 - 19 Jan 2021
Cited by 1 | Viewed by 784
Abstract
Recent studies have highlighted the therapeutic and ergogenic potential of the ketone body ester, (R)-3-hydroxybutyl-(R)-3-hydroxybutyrate. In the present work, the enzymatic synthesis of this biological active compound is reported. The (R)-3-hydroxybutyl-(R)-3-hydroxybutyrate has been produced through [...] Read more.
Recent studies have highlighted the therapeutic and ergogenic potential of the ketone body ester, (R)-3-hydroxybutyl-(R)-3-hydroxybutyrate. In the present work, the enzymatic synthesis of this biological active compound is reported. The (R)-3-hydroxybutyl-(R)-3-hydroxybutyrate has been produced through the transesterification of racemic ethyl 3-hydroxybutyrate with (R)-1,3-butanediol by exploiting the selectivity of Candida antarctica lipase B (CAL-B). The needed (R)-1,3-butanediol was in turn obtained from the kinetic resolution of the racemate achieved by acetylation with vinyl acetate, also in this case, thanks to the enantioselectivity of the CAL-B used as catalyst. Finally, the stereochemical inversion of the unreacted (S) enantiomers of the ethyl 3-hydroxybutyate and 1,3-butanediol accomplished by known procedure allowed to increase the overall yield of the synthetic pathway by incorporating up to 70% of the starting racemic reagents into the final product. Full article
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Article
Sustainable Synthesis of Omega-3 Fatty Acid Ethyl Esters from Monkfish Liver Oil
Catalysts 2021, 11(1), 100; https://doi.org/10.3390/catal11010100 - 13 Jan 2021
Cited by 2 | Viewed by 581
Abstract
The search for economic and sustainable sources of polyunsaturated fatty acids (PUFAs) within the framework of the circular economy is encouraged by their proven beneficial effects on health. The extraction of monkfish liver oil (MLO) for the synthesis of omega-3 ethyl esters was [...] Read more.
The search for economic and sustainable sources of polyunsaturated fatty acids (PUFAs) within the framework of the circular economy is encouraged by their proven beneficial effects on health. The extraction of monkfish liver oil (MLO) for the synthesis of omega-3 ethyl esters was performed to evaluate two blending systems and four green solvents in this work. Moreover, the potential solubility of the MLO in green solvents was studied using the predictive simulation software COnductor-like Screening MOdel for Realistic Solvents (COSMO-RS). The production of ethyl esters was performed by one or two-step reactions. Novozym 435, two resting cells (Aspergillus flavus and Rhizopus oryzae) obtained in our laboratory and a mix of them were used as biocatalysts in a solvent-free system. The yields for Novozym 435, R. oryzae and A. flavus in the one-step esterification were 63, 61 and 46%, respectively. The hydrolysis step in the two-step reaction led to 83, 88 and 93% of free fatty acids (FFA) for Novozym 435, R. oryzae and A. flavus, respectively. However, Novozym 435 showed the highest yield in the esterification step (85%), followed by R. oryzae (65%) and A. flavus (41%). Moreover, selectivity of polyunsaturated fatty acids of R. oryzae lipase was evidenced as it slightly esterified docosahexaenoic acid (DHA) in all the esterification reactions tested. Full article
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Article
Conformational Landscapes of Halohydrin Dehalogenases and Their Accessible Active Site Tunnels
Catalysts 2020, 10(12), 1403; https://doi.org/10.3390/catal10121403 - 01 Dec 2020
Cited by 3 | Viewed by 787
Abstract
Halohydrin dehalogenases (HHDH) are industrially relevant biocatalysts exhibiting a promiscuous epoxide-ring opening reactivity in the presence of small nucleophiles, thus giving access to novel carbon–carbon, carbon–oxygen, carbon–nitrogen, and carbon–sulfur bonds. Recently, the repertoire of HHDH has been expanded, providing access to some novel [...] Read more.
