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Enzymes, Biocatalysis and Chemical Biology
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Enzymes, Biocatalysis and Chemical Biology

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Chemical Biology".

Deadline for manuscript submissions: closed (31 October 2019) | Viewed by 41734

Printed Edition Available!
A printed edition of this Special Issue is available here.

Special Issue Editor

Prof. Dr. Stefano Serra

E-Mail Website
Guest Editor
Consiglio Nazionale delle Ricerche (C.N.R.), Istituto di Scienze e Tecnologie Chimiche (SCITEC), Milano, Italy
Interests: organic synthesis; stereoselective synthesis; development of new synthetic methods; biotransformations and use of enzymes in organic synthesis; biogeneration of flavours and fragrances; natural products; synthesis and chemical characterization of APIs; antibiotics and biological active compounds
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Chemical transformations that take advantage of biocatalysis are of great interest to chemists. The specific activity and selectivity of the enzymes allow them to perform different chemical reactions with high regio- and stereoselectivity, and a large number of biocatalysed industrial processes have been already established.

At the same time, we can observe the emergence of chemical biology, namely the scientific discipline spanning the fields of chemistry and biology and dealing with chemistry applied to biology.

The aim of this Special Issue is to collect original research papers, reviews and communications focused on biocatalysis applied to organic synthesis, as well as studies related to chemical biology. Contributions dealing with biotransformations, enzymology, the stereoselective synthesis of bioactive chemical compounds, and any study at the interface of chemistry and biology are welcome.

Prof. Dr. Stefano Serra
Guest Editor

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Enzymes
  • Biocatalysis and biotransformations;
  • Stereoselective synthesis;
  • Enzymes in organic synthesis;
  • Whole-cell biotransformations;
  • Chemical biology;
  • Biological activity;
  • Synthesis of bioactive chemical compounds;
  • Natural products

 

Published Papers (11 papers)

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Editorial

Jump to: Research

3 pages, 168 KiB  
Editorial
Enzymes, Biocatalysis and Chemical Biology
by Stefano Serra
Molecules 2020, 25(10), 2354; https://doi.org/10.3390/molecules25102354 - 18 May 2020
Cited by 5 | Viewed by 2310
Abstract
Chemical transformations that take advantage of biocatalysis are of great interest to chemists [...] Full article
(This article belongs to the Special Issue Enzymes, Biocatalysis and Chemical Biology)

