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Zhang L, Wang G, Li Z, Yang J, Li H, Wang W, Li Z, Li H. Molecular pharmacology and therapeutic advances of monoterpene perillyl alcohol. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 132:155826. [PMID: 38897045 DOI: 10.1016/j.phymed.2024.155826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 02/20/2024] [Accepted: 06/12/2024] [Indexed: 06/21/2024]
Abstract
BACKGROUND Perillyl alcohol (POH) is a aroma monoterpene commonly obtained from various plants' essential oil. Recently, increasing researches have demonstrated that POH may be useful, not only as flavor compound, but also as bioactive molecule because of a variety of biological activities. PURPOSE The aim of this review is to summarize the production, pharmacological activities and molecular mechanism, active derivatives, toxicity and parmacokinetics, and industrial application of POH. METHODS A systematic search of published articles up to January 2024 in Web of Science, China Knowledge Network, and PubMed databases is conducted using the following keywords: POH, POH derivatives, biological or pharmacological, production or synthesis, pharmacokinetics, toxicity and application. RESULTS Biotechnological production is considered to be a potential alternative approach to generate POH. POH provides diverse pharmacological benefits, including anticancer, antimicrobial, insecticidal, antioxidant, anti-inflammatory, hypotensive, vasorelaxant, antinociceptive, antiasthmatic, hepatoprotective effects, etc. The underlying mechanisms of action include modulation of NF-κB, JNK/c-Jun, Notch, Akt/mTOR, PI3K/Akt/eNOS, STAT3, Nrf2 and ERS response pathways, mitigation of mitochondrial dysfunction and membrane integrity damage, and inhibition of ROS accumulation, pro-inflammatory cytokines release and NLRP3 activation. What's more, the proteins or genes influenced by POH against diseases refer to Bax, Bcl-2, cyclin D1, CDK, p21, p53, HIF-1α, AP-1, caspase-3, M6P/IGF2R, PARP, VEGF, etc. Some clinical studies report that intranasal delivery of POH is a safe and effective treatment for cancer, but further clinical investigations are needed to confirm other health benefits of POH in human healthy. Depending on these health-promoting properties together with desirable flavor and safety, POH can be employed as dietary supplement, preservative and flavor additive in food and cosmetic fields, as building block in synthesis fields, as anticancer drug in medicinal fields, and as pesticides and herbicides in agricultural fields. CONCLUSION This review systematically summarizes the recent advances in POH and highlights its therapeutic effects and potential mechanisms as well as the clinical settings, which is helpful to develop POH into functional food and new candidate drug for prevention and management of diseases. Future studies are needed to conduct more biological activity studies of POH and its derivatives, and check their clinical efficacy and potential side effects.
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Affiliation(s)
- Lulu Zhang
- College of Food Science and Technology, Henan University of Technology, Zhengzhou, Henan 450001, PR China; Henan Province Wheat-flour Staple Food Engineering Technology Research Centre, Zhengzhou, Henan 450001, PR China.
| | - Guoguo Wang
- College of Food Science and Technology, Henan University of Technology, Zhengzhou, Henan 450001, PR China; Henan Province Wheat-flour Staple Food Engineering Technology Research Centre, Zhengzhou, Henan 450001, PR China
| | - Zehao Li
- College of Food Science and Technology, Henan University of Technology, Zhengzhou, Henan 450001, PR China; Henan Province Wheat-flour Staple Food Engineering Technology Research Centre, Zhengzhou, Henan 450001, PR China
| | - Jinchu Yang
- Technology Center, China Tobacco Henan Industrial Co., Ltd., Zhengzhou, Henan 450000, PR China.
| | - Haoliang Li
- Technology Center, China Tobacco Henan Industrial Co., Ltd., Zhengzhou, Henan 450000, PR China
| | - Wanying Wang
- College of Food Science and Technology, Henan University of Technology, Zhengzhou, Henan 450001, PR China; Henan Province Wheat-flour Staple Food Engineering Technology Research Centre, Zhengzhou, Henan 450001, PR China
| | - Zhijian Li
- College of Food Science and Technology, Henan University of Technology, Zhengzhou, Henan 450001, PR China; Henan Province Wheat-flour Staple Food Engineering Technology Research Centre, Zhengzhou, Henan 450001, PR China
| | - Hua Li
- College of Food Science and Technology, Henan University of Technology, Zhengzhou, Henan 450001, PR China; Henan Province Wheat-flour Staple Food Engineering Technology Research Centre, Zhengzhou, Henan 450001, PR China.
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2
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Fansher D, Besna JN, Fendri A, Pelletier JN. Choose Your Own Adventure: A Comprehensive Database of Reactions Catalyzed by Cytochrome P450 BM3 Variants. ACS Catal 2024; 14:5560-5592. [PMID: 38660610 PMCID: PMC11036407 DOI: 10.1021/acscatal.4c00086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 04/26/2024]
Abstract
Cytochrome P450 BM3 monooxygenase is the topic of extensive research as many researchers have evolved this enzyme to generate a variety of products. However, the abundance of information on increasingly diversified variants of P450 BM3 that catalyze a broad array of chemistry is not in a format that enables easy extraction and interpretation. We present a database that categorizes variants by their catalyzed reactions and includes details about substrates to provide reaction context. This database of >1500 P450 BM3 variants is downloadable and machine-readable and includes instructions to maximize ease of gathering information. The database allows rapid identification of commonly reported substitutions, aiding researchers who are unfamiliar with the enzyme in identifying starting points for enzyme engineering. For those actively engaged in engineering P450 BM3, the database, along with this review, provides a powerful and user-friendly platform to understand, predict, and identify the attributes of P450 BM3 variants, encouraging the further engineering of this enzyme.