Halohydrin dehalogenases (HHDH) are industrially relevant biocatalysts exhibiting a promiscuous epoxide-ring opening reactivity in the presence of small nucleophiles, thus giving access to novel carbon–carbon, carbon–oxygen, carbon–nitrogen, and carbon–sulfur bonds. Recently, the repertoire of HHDH has been expanded, providing access to some novel HHDH subclasses exhibiting a broader epoxide substrate scope. In this work, we develop a computational approach based on the application of linear and non-linear dimensionality reduction techniques to long time-scale Molecular Dynamics (MD) simulations to study the HHDH conformational landscapes. We couple the analysis of the conformational landscapes to CAVER calculations to assess their impact on the active site tunnels and potential ability towards bulky epoxide ring opening reaction. Our study indicates that the analyzed HHDHs subclasses share a common breathing motion of the halide binding pocket, but present large deviations in the loops adjacent to the active site pocket and N-terminal regions. Such conformational differences affect the available tunnels for epoxide binding to the active site. The superior activity of the HHDH G subclass towards bulkier substrates is explained by the additional structural elements delimiting the active site region, its rich conformational heterogeneity, and the substantially wider and frequently observed active site tunnels. This study therefore provides key information for HHDH promiscuity and engineering. Full article
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Article
Biocatalysis at Extreme Temperatures: Enantioselective Synthesis of both Enantiomers of Mandelic Acid by Transesterification Catalyzed by a Thermophilic Lipase in Ionic Liquids at 120 °C
Catalysts 2020, 10(9), 1055; https://doi.org/10.3390/catal10091055 - 14 Sep 2020
Cited by 5 | Viewed by 1007
Abstract
The use of biocatalysts in organic chemistry for catalyzing chemo-, regio- and stereoselective transformations has become an usual tool in the last years, both at lab and industrial scale. This is not only because of their exquisite precision, but also due to the [...] Read more.
The use of biocatalysts in organic chemistry for catalyzing chemo-, regio- and stereoselective transformations has become an usual tool in the last years, both at lab and industrial scale. This is not only because of their exquisite precision, but also due to the inherent increase in the process sustainability. Nevertheless, most of the interesting industrial reactions involve water-insoluble substrates, so the use of (generally not green) organic solvents is generally required. Although lipases are capable of maintaining their catalytic precision working in those solvents, reactions are usually very slow and consequently not very appropriate for industrial purposes. Increasing reaction temperature would accelerate the reaction rate, but this should require the use of lipases from thermophiles, which tend to be more enantioselective at lower temperatures, as they are more rigid than those from mesophiles. Therefore, the ideal scenario would require a thermophilic lipase capable of retaining high enantioselectivity at high temperatures. In this paper, we describe the use of lipase from Geobacillus thermocatenolatus as catalyst in the ethanolysis of racemic 2-(butyryloxy)-2-phenylacetic to furnish both enantiomers of mandelic acid, an useful intermediate in the synthesis of many drugs and active products. The catalytic performance at high temperature in a conventional organic solvent (isooctane) and four imidazolium-based ionic liquids was assessed. The best results were obtained using 1-ethyl-3-methyl imidazolium tetrafluoroborate (EMIMBF4) and 1-ethyl-3-methyl imidazolium hexafluorophosphate (EMIMPF6) at temperatures as high as 120 °C, observing in both cases very fast and enantioselective kinetic resolutions, respectively leading exclusively to the (S) or to the (R)-enantiomer of mandelic acid, depending on the anion component of the ionic liquid. Full article
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Article
Immobilization of Arabidopsis thaliana Hydroxynitrile Lyase (AtHNL) on EziG Opal
Catalysts 2020, 10(8), 899; https://doi.org/10.3390/catal10080899 - 08 Aug 2020
Cited by 3 | Viewed by 1035
Abstract
Arabidopsis thaliana hydroxynitrile lyase (AtHNL) catalyzes the selective synthesis of (R)-cyanohydrins. This enzyme is unstable under acidic conditions, therefore its immobilization is necessary for the synthesis of enantiopure cyanohydrins. EziG Opal is a controlled porosity glass material for the [...] Read more.