Research

Jump to: Editorial

12 pages, 1698 KiB  
Article
Effects of GGT and C-S Lyase on the Generation of Endogenous Formaldehyde in Lentinula edodes at Different Growth Stages
by Xiaoyu Lei, Shuangshuang Gao, Xi Feng, Zhicheng Huang, Yinbing Bian, Wen Huang and Ying Liu
Molecules 2019, 24(23), 4203; https://doi.org/10.3390/molecules24234203 - 20 Nov 2019
Cited by 12 | Viewed by 2804
Abstract
Endogenous formaldehyde is generated as a normal metabolite via bio-catalysis of γ-glutamyl transpeptidase (GGT) and L-cysteine sulfoxide lyase (C-S lyase) during the growth and development of Lentinula edodes. In this study, we investigated the mRNA and protein expression levels, the activities of [...] Read more.
Endogenous formaldehyde is generated as a normal metabolite via bio-catalysis of γ-glutamyl transpeptidase (GGT) and L-cysteine sulfoxide lyase (C-S lyase) during the growth and development of Lentinula edodes. In this study, we investigated the mRNA and protein expression levels, the activities of GGT and C-S lyase, and the endogenous formaldehyde content in L. edodes at different growth stages. With the growth of L. edodes, a decrease was found in the mRNA and protein expression levels of GGT, while an increase was observed in the mRNA and protein expression levels of C-S lyase as well as the activities of GGT and C-S lyase. Our results revealed for the first time a positive relationship of formaldehyde content with the expression levels of Csl (encoding Lecsl) and Lecsl (C-S lyase protein of Lentinula edodes) as well as the enzyme activities of C-S lyase and GGT during the growth of L. edodes. This research provided a molecular basis for understanding and controlling the endogenous formaldehyde formation in Lentinula edodes in the process of growth. Full article
(This article belongs to the Special Issue Enzymes, Biocatalysis and Chemical Biology)
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12 pages, 2349 KiB  
Article
A New Triterpenoid Glucoside from a Novel Acidic Glycosylation of Ganoderic Acid A via Recombinant Glycosyltransferase of Bacillus subtilis
by Te-Sheng Chang, Chien-Min Chiang, Yu-Han Kao, Jiumn-Yih Wu, Yu-Wei Wu and Tzi-Yuan Wang
Molecules 2019, 24(19), 3457; https://doi.org/10.3390/molecules24193457 - 24 Sep 2019
Cited by 10 | Viewed by 3750
Abstract
Ganoderic acid A (GAA) is a bioactive triterpenoid isolated from the medicinal fungus Ganoderma lucidum. Our previous study showed that the Bacillus subtilis ATCC (American type culture collection) 6633 strain could biotransform GAA into compound (1), GAA-15-O-β-glucoside, and [...] Read more.
Ganoderic acid A (GAA) is a bioactive triterpenoid isolated from the medicinal fungus Ganoderma lucidum. Our previous study showed that the Bacillus subtilis ATCC (American type culture collection) 6633 strain could biotransform GAA into compound (1), GAA-15-O-β-glucoside, and compound (2). Even though we identified two glycosyltransferases (GT) to catalyze the synthesis of GAA-15-O-β-glucoside, the chemical structure of compound (2) and its corresponding enzyme remain elusive. In the present study, we identified BsGT110, a GT from the same B. subtilis strain, for the biotransformation of GAA into compound (2) through acidic glycosylation. BsGT110 showed an optimal glycosylation activity toward GAA at pH 6 but lost most of its activity at pH 8. Through a scaled-up production, compound (2) was successfully isolated using preparative high-performance liquid chromatography and identified to be a new triterpenoid glucoside (GAA-26-O-β-glucoside) by mass and nuclear magnetic resonance spectroscopy. The results of kinetic experiments showed that the turnover number (kcat) of BsGT110 toward GAA at pH 6 (kcat = 11.2 min−1) was 3-fold higher than that at pH 7 (kcat = 3.8 min−1), indicating that the glycosylation activity of BsGT110 toward GAA was more active at acidic pH 6. In short, we determined that BsGT110 is a unique GT that plays a role in the glycosylation of triterpenoid at the C-26 position under acidic conditions, but loses most of this activity under alkaline ones, suggesting that acidic solutions may enhance the catalytic activity of this and similar types of GTs toward triterpenoids. Full article
(This article belongs to the Special Issue Enzymes, Biocatalysis and Chemical Biology)
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10 pages, 1846 KiB  
Article
Ultrasonic Processing Induced Activity and Structural Changes of Polyphenol Oxidase in Orange (Citrus sinensis Osbeck)
by Lijuan Zhu, Linhu Zhu, Ayesha Murtaza, Yan Liu, Siyu Liu, Junjie Li, Aamir Iqbal, Xiaoyun Xu, Siyi Pan and Wanfeng Hu
Molecules 2019, 24(10), 1922; https://doi.org/10.3390/molecules24101922 - 18 May 2019
Cited by 24 | Viewed by 3283
Abstract
Apart from non-enzymatic browning, polyphenol oxidase (PPO) also plays a role in the browning reaction of orange (Citrus sinensis Osbeck) juice, and needs to be inactivated during the processing. In this study, the protein with high PPO activity was purified from orange [...] Read more.