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Affiliation(s)
- Douglas
J. Fansher
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
| | - Jonathan N. Besna
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
- Department
of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada H3T 1J4
| | - Ali Fendri
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
| | - Joelle N. Pelletier
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
- Department
of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada H3T 1J4
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3
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Kim JH, Park CM, Jeong HC, Jeong GH, Cha GS, Lee S, Yun CH. Production of Mono-Hydroxylated Derivatives of Terpinen-4-ol by Bacterial CYP102A1 Enzymes. J Microbiol Biotechnol 2024; 34:725-734. [PMID: 38044690 PMCID: PMC11016761 DOI: 10.4014/jmb.2310.10018] [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: 10/13/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/05/2023]
Abstract
CYP102A1 from Bacillus megaterium is an important enzyme in biotechnology, because engineered CYP102A1 enzymes can react with diverse substrates and produce human cytochrome P450-like metabolites. Therefore, CYP102A1 can be applied to drug metabolite production. Terpinen-4-ol is a cyclic monoterpene and the primary component of essential tea tree oil. Terpinen-4-ol was known for therapeutic effects, including antibacterial, antifungal, antiviral, and anti-inflammatory. Because terpenes are natural compounds, examining novel terpenes and investigating the therapeutic effects of terpenes represent responses to social demands for eco-friendly compounds. In this study, we investigated the catalytic activity of engineered CYP102A1 on terpinen-4-ol. Among CYP102A1 mutants tested here, the R47L/F81I/F87V/E143G/L188Q/N213S/E267V mutant showed the highest activity to terpinen-4-ol. Two major metabolites of terpinen-4-ol were generated by engineered CYP102A1. Characterization of major metabolites was confirmed by liquid chromatography-mass spectrometry (LC-MS), gas chromatography-MS, and nuclear magnetic resonance spectroscopy (NMR). Based on the LC-MS results, the difference in mass-to-charge ratio of an ion (m/z) between terpinen-4-ol and its major metabolites was 16. One major metabolite was defined as 1,4-dihydroxy-p-menth-2-ene by NMR. Given these results, we speculate that another major metabolite is also a mono-hydroxylated product. Taken together, we suggest that CYP102A1 can be applied to make novel terpene derivatives.
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Affiliation(s)
- Jeong-Hoon Kim
- School of Biological Sciences and Biotechnology, Graduate School, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Chan Mi Park
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Hae Chan Jeong
- School of Biological Sciences and Biotechnology, Graduate School, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Gyeong Han Jeong
- Research Division for Biotechnology, Advanced Radiation Technology Institute (ARTI), Korea Atomic Energy Research Institute (KAERI), Jeongeup 56212, Republic of Korea
| | - Gun Su Cha
- Namhae Garlic Research Institute, Namhae 52430, Republic of Korea
| | - Sungbeom Lee
- Research Division for Biotechnology, Advanced Radiation Technology Institute (ARTI), Korea Atomic Energy Research Institute (KAERI), Jeongeup 56212, Republic of Korea
- Department of Radiation Science and Technology, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Chul-Ho Yun
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
- Institute of Synthetic Biology for Carbon Neutralization, Chonnam National University, Gwangju 61186, Republic of Korea
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4
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Taher M, Dubey KD, Mazumdar S. Computationally guided bioengineering of the active site, substrate access pathway, and water channels of thermostable cytochrome P450, CYP175A1, for catalyzing the alkane hydroxylation reaction. Chem Sci 2023; 14:14316-14326. [PMID: 38098704 PMCID: PMC10718072 DOI: 10.1039/d3sc02857g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 11/10/2023] [Indexed: 12/17/2023] Open
Abstract
Understanding structure-function relationships in proteins is pivotal in their development as industrial biocatalysts. In this regard, rational engineering of protein active site access pathways and various tunnels and channels plays a central role in designing competent enzymes with high stability and enhanced efficiency. Here, we report the rational evolution of a thermostable cytochrome P450, CYP175A1, to catalyze the C-H activation reaction of longer-chain alkanes. A strategy combining computational tools with experiments has shown that the substrate scope and enzymatic activity can be enhanced by rational engineering of certain important channels such as the substrate entry and water channels along with the active site of the enzyme. The evolved enzymes showed an improved catalytic rate for hexadecane hydroxylation with high regioselectivity. The Q67L/Y68F mutation showed binding of the substrate in the active site, water channel mutation L80F/V220T showed improved catalytic activity through the peroxide shunt pathway and substrate entry channel mutation W269F/I270A showed better substrate accessibility to the active pocket. All-atom MD simulations provided the rationale for the inactivity of the wild-type CYP175A1 for hexadecane hydroxylation and predicted the above hot-spot residues to enhance the activity. The reaction mechanism was studied by QM/MM calculations for enzyme-substrate complexes and reaction intermediates. Detailed thermal and thermodynamic stability of all the mutants were analyzed and the results showed that the evolved enzymes were thermally stable. The present strategy showed promising results, and insights gained from this work can be applied to the general enzymatic system to expand substrate scope and improve catalytic activity.
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Affiliation(s)
- Mohd Taher
- Department of Chemical Sciences, Tata Institute of Fundamental Research Homi Bhabha Road, Colaba Mumbai 400005 India
| | - Kshatresh Dutta Dubey
- Department of Chemistry, School of Natural Science, Shiv Nadar Institution of Eminence Delhi-NCR NH91, Tehsil Dadri Greater Noida Uttar Pradesh 201314 India
| | - Shyamalava Mazumdar
- Department of Chemical Sciences, Tata Institute of Fundamental Research Homi Bhabha Road, Colaba Mumbai 400005 India
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5
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Ashworth MA, Bombino E, de Jong RM, Wijma HJ, Janssen DB, McLean KJ, Munro AW. Computation-Aided Engineering of Cytochrome P450 for the Production of Pravastatin. ACS Catal 2022; 12:15028-15044. [PMID: 36570080 PMCID: PMC9764288 DOI: 10.1021/acscatal.2c03974] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/22/2022] [Indexed: 11/29/2022]
Abstract
CYP105AS1 is a cytochrome P450 from Amycolatopsis orientalis that catalyzes monooxygenation of compactin to 6-epi-pravastatin. For fermentative production of the cholesterol-lowering drug pravastatin, the stereoselectivity of the enzyme needs to be inverted, which has been partially achieved by error-prone PCR mutagenesis and screening. In the current study, we report further optimization of the stereoselectivity by a computationally aided approach. Using the CoupledMoves protocol of Rosetta, a virtual library of mutants was designed to bind compactin in a pro-pravastatin orientation. By examining the frequency of occurrence of beneficial substitutions and rational inspection of their interactions, a small set of eight mutants was predicted to show the desired selectivity and these variants were tested experimentally. The best CYP105AS1 variant gave >99% stereoselective hydroxylation of compactin to pravastatin, with complete elimination of the unwanted 6-epi-pravastatin diastereomer. The enzyme-substrate complexes were also examined by ultrashort molecular dynamics simulations of 50 × 100 ps and 5 × 22 ns, which revealed that the frequency of occurrence of near-attack conformations agreed with the experimentally observed stereoselectivity. These results show that a combination of computational methods and rational inspection could improve CYP105AS1 stereoselectivity beyond what was obtained by directed evolution. Moreover, the work lays out a general in silico framework for specificity engineering of enzymes of known structure.