Arabidopsis thaliana hydroxynitrile lyase (AtHNL) catalyzes the selective synthesis of (R)-cyanohydrins. This enzyme is unstable under acidic conditions, therefore its immobilization is necessary for the synthesis of enantiopure cyanohydrins. EziG Opal is a controlled porosity glass material for the immobilization of His-tagged enzymes. The immobilization of His6-tagged AtHNL on EziG Opal was optimized for higher enzyme stability and tested for the synthesis of (R)-mandelonitrile in batch and continuous flow systems. AtHNL-EziG Opal achieved 95% of conversion after 30 min of reaction time in batch and it was recycled up to eight times with a final conversion of 80% and excellent enantioselectivity. The EziG Opal carrier catalyzed the racemic background reaction; however, the high enantioselectivity observed in the recycling study demonstrated that this was efficiently suppressed by using citrate/phosphate buffer saturated methyl-tert-butylether (MTBE) pH 5 as reaction medium. The continuous flow system achieved 96% of conversion and excellent enantioselectivity at 0.1 mL min−1. Lower conversion and enantioselectivity were observed at higher flow rates. The specific rate of AtHNL-EziG Opal in flow was 0.26 mol h−1 genzyme−1 at 0.1 mL min−1 and 96% of conversion whereas in batch, the immobilized enzyme displayed a specific rate of 0.51 mol h−1 genzyme−1 after 30 min of reaction time at a similar level of conversion. However, in terms of productivity the continuous flow system proved to be almost four times more productive than the batch approach, displaying a space-time-yield (STY) of 690 molproduct h−1 L−1 genzyme−1 compared to 187 molproduct h−1 L−1 genzyme−1 achieved with the batch system. Full article
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Article
Enzymatic Synthesis of Estolides from Castor Oil
Catalysts 2020, 10(8), 835; https://doi.org/10.3390/catal10080835 - 24 Jul 2020
Cited by 2 | Viewed by 919
Abstract
Estolides are fatty acid polyesters with applications in both industry and consumer products. Recently, reports have emerged detailing lipase-catalyzed synthesis of estolides from free hydroxy fatty acids. In this paper, we describe a simple alternative enzymatic process, in which castor oil is directly [...] Read more.
Estolides are fatty acid polyesters with applications in both industry and consumer products. Recently, reports have emerged detailing lipase-catalyzed synthesis of estolides from free hydroxy fatty acids. In this paper, we describe a simple alternative enzymatic process, in which castor oil is directly converted to an estolide mixture by Candida antarctica lipase A (CALA) catalyzed transesterification. The reaction mixture is analyzed by NMR to determine the estolide number (EN) and MALDI MS to identify individual components, in addition to titration to determine the acid value (AV). Estolide trimers and tetramers (EN 2–3) were formed over 24 h in a system with 2:1 (v/v) castor oil–water. Further, utilizing different lipase specificities, addition of Thermomyces lanuginosus lipase (TLL), allowed the CALA product mixture to be cleaned up by hydrolyzing attached glycerol. In addition, a three-enzyme process is suggested, in which a simple alcohol is added and Candida antarctica lipase B (CALB) is used to esterify carboxylic acids to lower AV. Full article
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Article
Penicillin Acylase from Streptomyces lavendulae and Aculeacin A Acylase from Actinoplanes utahensis: Two Versatile Enzymes as Useful Tools for Quorum Quenching Processes
Catalysts 2020, 10(7), 730; https://doi.org/10.3390/catal10070730 - 01 Jul 2020
Cited by 5 | Viewed by 1002
Abstract
Many Gram-negative bacteria produce N-acyl-homoserine lactones (AHLs), quorum sensing (QS) molecules that can be enzymatically inactivated by quorum quenching (QQ) processes; this approach is considered an emerging antimicrobial alternative. In this study, kinetic parameters of several AHLs hydrolyzed by penicillin acylase from [...] Read more.