Apart from non-enzymatic browning, polyphenol oxidase (PPO) also plays a role in the browning reaction of orange (Citrus sinensis Osbeck) juice, and needs to be inactivated during the processing. In this study, the protein with high PPO activity was purified from orange (Citrus sinensis Osbeck) and inactivated by ultrasonic processing. Fluorescence spectroscopy, circular dichroism (CD) and Dynamic light scattering (DLS) were used to investigate the ultrasonic effect on PPO activity and structural changes on purified PPO. DLS analysis illustrated that ultrasonic processing leads to initial dissociation and final aggregation of the protein. Fluorescence spectroscopy analysis showed the decrease in fluorescence intensity leading to the exposure of Trp residues to the polar environment, thereby causing the disruption of the tertiary structure after ultrasonic processing. Loss of α-helix conformation leading to the reorganization of secondary structure was triggered after the ultrasonic processing, according to CD analysis. Ultrasonic processing could induce aggregation and modification in the tertiary and secondary structure of a protein containing high PPO activity in orange (Citrus sinensis Osbeck), thereby causing inactivation of the enzyme. Full article
(This article belongs to the Special Issue Enzymes, Biocatalysis and Chemical Biology)
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15 pages, 2149 KiB  
Article
Engineering the Enantioselectivity of Yeast Old Yellow Enzyme OYE2y in Asymmetric Reduction of (E/Z)-Citral to (R)-Citronellal
by Xiangxian Ying, Shihua Yu, Meijuan Huang, Ran Wei, Shumin Meng, Feng Cheng, Meilan Yu, Meirong Ying, Man Zhao and Zhao Wang
Molecules 2019, 24(6), 1057; https://doi.org/10.3390/molecules24061057 - 18 Mar 2019
Cited by 17 | Viewed by 4694
Abstract
The members of the Old Yellow Enzyme (OYE) family are capable of catalyzing the asymmetric reduction of (E/Z)-citral to (R)-citronellal—a key intermediate in the synthesis of L-menthol. The applications of OYE-mediated biotransformation are usually hampered by its [...] Read more.
The members of the Old Yellow Enzyme (OYE) family are capable of catalyzing the asymmetric reduction of (E/Z)-citral to (R)-citronellal—a key intermediate in the synthesis of L-menthol. The applications of OYE-mediated biotransformation are usually hampered by its insufficient enantioselectivity and low activity. Here, the (R)-enantioselectivity of Old Yellow Enzyme from Saccharomyces cerevisiae CICC1060 (OYE2y) was enhanced through protein engineering. The single mutations of OYE2y revealed that the sites R330 and P76 could act as the enantioselectivity switch of OYE2y. Site-saturation mutagenesis was conducted to generate all possible replacements for the sites R330 and P76, yielding 17 and five variants with improved (R)-enantioselectivity in the (E/Z)-citral reduction, respectively. Among them, the variants R330H and P76C partly reversed the neral derived enantioselectivity from 32.66% e.e. (S) to 71.92% e.e. (R) and 37.50% e.e. (R), respectively. The docking analysis of OYE2y and its variants revealed that the substitutions R330H and P76C enabled neral to bind with a flipped orientation in the active site and thus reverse the enantioselectivity. Remarkably, the double substitutions of R330H/P76M, P76G/R330H, or P76S/R330H further improved (R)-enantioselectivity to >99% e.e. in the reduction of (E)-citral or (E/Z)-citral. The results demonstrated that it was feasible to alter the enantioselectivity of OYEs through engineering key residue distant from active sites, e.g., R330 in OYE2y. Full article
(This article belongs to the Special Issue Enzymes, Biocatalysis and Chemical Biology)
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12 pages, 1505 KiB  
Article
Antifungal Activity against Botrytis cinerea of 2,6-Dimethoxy-4-(phenylimino)cyclohexa-2,5-dienone Derivatives
by Paulo Castro, Leonora Mendoza, Claudio Vásquez, Paz Cornejo Pereira, Freddy Navarro, Karin Lizama, Rocío Santander and Milena Cotoras
Molecules 2019, 24(4), 706; https://doi.org/10.3390/molecules24040706 - 15 Feb 2019
Cited by 11 | Viewed by 2803
Abstract
In this work the enzyme laccase from Trametes versicolor was used to synthetize 2,6-dimethoxy-4-(phenylimino)cyclohexa-2,5-dienone derivatives. Ten products with different substitutions in the aromatic ring were synthetized and characterized using 1H- and 13C-NMR and mass spectrometry. The 3,5-dichlorinated compound showed highest antifungal [...] Read more.
In this work the enzyme laccase from Trametes versicolor was used to synthetize 2,6-dimethoxy-4-(phenylimino)cyclohexa-2,5-dienone derivatives. Ten products with different substitutions in the aromatic ring were synthetized and characterized using 1H- and 13C-NMR and mass spectrometry. The 3,5-dichlorinated compound showed highest antifungal activity against the phytopathogen Botrytis cinerea, while the p-methoxylated compound had the lowest activity; however, the antifungal activity of the products was higher than the activity of the substrates of the reactions. Finally, the results suggested that these compounds produced damage in the fungal cell wall. Full article