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Affiliation(s)
- Mark A. Ashworth
- Manchester
Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Elvira Bombino
- Department
of Biochemistry, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Nijenborgh 4, Groningen 9747 AG, Netherlands
| | - René M. de Jong
- DSM
Food & Beverage, Alexander Fleminglaan 1, 2613 AX Delft, the Netherlands
| | - Hein J. Wijma
- Department
of Biochemistry, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Nijenborgh 4, Groningen 9747 AG, Netherlands
| | - Dick B. Janssen
- Department
of Biochemistry, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Nijenborgh 4, Groningen 9747 AG, Netherlands,
| | - Kirsty J. McLean
- Manchester
Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester M1 7DN, United Kingdom,Department
of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, United Kingdom
| | - Andrew W. Munro
- Manchester
Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester M1 7DN, United Kingdom
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6
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Correddu D, Helmy Aly S, Di Nardo G, Catucci G, Prandi C, Blangetti M, Bellomo C, Bonometti E, Viscardi G, Gilardi G. Enhanced and specific epoxidation activity of P450 BM3 mutants for the production of high value terpene derivatives. RSC Adv 2022; 12:33964-33969. [PMID: 36505709 PMCID: PMC9703296 DOI: 10.1039/d2ra06029a] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
Terpenes are natural molecules of valuable interest for different industrial applications. Cytochromes P450 enzymes can functionalize terpenoids to form high value oxidized derivatives in a green and sustainable manner, representing a valid alternative to chemical catalysis. In this work, an enhanced and specific epoxidation activity of cytochrome P450 BM3 mutants was found for the terpenes geraniol and linalool. This is the first report showing the epoxidation of linalool by P450 BM3 and its mutant A2 (Asp251Gly/Gln307His) with the formation of valuable oxide derivatives, highlighting the relevance of this enzymes for industrial applications.
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Affiliation(s)
- Danilo Correddu
- Department of Life Sciences and Systems Biology, University of TorinoVia Accademia Albertina 1310123TorinoItaly
| | - Sabrina Helmy Aly
- Department of Life Sciences and Systems Biology, University of TorinoVia Accademia Albertina 1310123TorinoItaly
| | - Giovanna Di Nardo
- Department of Life Sciences and Systems Biology, University of TorinoVia Accademia Albertina 1310123TorinoItaly
| | - Gianluca Catucci
- Department of Life Sciences and Systems Biology, University of TorinoVia Accademia Albertina 1310123TorinoItaly
| | - Cristina Prandi
- Department of Chemistry, University of TorinoVia P. Giuria 710125TorinoItaly
| | - Marco Blangetti
- Department of Chemistry, University of TorinoVia P. Giuria 710125TorinoItaly
| | - Chiara Bellomo
- Department of Chemistry, University of TorinoVia P. Giuria 710125TorinoItaly
| | | | - Guido Viscardi
- Department of Chemistry, University of TorinoVia P. Giuria 710125TorinoItaly
| | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology, University of TorinoVia Accademia Albertina 1310123TorinoItaly
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7
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Wang M, Zhou X, Wang Z, Chen Y. Enzyme-catalyzed allylic oxidation reactions: A mini-review. Front Chem 2022; 10:950149. [PMID: 36046724 PMCID: PMC9420900 DOI: 10.3389/fchem.2022.950149] [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: 05/22/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
Chiral allylic oxidized products play an increasingly important role in the pharmaceutical, agrochemical, and pharmaceutical industries. Biocatalytic C–H oxyfunctionalization to synthesize allylic oxidized products has attracted great attention in recent years, with the ability to simplify synthetic approaches toward complex compounds. As a result, scientists have found some new enzymes and mutants through techniques of gene mining and enzyme-directed evolution in recent years. This review summarizes the recent developments in biocatalytic selective oxidation of olefins by different kinds of biocatalysts.
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Affiliation(s)
- Maoyao Wang
- Key Laboratory of Biocatalysis and Chiral Drug Synthesis of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, Zunyi Medical University, Zunyi, China
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Xiaojian Zhou
- Key Laboratory of Biocatalysis and Chiral Drug Synthesis of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, Zunyi Medical University, Zunyi, China
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Zhongqiang Wang
- Key Laboratory of Biocatalysis and Chiral Drug Synthesis of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, Zunyi Medical University, Zunyi, China
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Yongzheng Chen
- Key Laboratory of Biocatalysis and Chiral Drug Synthesis of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, Zunyi Medical University, Zunyi, China
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
- *Correspondence: Yongzheng Chen,
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8
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Reetz M. Witnessing the Birth of Directed Evolution of Stereoselective Enzymes as Catalysts in Organic Chemistry. Adv Synth Catal 2022. [DOI: 10.1002/adsc.202200466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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9
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Reetz MT. Making Enzymes Suitable for Organic Chemistry by Rational Protein Design. Chembiochem 2022; 23:e202200049. [PMID: 35389556 PMCID: PMC9401064 DOI: 10.1002/cbic.202200049] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/07/2022] [Indexed: 11/25/2022]
Abstract
This review outlines recent developments in protein engineering of stereo‐ and regioselective enzymes, which are of prime interest in organic and pharmaceutical chemistry as well as biotechnology. The widespread application of enzymes was hampered for decades due to limited enantio‐, diastereo‐ and regioselectivity, which was the reason why most organic chemists were not interested in biocatalysis. This attitude began to change with the advent of semi‐rational directed evolution methods based on focused saturation mutagenesis at sites lining the binding pocket. Screening constitutes the labor‐intensive step (bottleneck), which is the reason why various research groups are continuing to develop techniques for the generation of small and smart mutant libraries. Rational enzyme design, traditionally an alternative to directed evolution, provides small collections of mutants which require minimal screening. This approach first focused on thermostabilization, and did not enter the field of stereoselectivity until later. Computational guides such as the Rosetta algorithms, HotSpot Wizard metric, and machine learning (ML) contribute significantly to decision making. The newest advancements show that semi‐rational directed evolution such as CAST/ISM and rational enzyme design no longer develop on separate tracks, instead, they have started to merge. Indeed, researchers utilizing the two approaches have learned from each other. Today, the toolbox of organic chemists includes enzymes, primarily because the possibility of controlling stereoselectivity by protein engineering has ensured reliability when facing synthetic challenges. This review was also written with the hope that undergraduate and graduate education will include enzymes more so than in the past.