Many Gram-negative bacteria produce N-acyl-homoserine lactones (AHLs), quorum sensing (QS) molecules that can be enzymatically inactivated by quorum quenching (QQ) processes; this approach is considered an emerging antimicrobial alternative. In this study, kinetic parameters of several AHLs hydrolyzed by penicillin acylase from Streptomyces lavendulae (SlPA) and aculeacin A acylase from Actinoplanes utahensis (AuAAC) have been determined. Both enzymes catalyze efficiently the amide bond hydrolysis in AHLs with different acyl chain moieties (with or without 3-oxo modification) and exhibit a clear preference for AHLs with long acyl chains (C12-HSL > C14-HSL > C10-HSL > C8-HSL for SlPA, whereas C14-HSL > C12-HSL > C10-HSL > C8-HSL for AuAAC). Involvement of SlPA and AuAAC in QQ processes was demonstrated by Chromobacterium violaceum CV026-based bioassays and inhibition of biofilm formation by Pseudomonas aeruginosa, a process controlled by QS molecules, suggesting the application of these multifunctional enzymes as quorum quenching agents, this being the first time that quorum quenching activity was shown by an aculeacin A acylase. In addition, a phylogenetic study suggests that SlPA and AuAAC could be part of a new family of actinomycete acylases, with a preference for substrates with long aliphatic acyl chains, and likely involved in QQ processes. Full article
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Article
A Three-Step Process for the Bioconversion of Whey Permeate into a Glucose-Free D-Tagatose Syrup
Catalysts 2020, 10(6), 647; https://doi.org/10.3390/catal10060647 - 09 Jun 2020
Cited by 5 | Viewed by 1054
Abstract
We have developed a sustainable three-stage process for the revaluation of cheese whey permeate into D-tagatose, a rare sugar with functional properties used as sweetener. The experimental conditions (pH, temperature, cofactors, etc.) for each step were independently optimized. In the first step, concentrated [...] Read more.
We have developed a sustainable three-stage process for the revaluation of cheese whey permeate into D-tagatose, a rare sugar with functional properties used as sweetener. The experimental conditions (pH, temperature, cofactors, etc.) for each step were independently optimized. In the first step, concentrated whey containing 180–200 g/L of lactose was fully hydrolyzed by β-galactosidase from Bifidobacterium bifidum (Saphera®) in 3 h at 45 °C. Secondly, glucose was selectively removed by treatment with Pichia pastoris cells for 3 h at 30 °C. The best results were obtained with 350 mg of cells (previously grown for 16 h) per mL of solution. Finally, L-arabinose isomerase US100 from Bacillus stearothermophilus was employed to isomerize D-galactose into D-tagatose at pH 7.5 and 65 °C, in presence of 0.5 mM MnSO4. After 7 h, the concentration of D-tagatose was approximately 30 g/L (33.3% yield, referred to the initial D-galactose present in whey). The proposed integrated process takes place under mild conditions (neutral pH, moderate temperatures) in a short time (13 h), yielding a glucose-free syrup containing D-tagatose and galactose in a ratio 1:2 (w/w). Full article
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Review

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Review
Aspergillus: A Powerful Protein Production Platform
Catalysts 2020, 10(9), 1064; https://doi.org/10.3390/catal10091064 - 16 Sep 2020
Cited by 6 | Viewed by 1318
Abstract
Aspergilli have been widely used in the production of organic acids, enzymes, and secondary metabolites for almost a century. Today, several GRAS (generally recognized as safe) Aspergillus species hold a central role in the field of industrial biotechnology with multiple profitable applications. Since [...] Read more.
Aspergilli have been widely used in the production of organic acids, enzymes, and secondary metabolites for almost a century. Today, several GRAS (generally recognized as safe) Aspergillus species hold a central role in the field of industrial biotechnology with multiple profitable applications. Since the 1990s, research has focused on the use of Aspergillus species in the development of cell factories for the production of recombinant proteins mainly due to their natively high secretion capacity. Advances in the Aspergillus-specific molecular toolkit and combination of several engineering strategies (e.g., protease-deficient strains and fusions to carrier proteins) resulted in strains able to generate high titers of recombinant fungal proteins. However, the production of non-fungal proteins appears to still be inefficient due to bottlenecks in fungal expression and secretion machinery. After a brief overview of the different heterologous expression systems currently available, this review focuses on the filamentous fungi belonging to the genus Aspergillus and their use in recombinant protein production. We describe key steps in protein synthesis and secretion that may limit production efficiency in Aspergillus systems and present genetic engineering approaches and bioprocessing strategies that have been adopted in order to improve recombinant protein titers and expand the potential of Aspergilli as competitive production platforms. Full article
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Erratum
Erratum: Ntana, F., et al. Aspergillus: A Powerful Protein Production Platform. Catalysts 2020, 10, 1064
Catalysts 2020, 10(12), 1400; https://doi.org/10.3390/catal10121400 - 30 Nov 2020
Viewed by 390
Abstract
The author wishes to make the following erratum to this paper [...] Full article
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