(This article belongs to the Special Issue Enzymes, Biocatalysis and Chemical Biology)
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10 pages, 1354 KiB  
Article
A Convenient, Rapid, Sensitive, and Reliable Spectrophotometric Assay for Adenylate Kinase Activity
by Kai Song, Yejing Wang, Yu Li, Chaoxiang Ding, Rui Cai, Gang Tao, Ping Zhao, Qingyou Xia and Huawei He
Molecules 2019, 24(4), 663; https://doi.org/10.3390/molecules24040663 - 13 Feb 2019
Cited by 4 | Viewed by 4529
Abstract
Enzymatic activity assays are essential and critical for the study of enzyme kinetics. Adenylate kinase (Adk) plays a fundamental role in cellular energy and nucleotide homeostasis. To date, assays based on different principles have been used for the determination of Adk activity. Here, [...] Read more.
Enzymatic activity assays are essential and critical for the study of enzyme kinetics. Adenylate kinase (Adk) plays a fundamental role in cellular energy and nucleotide homeostasis. To date, assays based on different principles have been used for the determination of Adk activity. Here, we show a spectrophotometric analysis technique to determine Adk activity with bromothymol blue as a pH indicator. We analyzed the effects of substrates and the pH indicator on the assay using orthogonal design and then established the most optimal assay for Adk activity. Subsequently, we evaluated the thermostability of Adk and the inhibitory effect of KCl on Adk activity with this assay. Our results show that this assay is simple, rapid, and precise. It shows great potential as an alternative to the conventional Adk activity assay. Our results also suggest that orthogonal design is an effective approach, which is very suitable for the optimization of complex enzyme reaction conditions. Full article
(This article belongs to the Special Issue Enzymes, Biocatalysis and Chemical Biology)
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18 pages, 940 KiB  
Article
Fungi-Mediated Biotransformation of the Isomeric Forms of the Apocarotenoids Ionone, Damascone and Theaspirane
by Stefano Serra and Davide De Simeis
Molecules 2019, 24(1), 19; https://doi.org/10.3390/molecules24010019 - 21 Dec 2018
Cited by 12 | Viewed by 5062
Abstract
In this work, we describe a study on the biotransformation of seven natural occurring apocarotenoids by means of eleven selected fungal species. The substrates, namely ionone (α-, β- and γ-isomers), 3,4-dehydroionone, damascone (α- and β-isomers) and theaspirane are relevant flavour and fragrances components. [...] Read more.
In this work, we describe a study on the biotransformation of seven natural occurring apocarotenoids by means of eleven selected fungal species. The substrates, namely ionone (α-, β- and γ-isomers), 3,4-dehydroionone, damascone (α- and β-isomers) and theaspirane are relevant flavour and fragrances components. We found that most of the investigated biotransformation reactions afforded oxidized products such as hydroxy- keto- or epoxy-derivatives. On the contrary, the reduction of the keto groups or the reduction of the double bond functional groups were observed only for few substrates, where the reduced products are however formed in minor amount. When starting apocarotenoids are isomers of the same chemical compound (e.g., ionone isomers) their biotransformation can give products very different from each other, depending both on the starting substrate and on the fungal species used. Since the majority of the starting apocarotenoids are often available in natural form and the described products are natural compounds, identified in flavours or fragrances, our biotransformation procedures can be regarded as prospective processes for the preparation of high value olfactory active compounds. Full article
(This article belongs to the Special Issue Enzymes, Biocatalysis and Chemical Biology)
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13 pages, 2503 KiB  
Article
Characterization of a Carbonyl Reductase from Rhodococcus erythropolis WZ010 and Its Variant Y54F for Asymmetric Synthesis of (S)-N-Boc-3-Hydroxypiperidine
by Xiangxian Ying, Jie Zhang, Can Wang, Meijuan Huang, Yuting Ji, Feng Cheng, Meilan Yu, Zhao Wang and Meirong Ying
Molecules 2018, 23(12), 3117; https://doi.org/10.3390/molecules23123117 - 28 Nov 2018
Cited by 15 | Viewed by 4569
Abstract
The recombinant carbonyl reductase from Rhodococcus erythropolis WZ010 (ReCR) demonstrated strict (S)-stereoselectivity and catalyzed the irreversible reduction of N-Boc-3-piperidone (NBPO) to (S)-N-Boc-3-hydroxypiperidine [(S)-NBHP], a key chiral intermediate in the synthesis of ibrutinib. The NAD(H)-specific [...] Read more.