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Affiliation(s)
- Manfred T Reetz
- Max-Planck-Institut fur Kohlenforschung, Biocatalysis, Kaiser-Wilhelm-Platz 1, 45470, Muelheim an der Ruhr, GERMANY
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10
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Fessner ND, Weber H, Glieder A. Regiospecific 7-hydroxylation of ten-carbon monoterpenes by detoxifying CYP5035S7 monooxygenase of the white-rot fungus Polyporus arcularius. Biochem Biophys Res Commun 2022; 595:35-40. [DOI: 10.1016/j.bbrc.2022.01.072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/18/2022] [Indexed: 12/22/2022]
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11
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Ikebe J, Suzuki M, Komori A, Kobayashi K, Kameda T. Enzyme modification using mutation site prediction method for enhancing the regioselectivity of substrate reaction sites. Sci Rep 2021; 11:19004. [PMID: 34602611 PMCID: PMC8488038 DOI: 10.1038/s41598-021-98433-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/02/2021] [Indexed: 11/16/2022] Open
Abstract
Enzymes with low regioselectivity of substrate reaction sites may produce multiple products from a single substrate. When a target product is produced industrially using these enzymes, the production of non-target products (byproducts) causes adverse effects such as increased processing costs for purification and the amount of raw material. Thus it is required the development of modified enzymes to reduce the amount of byproducts’ production. In this paper, we report a method called mutation site prediction for enhancing the regioselectivity of substrate reaction sites (MSPER). MSPER takes conformational data for docking poses of an enzyme and a substrate as input and automatically generates a ranked list of mutation sites to destabilize docking poses for byproducts while maintaining those for target products in silico. We applied MSPER to the enzyme cytochrome P450 CYP102A1 (BM3) and the two substrates to enhance the regioselectivity for four target products with different reaction sites. The 13 of the total 14 top-ranked mutation sites predicted by MSPER for the four target products succeeded in selectively enhancing the regioselectivity up to 6.4-fold. The results indicate that MSPER can distinguish differences of substrate structures and the reaction sites, and can accurately predict mutation sites to enhance regioselectivity without selection by directed evolution screening.
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Affiliation(s)
- Jinzen Ikebe
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Munenori Suzuki
- KNC Bio-Research Center, KNC Laboratories Co., Ltd., 1-1-1 Murotani, Nishi-ku, Kobe, Hyogo, 651-2241, Japan
| | - Aya Komori
- KNC Bio-Research Center, KNC Laboratories Co., Ltd., 1-1-1 Murotani, Nishi-ku, Kobe, Hyogo, 651-2241, Japan
| | - Kaito Kobayashi
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Tomoshi Kameda
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.
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12
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Advances in enzymatic oxyfunctionalization of aliphatic compounds. Biotechnol Adv 2021; 51:107703. [PMID: 33545329 DOI: 10.1016/j.biotechadv.2021.107703] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 01/17/2021] [Accepted: 01/25/2021] [Indexed: 12/27/2022]
Abstract
Selective oxyfunctionalizations of aliphatic compounds are difficult chemical reactions, where enzymes can play an important role due to their stereo- and regio-selectivity and operation under mild reaction conditions. P450 monooxygenases are well-known biocatalysts that mediate oxyfunctionalization reactions in different living organisms (from bacteria to humans). Unspecific peroxygenases (UPOs), discovered in fungi, have arisen as "dream biocatalysts" of great biotechnological interest because they catalyze the oxyfunctionalization of aliphatic and aromatic compounds, avoiding the necessity of expensive cofactors and regeneration systems, and only depending on H2O2 for their catalysis. Here, we summarize recent advances in aliphatic oxyfunctionalization reactions by UPOs, as well as the molecular determinants of the enzyme structures responsible for their activities, emphasizing the differences found between well-known P450s and the novel fungal peroxygenases.
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13
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Microbial production of limonene and its derivatives: Achievements and perspectives. Biotechnol Adv 2020; 44:107628. [DOI: 10.1016/j.biotechadv.2020.107628] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 12/14/2022]
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14
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Bokel A, Rühlmann A, Hutter MC, Urlacher VB. Enzyme-Mediated Two-Step Regio- and Stereoselective Synthesis of Potential Rapid-Acting Antidepressant (2S,6S)-Hydroxynorketamine. ACS Catal 2020. [DOI: 10.1021/acscatal.9b05384] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ansgar Bokel
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Ansgar Rühlmann
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Michael C. Hutter
- Center for Bioinformatics, Saarland University, Campus E2.1, 66123 Saarbruecken, Germany
| | - Vlada B. Urlacher
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
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15
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Arabnejad H, Bombino E, Colpa DI, Jekel PA, Trajkovic M, Wijma HJ, Janssen DB. Computational Design of Enantiocomplementary Epoxide Hydrolases for Asymmetric Synthesis of Aliphatic and Aromatic Diols. Chembiochem 2020; 21:1893-1904. [PMID: 31961471 PMCID: PMC7383614 DOI: 10.1002/cbic.201900726] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/16/2020] [Indexed: 12/13/2022]
Abstract
The use of enzymes in preparative biocatalysis often requires tailoring enzyme selectivity by protein engineering. Herein we explore the use of computational library design and molecular dynamics simulations to create variants of limonene epoxide hydrolase that produce enantiomeric diols from meso‐epoxides. Three substrates of different sizes were targeted: cis‐2,3‐butene oxide, cyclopentene oxide, and cis‐stilbene oxide. Most of the 28 designs tested were active and showed the predicted enantioselectivity. Excellent enantioselectivities were obtained for the bulky substrate cis‐stilbene oxide, and enantiocomplementary mutants produced (S,S)‐ and (R,R)‐stilbene diol with >97 % enantiomeric excess. An (R,R)‐selective mutant was used to prepare (R,R)‐stilbene diol with high enantiopurity (98 % conversion into diol, >99 % ee). Some variants displayed higher catalytic rates (kcat) than the original enzyme, but in most cases KM values increased as well. The results demonstrate the feasibility of computational design and screening to engineer enantioselective epoxide hydrolase variants with very limited laboratory screening.
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Affiliation(s)
- Hesam Arabnejad
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Elvira Bombino
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Dana I. Colpa
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Peter A. Jekel
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Milos Trajkovic
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Hein J. Wijma
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Dick B. Janssen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
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16
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Rousseau O, Ebert MCCJC, Quaglia D, Fendri A, Parisien AH, Besna JN, Iyathurai S, Pelletier JN. Indigo Formation and Rapid NADPH Consumption Provide Robust Prediction of Raspberry Ketone Synthesis by Engineered Cytochrome P450 BM3. ChemCatChem 2019. [DOI: 10.1002/cctc.201901974] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Olivier Rousseau
- Department of ChemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
| | - Maximilian C. C. J. C. Ebert
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
- Department of BiochemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
| | - Daniela Quaglia
- Department of ChemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
| | - Ali Fendri
- Department of ChemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
| | - Adem H. Parisien
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
- Department of BiochemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
| | - Jonathan N. Besna
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
- Department of BiochemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
| | - Saathanan Iyathurai
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
- Department of BiochemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
| | - Joelle N. Pelletier
- Department of ChemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
- Department of BiochemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
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17
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Ferrario V, Fischer M, Zhu Y, Pleiss J. Modelling of substrate access and substrate binding to cephalosporin acylases. Sci Rep 2019; 9:12402. [PMID: 31455800 PMCID: PMC6712217 DOI: 10.1038/s41598-019-48849-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 08/14/2019] [Indexed: 01/16/2023] Open
Abstract
Semisynthetic cephalosporins are widely used antibiotics currently produced by different chemical steps under harsh conditions, which results in a considerable amount of toxic waste. Biocatalytic synthesis by the cephalosporin acylase from Pseudomonas sp. strain N176 is a promising alternative. Despite intensive engineering of the enzyme, the catalytic activity is still too low for a commercially viable process. To identify the bottlenecks which limit the success of protein engineering efforts, a series of MD simulations was performed to study for two acylase variants (WT, M6) the access of the substrate cephalosporin C from the bulk to the active site and the stability of the enzyme-substrate complex. In both variants, cephalosporin C was binding to a non-productive substrate binding site (E86α, S369β, S460β) at the entrance to the binding pocket, preventing substrate access. A second non-productive binding site (G372β, W376β, L457β) was identified within the binding pocket, which competes with the active site for substrate binding. Noteworthy, substrate binding to the protein surface followed a Langmuir model resulting in binding constants K = 7.4 and 9.2 mM for WT and M6, respectively, which were similar to the experimentally determined Michaelis constants KM = 11.0 and 8.1 mM, respectively.
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Affiliation(s)
- Valerio Ferrario
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Mona Fischer
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Yushan Zhu
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
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18
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Farhat W, Stamm A, Robert-Monpate M, Biundo A, Syrén PO. Biocatalysis for terpene-based polymers. ACTA ACUST UNITED AC 2019; 74:91-100. [PMID: 30789828 DOI: 10.1515/znc-2018-0199] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 01/24/2019] [Indexed: 12/11/2022]
Abstract
Accelerated generation of bio-based materials is vital to replace current synthetic polymers obtained from petroleum with more sustainable options. However, many building blocks available from renewable resources mainly contain unreactive carbon-carbon bonds, which obstructs their efficient polymerization. Herein, we highlight the potential of applying biocatalysis to afford tailored functionalization of the inert carbocyclic core of multicyclic terpenes toward advanced materials. As a showcase, we unlock the inherent monomer reactivity of norcamphor, a bicyclic ketone used as a monoterpene model system in this study, to afford polyesters with unprecedented backbones. The efficiencies of the chemical and enzymatic Baeyer-Villiger transformation in generating key lactone intermediates are compared. The concepts discussed herein are widely applicable for the valorization of terpenes and other cyclic building blocks using chemoenzymatic strategies.
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Affiliation(s)
- Wissam Farhat
- Department of Fibre and Polymer Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Teknikringen 56-58, 100 44 Stockholm, Sweden.,Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Tomtebodavägen 23, Box 1031, 171 21 Solna, Stockholm, Sweden
| | - Arne Stamm
- Department of Fibre and Polymer Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Teknikringen 56-58, 100 44 Stockholm, Sweden.,Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Tomtebodavägen 23, Box 1031, 171 21 Solna, Stockholm, Sweden
| | - Maxime Robert-Monpate
- Department of Fibre and Polymer Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Teknikringen 56-58, 100 44 Stockholm, Sweden.,Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Tomtebodavägen 23, Box 1031, 171 21 Solna, Stockholm, Sweden
| | - Antonino Biundo
- Department of Fibre and Polymer Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Teknikringen 56-58, 100 44 Stockholm, Sweden.,Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Tomtebodavägen 23, Box 1031, 171 21 Solna, Stockholm, Sweden
| | - Per-Olof Syrén
- Department of Fibre and Polymer Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Teknikringen 56-58, 100 44 Stockholm, Sweden.,Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Tomtebodavägen 23, Box 1031, 171 21 Solna, Stockholm, Sweden.,Wallenberg Wood Science Center, Teknikringen 56-58, SE-100 44 Stockholm, Sweden
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19
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Abstract
A novel approach for the synthesis of vanillin employing a three-step two-enzymatic cascade sequence is reported. Cytochrome P450 monooxygenases are known to catalyse the selective hydroxylation of aromatic compounds, which is one of the most challenging chemical reactions. A set of rationally designed variants of CYP102A1 (P450 BM3) from Bacillus megaterium at the amino acid positions 47, 51, 87, 328 and 437 was screened for conversion of the substrate 3-methylanisole to vanillyl alcohol via the intermediate product 4-methylguaiacol. Furthermore, a vanillyl alcohol oxidase (VAO) variant (F454Y) was selected as an alternative enzyme for the transformation of one of the intermediate compounds via vanillyl alcohol to vanillin. As a proof of concept, the bi-enzymatic three-step cascade conversion of 3-methylanisole to vanillin was successfully evaluated both in vitro and in vivo.
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20
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Abstract
The successful implementation of synthetic biology for chemicals biosynthesis relies on the availability of large libraries of well-characterized enzymatic building blocks. Here we present a scalable pipeline that applies the methodology of synthetic biology itself to bootstrap the creation of such a library. By designing and building a cytochrome P450 enzyme collection and testing it in a custom-made untargeted GC/MS-metabolomics-based approach, we were able to rapidly create and characterize a comprehensive enzyme library for the controlled oxyfunctionalisation of terpene scaffolds with a wide range of activities and selectivities towards several monoterpenes. This novel resource can now be used to access the extensive chemical diversity of terpenoids by pathway engineering and the assembly of biocatalytic cascades to subsequently produce libraries of oxygenated terpenoids and their derivatives for diverse applications, including drug discovery.