The recombinant carbonyl reductase from Rhodococcus erythropolis WZ010 (ReCR) demonstrated strict (S)-stereoselectivity and catalyzed the irreversible reduction of N-Boc-3-piperidone (NBPO) to (S)-N-Boc-3-hydroxypiperidine [(S)-NBHP], a key chiral intermediate in the synthesis of ibrutinib. The NAD(H)-specific enzyme was active within broad ranges of pH and temperature and had remarkable activity in the presence of higher concentration of organic solvents. The amino acid residue at position 54 was critical for the activity and the substitution of Tyr54 to Phe significantly enhanced the catalytic efficiency of ReCR. The kcat/Km values of ReCR Y54F for NBPO, (R/S)-2-octanol, and 2-propanol were 49.17 s−1 mM−1, 56.56 s−1 mM−1, and 20.69 s−1 mM−1, respectively. In addition, the (S)-NBHP yield was as high as 95.92% when whole cells of E. coli overexpressing ReCR variant Y54F catalyzed the asymmetric reduction of 1.5 M NBPO for 12 h in the aqueous/(R/S)-2-octanol biphasic system, demonstrating the great potential of ReCR variant Y54F for practical applications. Full article
(This article belongs to the Special Issue Enzymes, Biocatalysis and Chemical Biology)
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14 pages, 2186 KiB  
Article
Chemical Modification of Sweet Potato β-amylase by Mal-mPEG to Improve Its Enzymatic Characteristics
by Xinhong Liang, Wanli Zhang, Junjian Ran, Junliang Sun, Lingxia Jiao, Longfei Feng and Benguo Liu
Molecules 2018, 23(11), 2754; https://doi.org/10.3390/molecules23112754 - 24 Oct 2018
Cited by 8 | Viewed by 2810
Abstract
The sweet potato β-amylase (SPA) was modified by 6 types of methoxy polyethylene glycol to enhance its specific activity and thermal stability. The aims of the study were to select the optimum modifier, optimize the modification parameters, and further investigate the characterization of [...] Read more.
The sweet potato β-amylase (SPA) was modified by 6 types of methoxy polyethylene glycol to enhance its specific activity and thermal stability. The aims of the study were to select the optimum modifier, optimize the modification parameters, and further investigate the characterization of the modified SPA. The results showed that methoxy polyethylene glycol maleimide (molecular weight 5000, Mal-mPEG5000) was the optimum modifier of SPA; Under the optimal modification conditions, the specific activity of Mal-mPEG5000-SPA was 24.06% higher than that of the untreated SPA. Mal-mPEG5000-SPA was monomeric with a molecular weight of about 67 kDa by SDS-PAGE. The characteristics of Mal-mPEG5000-SPA were significantly improved. The Km value, Vmax and Ea in Mal-mPEG5000-SPA for sweet potato starch showed that Mal-mPEG5000-SPA had greater affinity for sweet potato starch and higher speed of hydrolysis than SPA. There was no significant difference of the metal ions’ effect on Mal-mPEG5000-SPA and SPA. Full article
(This article belongs to the Special Issue Enzymes, Biocatalysis and Chemical Biology)
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19 pages, 2598 KiB  
Article
Biodegradation of 7-Hydroxycoumarin in Pseudomonas mandelii 7HK4 via ipso-Hydroxylation of 3-(2,4-Dihydroxyphenyl)-propionic Acid
by Arūnas Krikštaponis and Rolandas Meškys
Molecules 2018, 23(10), 2613; https://doi.org/10.3390/molecules23102613 - 12 Oct 2018
Cited by 10 | Viewed by 4294
Abstract
A gene cluster, denoted as hcdABC, required for the degradation of 3-(2,4-dihydroxyphenyl)-propionic acid has been cloned from 7-hydroxycoumarin-degrading Pseudomonas mandelii 7HK4 (DSM 107615), and sequenced. Bioinformatic analysis shows that the operon hcdABC encodes a flavin-binding hydroxylase (HcdA), an extradiol dioxygenase (HcdB), and [...] Read more.
A gene cluster, denoted as hcdABC, required for the degradation of 3-(2,4-dihydroxyphenyl)-propionic acid has been cloned from 7-hydroxycoumarin-degrading Pseudomonas mandelii 7HK4 (DSM 107615), and sequenced. Bioinformatic analysis shows that the operon hcdABC encodes a flavin-binding hydroxylase (HcdA), an extradiol dioxygenase (HcdB), and a putative hydroxymuconic semialdehyde hydrolase (HcdC). The analysis of the recombinant HcdA activity in vitro confirms that this enzyme belongs to the group of ipso-hydroxylases. The activity of the proteins HcdB and HcdC has been analyzed by using recombinant Escherichia coli cells. Identification of intermediate metabolites allowed us to confirm the predicted enzyme functions and to reconstruct the catabolic pathway of 3-(2,4-dihydroxyphenyl)-propionic acid. HcdA catalyzes the conversion of 3-(2,4-dihydroxyphenyl)-propionic acid to 3-(2,3,5-trihydroxyphenyl)-propionic acid through an ipso-hydroxylation followed by an internal (1,2-C,C)-shift of the alkyl moiety. Then, in the presence of HcdB, a subsequent oxidative meta-cleavage of the aromatic ring occurs, resulting in the corresponding linear product (2E,4E)-2,4-dihydroxy-6-oxonona-2,4-dienedioic acid. Here, we describe a Pseudomonas mandelii strain 7HK4 capable of degrading 7-hydroxycoumarin via 3-(2,4-dihydroxyphenyl)-propionic acid pathway. Full article
(This article belongs to the Special Issue Enzymes, Biocatalysis and Chemical Biology)
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