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21
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Affiliation(s)
- Yujie Liang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road 38, Beijing 100191, China
| | - Jialiang Wei
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road 38, Beijing 100191, China
| | - Xu Qiu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road 38, Beijing 100191, China
| | - Ning Jiao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road 38, Beijing 100191, China
- State Key Laboratory of Organometallic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
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22
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Xiong S, Wang Y, Yao M, Liu H, Zhou X, Xiao W, Yuan Y. Cell foundry with high product specificity and catalytic activity for 21-deoxycortisol biotransformation. Microb Cell Fact 2017; 16:105. [PMID: 28610588 PMCID: PMC5470312 DOI: 10.1186/s12934-017-0720-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 06/06/2017] [Indexed: 12/22/2022] Open
Abstract
Background 21-deoxycortisol (21-DF) is the key intermediate to manufacture pharmaceutical glucocorticoids. Recently, a Japan patent has realized 21-DF production via biotransformation of 17-hydroxyprogesterone (17-OHP) by purified steroid 11β-hydroxylase CYP11B1. Due to the less costs on enzyme isolation, purification and stabilization as well as cofactors supply, whole-cell should be preferentially employed as the biocatalyst over purified enzymes. No reports as so far have demonstrated a whole-cell system to produce 21-DF. Therefore, this study aimed to establish a whole-cell biocatalyst to achieve 21-DF transformation with high catalytic activity and product specificity. Results In this study, Escherichia coli MG1655(DE3), which exhibited the highest substrate transportation rate among other tested chassises, was employed as the host cell to construct our biocatalyst by co-expressing heterologous CYP11B1 together with bovine adrenodoxin and adrenodoxin reductase. Through screening CYP11B1s (with mutagenesis at N-terminus) from nine sources, Homo sapiens CYP11B1 mutant (G25R/G46R/L52 M) achieved the highest 21-DF transformation rate at 10.6 mg/L/h. Furthermore, an optimal substrate concentration of 2.4 g/L and a corresponding transformation rate of 16.2 mg/L/h were obtained by screening substrate concentrations. To be noted, based on structural analysis of the enzyme-substrate complex, two types of site-directed mutations were designed to adjust the relative position between the catalytic active site heme and the substrate. Accordingly, 1.96-fold enhancement on 21-DF transformation rate (to 47.9 mg/L/h) and 2.78-fold improvement on product/by-product ratio (from 0.36 to 1.36) were achieved by the combined mutagenesis of F381A/L382S/I488L. Eventually, after 38-h biotransformation in shake-flask, the production of 21-DF reached to 1.42 g/L with a yield of 52.7%, which is the highest 21-DF production as known. Conclusions Heterologous CYP11B1 was manipulated to construct E. coli biocatalyst converting 17-OHP to 21-DF. Through the strategies in terms of (1) screening enzymes (with N-terminal mutagenesis) sources, (2) optimizing substrate concentration, and most importantly (3) rational design novel mutants aided by structural analysis, the 21-DF transformation rate was stepwise improved by 19.5-fold along with 4.67-fold increase on the product/byproduct ratio. Eventually, the highest 21-DF reported production was achieved in shake-flask after 38-h biotransformation. This study highlighted above described methods to obtain a high efficient and specific biocatalyst for the desired biotransformation. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0720-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shuting Xiong
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Ying Wang
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Mingdong Yao
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Hong Liu
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Xiao Zhou
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Wenhai Xiao
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, People's Republic of China. .,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.
| | - Yingjin Yuan
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
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23
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An engineered outer membrane pore enables an efficient oxygenation of aromatics and terpenes. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.11.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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24
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Ciaramella A, Minerdi D, Gilardi G. Catalytically self-sufficient cytochromes P450 for green production of fine chemicals. RENDICONTI LINCEI-SCIENZE FISICHE E NATURALI 2016. [DOI: 10.1007/s12210-016-0581-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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25
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Girvan HM, Munro AW. Applications of microbial cytochrome P450 enzymes in biotechnology and synthetic biology. Curr Opin Chem Biol 2016; 31:136-45. [PMID: 27015292 DOI: 10.1016/j.cbpa.2016.02.018] [Citation(s) in RCA: 167] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 02/23/2016] [Accepted: 02/24/2016] [Indexed: 12/11/2022]
Abstract
Cytochrome P450 enzymes (P450s) are a superfamily of monooxygenase enzymes with enormous potential for synthetic biology applications. Across Nature, their substrate range is vast and exceeds that of other enzymes. The range of different chemical transformations performed by P450s is also substantial, and continues to expand through interrogation of the properties of novel P450s and by protein engineering studies. The ability of P450s to introduce oxygen atoms at specific positions on complex molecules makes these enzymes particularly valuable for applications in synthetic biology. This review focuses on the enzymatic properties and reaction mechanisms of P450 enzymes, and on recent studies that highlight their broad applications in the production of oxychemicals. For selected soluble bacterial P450s (notably the high-activity P450-cytochrome P450 reductase enzyme P450 BM3), variants with a multitude of diverse substrate selectivities have been generated both rationally and by random mutagenesis/directed evolution approaches. This highlights the robustness and malleability of the P450 fold, and the capacity of these biocatalysts to oxidise a wide range of chemical scaffolds. This article reviews recent research on the application of wild-type and engineered P450s in the production of important chemicals, including pharmaceuticals and drug metabolites, steroids and antibiotics. In addition, the properties of unusual members of the P450 superfamily that do not follow the canonical P450 catalytic pathway are described.
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Affiliation(s)
- Hazel M Girvan
- Manchester Institute of Biotechnology, Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Faculty of Life Sciences, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Andrew W Munro
- Manchester Institute of Biotechnology, Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Faculty of Life Sciences, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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26
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Eichler A, Gricman Ł, Herter S, Kelly PP, Turner NJ, Pleiss J, Flitsch SL. Enantioselective Benzylic Hydroxylation Catalysed by P450 Monooxygenases: Characterisation of a P450cam Mutant Library and Molecular Modelling. Chembiochem 2016; 17:426-32. [DOI: 10.1002/cbic.201500536] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Indexed: 12/30/2022]
Affiliation(s)
- Anja Eichler
- School of Chemistry; Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Łukasz Gricman
- Institute for Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Susanne Herter
- School of Chemistry; Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Paul P. Kelly
- School of Chemistry; Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Nicholas J. Turner
- School of Chemistry; Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Jürgen Pleiss
- Institute for Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Sabine L. Flitsch
- School of Chemistry; Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
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27
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Roccatano D. Structure, dynamics, and function of the monooxygenase P450 BM-3: insights from computer simulations studies. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:273102. [PMID: 26061496 DOI: 10.1088/0953-8984/27/27/273102] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The monooxygenase P450 BM-3 is a NADPH-dependent fatty acid hydroxylase enzyme isolated from soil bacterium Bacillus megaterium. As a pivotal member of cytochrome P450 superfamily, it has been intensely studied for the comprehension of structure-dynamics-function relationships in this class of enzymes. In addition, due to its peculiar properties, it is also a promising enzyme for biochemical and biomedical applications. However, despite the efforts, the full understanding of the enzyme structure and dynamics is not yet achieved. Computational studies, particularly molecular dynamics (MD) simulations, have importantly contributed to this endeavor by providing new insights at an atomic level regarding the correlations between structure, dynamics, and function of the protein. This topical review summarizes computational studies based on MD simulations of the cytochrome P450 BM-3 and gives an outlook on future directions.
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Affiliation(s)
- Danilo Roccatano
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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28
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Ilie A, Lonsdale R, Agudo R, Reetz MT. A diastereoselective P450-catalyzed epoxidation reaction: anti versus syn reactivity. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.03.076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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29
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Ko S, Yang YH, Choi KY, Kim BG. rational design and directed evolution of CYP102A1 (BM3) for regio-specific hydroxylation of isoflavone. BIOTECHNOL BIOPROC E 2015. [DOI: 10.1007/s12257-014-0718-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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30
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Currin A, Swainston N, Day PJ, Kell DB. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem Soc Rev 2015; 44:1172-239. [PMID: 25503938 PMCID: PMC4349129 DOI: 10.1039/c4cs00351a] [Citation(s) in RCA: 251] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/21/2022]
Abstract
The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust.
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Affiliation(s)
- Andrew Currin
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
| | - Neil Swainston
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- School of Computer Science , The University of Manchester , Manchester M13 9PL , UK
| | - Philip J. Day
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- Faculty of Medical and Human Sciences , The University of Manchester , Manchester M13 9PT , UK
| | - Douglas B. Kell
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
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Le-Huu P, Heidt T, Claasen B, Laschat S, Urlacher VB. Chemo-, Regio-, and Stereoselective Oxidation of the Monocyclic Diterpenoid β-Cembrenediol by P450 BM3. ACS Catal 2015. [DOI: 10.1021/cs5020404] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Priska Le-Huu
- Institute of Biochemistry, Heinrich-Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Tanja Heidt
- Institute of Organic Chemistry, University Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Birgit Claasen
- Institute of Organic Chemistry, University Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Sabine Laschat
- Institute of Organic Chemistry, University Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Vlada B. Urlacher
- Institute of Biochemistry, Heinrich-Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
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Guidelines for development and implementation of biocatalytic P450 processes. Appl Microbiol Biotechnol 2015; 99:2465-83. [PMID: 25652652 DOI: 10.1007/s00253-015-6403-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 01/09/2015] [Accepted: 01/12/2015] [Indexed: 01/17/2023]
Abstract
Biocatalytic reactions performed by cytochrome P450 monooxygenases are interesting in pharmaceutical research since they are involved in human drug metabolism. Furthermore, they are potentially interesting as biocatalysts for synthetic chemistry because of the exquisite selectivity of the chemistry they undertake. For example, selective hydroxylation can be undertaken on a highly functionalized molecule without the need for functional group protection. Recent progress in the discovery of novel P450s as well as protein engineering of these enzymes strongly encourages further development of their application, including use in synthetic processes. The biological characteristics of P450s (e.g., cofactor dependence) motivate the use of whole-cell systems for synthetic processes, and those processes implemented in industry are so far dominated by growing cells and native host systems. However, for an economically feasible process, the expression of P450 systems in a heterologous host with sufficient biocatalyst yield (g/g cdw) for non-growing systems or space-time yield (g/L/h) for growing systems remains a major challenge. This review summarizes the opportunities to improve P450 whole-cell processes and strategies in order to apply and implement them in industrial processes, both from a biological and process perspective. Indeed, a combined approach of host selection and cell engineering, integrated with process engineering, is suggested as the most effective route to implementation.
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Janocha S, Schmitz D, Bernhardt R. Terpene hydroxylation with microbial cytochrome P450 monooxygenases. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 148:215-50. [PMID: 25682070 DOI: 10.1007/10_2014_296] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Terpenoids comprise a highly diverse group of natural products. In addition to their basic carbon skeleton, they differ from one another in their functional groups. Functional groups attached to the carbon skeleton are the basis of the terpenoids' diverse properties. Further modifications of terpene olefins include the introduction of acyl-, aryl-, or sugar moieties and usually start with oxidations catalyzed by cytochrome P450 monooxygenases (P450s, CYPs). P450s are ubiquitously distributed throughout nature, involved in essential biological pathways such as terpenoid biosynthesis as well as the tailoring of terpenoids and other natural products. Their ability to introduce oxygen into nonactivated C-H bonds is unique and makes P450s very attractive for applications in biotechnology. Especially in the field of terpene oxidation, biotransformation methods emerge as an attractive alternative to classical chemical synthesis. For this reason, microbial P450s depict a highly interesting target for protein engineering approaches in order to increase selectivity and activity, respectively. Microbial P450s have been described to convert industrial and pharmaceutically interesting terpenoids such as ionones, limone, valencene, resin acids, and triterpenes (including steroids) as well as vitamin D3. Highly selective and active mutants have been evolved by applying classical site-directed mutagenesis as well as directed evolution of proteins. As P450s usually depend on electron transfer proteins, mutagenesis has also been applied to improve the interactions between P450s and their respective redox partners. This chapter provides an overview of terpenoid hydroxylation reactions catalyzed by bacterial P450s and highlights the achievements made by protein engineering to establish productive hydroxylation processes.
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Affiliation(s)
- Simon Janocha
- Department of Biochemistry, Saarland University, Campus B2 2, 66123, Saarbruecken, Germany
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Ilie A, Agudo R, Roiban GD, Reetz MT. P450-catalyzed regio- and stereoselective oxidative hydroxylation of disubstituted cyclohexanes: creation of three centers of chirality in a single CH-activation event. Tetrahedron 2015. [DOI: 10.1016/j.tet.2014.11.067] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Roiban GD, Reetz MT. Expanding the toolbox of organic chemists: directed evolution of P450 monooxygenases as catalysts in regio- and stereoselective oxidative hydroxylation. Chem Commun (Camb) 2015; 51:2208-24. [DOI: 10.1039/c4cc09218j] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cytochrome P450 enzymes (CYPs) have been used for more than six decades as catalysts for the CH-activating oxidative hydroxylation of organic compounds with formation of added-value products.
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Affiliation(s)
| | - Manfred T. Reetz
- Department of Chemistry
- Philipps-Universität Marburg
- 35032 Marburg
- Germany
- Max-Planck-Institut für Kohlenforschung
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Brühlmann F, Fourage L, Ullmann C, Haefliger OP, Jeckelmann N, Dubois C, Wahler D. Engineering cytochrome P450 BM3 of Bacillus megaterium for terminal oxidation of palmitic acid. J Biotechnol 2014; 184:17-26. [DOI: 10.1016/j.jbiotec.2014.05.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 04/09/2014] [Accepted: 05/04/2014] [Indexed: 01/10/2023]
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Wijma HJ, Marrink SJ, Janssen DB. Computationally efficient and accurate enantioselectivity modeling by clusters of molecular dynamics simulations. J Chem Inf Model 2014; 54:2079-92. [PMID: 24916632 DOI: 10.1021/ci500126x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Computational approaches could decrease the need for the laborious high-throughput experimental screening that is often required to improve enzymes by mutagenesis. Here, we report that using multiple short molecular dynamics (MD) simulations makes it possible to accurately model enantioselectivity for large numbers of enzyme-substrate combinations at low computational costs. We chose four different haloalkane dehalogenases as model systems because of the availability of a large set of experimental data on the enantioselective conversion of 45 different substrates. To model the enantioselectivity, we quantified the frequency of occurrence of catalytically productive conformations (near attack conformations) for pairs of enantiomers during MD simulations. We found that the angle of nucleophilic attack that leads to carbon-halogen bond cleavage was a critical variable that limited the occurrence of productive conformations; enantiomers for which this angle reached values close to 180° were preferentially converted. A cluster of 20-40 very short (10 ps) MD simulations allowed adequate conformational sampling and resulted in much better agreement to experimental enantioselectivities than single long MD simulations (22 ns), while the computational costs were 50-100 fold lower. With single long MD simulations, the dynamics of enzyme-substrate complexes remained confined to a conformational subspace that rarely changed significantly, whereas with multiple short MD simulations a larger diversity of conformations of enzyme-substrate complexes was observed.
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Affiliation(s)
- Hein J Wijma
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
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Bogazkaya AM, von Bühler CJ, Kriening S, Busch A, Seifert A, Pleiss J, Laschat S, Urlacher VB. Selective allylic hydroxylation of acyclic terpenoids by CYP154E1 from Thermobifida fusca YX. Beilstein J Org Chem 2014; 10:1347-1353. [PMID: 24991288 PMCID: PMC4077532 DOI: 10.3762/bjoc.10.137] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Accepted: 05/20/2014] [Indexed: 12/22/2022] Open
Abstract
Allylic alcohols are valuable precursors in the synthesis of pharmaceutical intermediates, agrochemicals and natural products. Regioselective oxidation of parental alkenes is a challenging task for chemical catalysts and requires several steps including protection and deprotection. Many cytochrome P450 enzymes are known to catalyse selective allylic hydroxylation under mild conditions. Here, we describe CYP154E1 from Thermobifida fusca YX that enables this type of oxidation. Several acyclic terpenoids were tested as possible substrates for CYP154E1, and the regio- and chemoselectivity of their oxidation was investigated. Using a previously established bioinformatics approach we identified position 286 in the active site of CYP154E1 which is putatively involved in substrate binding and thereby might have an effect on enzyme selectivity. To tune regio- and chemoselectivity of the enzyme three mutants at position 286 were constructed and used for substrate oxidation. All formed products were analysed with GC-MS and identified using chemically synthesised authentic samples and known compounds as references. Best regioselectivity towards geraniol and nerol was observed with the wild type enzyme mainly leading to 8-hydroxy derivatives (8-hydroxygeraniol or 8-hydroxynerol) with high selectivity (100% and 96% respectively). Highest selectivities during the oxidation of geranylacetone and nerylacetone were observed with the following variants: V286F led mainly to 7-hydroxygeranylacetone (60% of the total product) and V286A produced predominantly 12-hydroxynerylacetone (75% of total product). Thus, CYP154E1 and its mutants expand the tool-box for allylic hydroxylation in synthetic chemistry.
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Affiliation(s)
- Anna M Bogazkaya
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Clemens J von Bühler
- Institute of Biochemistry, Heinrich-Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf
| | - Sebastian Kriening
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Alexandrine Busch
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Alexander Seifert
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Jürgen Pleiss
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Sabine Laschat
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Vlada B Urlacher
- Institute of Biochemistry, Heinrich-Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf
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Ardashov OV, Volcho KP, Salakhutdinov NF. Synthesis of hydroxy derivatives of limonene. RUSSIAN CHEMICAL REVIEWS 2014. [DOI: 10.1070/rc2014v083n04abeh004383] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Pleiss J. Systematic Analysis of Large Enzyme Families: Identification of Specificity- and Selectivity-Determining Hotspots. ChemCatChem 2014. [DOI: 10.1002/cctc.201300950] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Zharkova MS, Sobolev BN, Yu Oparina N, Veselovsky AV, Archakov AI. Prediction of amino acid residues participated in substrate recognition by cytochrome P450 subfamilies with broad substrate specificity. J Mol Recognit 2013; 26:86-91. [PMID: 23334916 DOI: 10.1002/jmr.2251] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 10/12/2012] [Accepted: 10/26/2012] [Indexed: 12/12/2022]
Abstract
Cytochromes P450 comprise a large superfamily and several of their isoforms play a crucial role in metabolism of xenobiotics, including drugs. Although these enzymes demonstrate broad and cross-substrate specificity, different cytochrome P450 subfamilies exhibit certain selectivity for some types of substrates. Analysis of amino acid residues of the active sites of six cytochrome subfamilies (CYP1А, CYP2А, CYP2С, CYP2D, CYP2E and CYP3А) enables to define subfamily-specific patterns that consist of four residues. These residues are located on the periphery of the active sites of these cytochromes. We suggest that they can form a primary binding site at the entrance to the active site, defining cytochrome substrate recognition.
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Affiliation(s)
- Maria S Zharkova
- Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences, Pogodinskaya str 10, Moscow 119121, Russia
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Müller CA, Akkapurathu B, Winkler T, Staudt S, Hummel W, Gröger H, Schwaneberg U. In VitroDouble Oxidation ofn-Heptane with Direct Cofactor Regeneration. Adv Synth Catal 2013. [DOI: 10.1002/adsc.201300143] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Roduner E, Kaim W, Sarkar B, Urlacher VB, Pleiss J, Gläser R, Einicke WD, Sprenger GA, Beifuß U, Klemm E, Liebner C, Hieronymus H, Hsu SF, Plietker B, Laschat S. Selective Catalytic Oxidation of CH Bonds with Molecular Oxygen. ChemCatChem 2012. [DOI: 10.1002/cctc.201200266] [Citation(s) in RCA: 211] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Venkataraman H, Beer SBAD, Geerke DP, Vermeulen NPE, Commandeur JNM. Regio- and Stereoselective Hydroxylation of Optically Active α-Ionone Enantiomers by Engineered Cytochrome P450 BM3 Mutants. Adv Synth Catal 2012. [DOI: 10.1002/adsc.201200067] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Affiliation(s)
- Rudi Fasan
- Department of Chemistry,
Hutchison Hall, University of Rochester, Rochester, New York 14627,
United States
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47
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Clouthier CM, Pelletier JN. Expanding the organic toolbox: a guide to integrating biocatalysis in synthesis. Chem Soc Rev 2012; 41:1585-605. [DOI: 10.1039/c2cs15286j] [Citation(s) in RCA: 251] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Abstract
P450(BM3) (CYP102A1), a fatty acid hydroxylase from Bacillus megaterium, has been extensively studied over a period of almost forty years. The enzyme has been redesigned to catalyse the oxidation of non-natural substrates as diverse as pharmaceuticals, terpenes and gaseous alkanes using a variety of engineering strategies. Crystal structures have provided a basis for several of the catalytic effects brought about by mutagenesis, while changes to reduction potentials, inter-domain electron transfer rates and catalytic parameters have yielded functional insights. Areas of active research interest include drug metabolite production, the development of process-scale techniques, unravelling general mechanistic aspects of P450 chemistry, methane oxidation, and improving selectivity control to allow the synthesis of fine chemicals. This review draws together the disparate research themes and places them in a historical context with the aim of creating a resource that can be used as a gateway to the field.
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Affiliation(s)
- Christopher J C Whitehouse
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, UK
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49
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Wong LL. P450BM3 on Steroids: The Swiss Army Knife P450 Enzyme Just Gets Better. Chembiochem 2011; 12:2537-9. [DOI: 10.1002/cbic.201100606] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Indexed: 11/10/2022]
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