1
|
Jain S, Ospina F, Hammer SC. A New Age of Biocatalysis Enabled by Generic Activation Modes. JACS AU 2024; 4:2068-2080. [PMID: 38938808 PMCID: PMC11200230 DOI: 10.1021/jacsau.4c00247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 06/29/2024]
Abstract
Biocatalysis is currently undergoing a profound transformation. The field moves from relying on nature's chemical logic to a discipline that exploits generic activation modes, allowing for novel biocatalytic reactions and, in many instances, entirely new chemistry. Generic activation modes enable a wide range of reaction types and played a pivotal role in advancing the fields of organo- and photocatalysis. This perspective aims to summarize the principal activation modes harnessed in enzymes to develop new biocatalysts. Although extensively researched in the past, the highlighted activation modes, when applied within enzyme active sites, facilitate chemical transformations that have largely eluded efficient and selective catalysis. This advance is attributed to multiple tunable interactions in the substrate binding pocket that precisely control competing reaction pathways and transition states. We will highlight cases of new synthetic methodologies achieved by engineered enzymes and will provide insights into potential future developments in this rapidly evolving field.
Collapse
Affiliation(s)
| | | | - Stephan C. Hammer
- Research Group for Organic Chemistry
and Biocatalysis, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| |
Collapse
|
2
|
Sarkar R, Korell A, Schneider C. Organocatalytic enantioselective oxa-Piancatelli rearrangement. Chem Commun (Camb) 2024; 60:3063-3066. [PMID: 38385217 DOI: 10.1039/d4cc00708e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
The first highly enantioselective oxa-Piancatelli rearrangement has been developed. This process which is catalyzed by a chiral BINOL-derived phosphoric acid rearranges a wide range of furylcarbinols into densely substituted γ-hydroxy cyclopentenones in high yield with excellent diastereo- and enantioselectivities (up to 99 : 1 er). This reaction exhibits a high functional group tolerance and was applied to complex bioactive molecules as well. The products were further manipulated into value-added molecular scaffolds further highlighting their versatility and synthetic utility.
Collapse
Affiliation(s)
- Rahul Sarkar
- Institut für Organische Chemie, Universität Leipzig, Leipzig D-04103, Germany.
| | - Alexander Korell
- Institut für Organische Chemie, Universität Leipzig, Leipzig D-04103, Germany.
| | - Christoph Schneider
- Institut für Organische Chemie, Universität Leipzig, Leipzig D-04103, Germany.
| |
Collapse
|
3
|
Fan S, Cong Z. Emerging Strategies for Modifying Cytochrome P450 Monooxygenases into Peroxizymes. Acc Chem Res 2024. [PMID: 38293787 DOI: 10.1021/acs.accounts.3c00746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
ConspectusCytochrome P450 monooxygenase is a versatile oxidizing enzyme with great potential in synthetic chemistry and biology. However, the dependence of its catalytic function on the nicotinamide cofactor NAD(P)H and redox partner proteins limits the practical catalytic application of P450 in vitro. An alternative to expensive cofactors is low-cost H2O2, which can be used directly to exploit the catalytic potential of P450s. However, the peroxide shunt pathway is generally inefficient at driving P450 catalysis compared to normal NAD(P)H-dependent activity. Over the last few decades, the scientific community has made continuous efforts to use directed evolution or site-directed mutagenesis to modify P450 monooxygenases into their peroxizyme modes─peroxygenase and peroxidase. Despite significant progress, obtaining efficient P450 peroxizymes remains a huge challenge. Here, we summarize our efforts to modulate peroxizyme activity in P450 monooxygenases and exploit their catalytic applications in challenging selective C-H oxidation, oxygenation, and oxyfunctionalization over the past seven years. We first developed a dual-functional small molecule (DFSM) strategy for transforming P450BM3 monooxygenase into peroxygenase. In this strategy, the typical DFSM, such as N-(ω-imidazolyl)-hexanoyl-l-phenylalanine (Im-C6-Phe), binds to the P450BM3 protein with an anchoring group at one end and plays a general acid-base catalytic role in the activation of H2O2 with an imidazolyl group at the other end. Compared with the O-O homolysis mechanism in the absence of DFSM, the addition of DFSM efficiently enables the heterolytic O-O cleavage of the adduct Fe-O-OH, thus being favored for the formation of active species compound I, which has been demonstrated by combining crystallographic and theoretical calculations. Furthermore, protein engineering showed the unique catalytic performance of DFSM-facilitated P450 peroxygenase for the highly difficult selective oxidation of C-H bonds. This catalytic performance was demonstrated during the chemoselective hydroxylation of gaseous alkanes, regioselective O-demethylation of aryl ethers, highly (R)-enantioselective epoxidation of styrene, and regio- and enantiomerically diverse hydroxylation of alkylbenzenes. Second, we demonstrated that DFSM-facilitated P450BM3 peroxygenase could be effectively switched to an efficient peroxidase mode through mechanism-guided protein engineering of redox-sensitive residues. Utilizing the peroxidase function of P450 enabled the direct nitration of unsaturated hydrocarbons including phenols, aromatic amines, and styrene derivatives, which was not only the P450-catalyzed direct nitration of phenols and aromatic amines for the first time but also the first example of the direct biological nitration of olefins. Finally, we report an H2O2 tunnel engineering strategy to enable peroxygenase activity in several different P450 monooxygenases for the first time, providing a general approach for accessing engineered P450 peroxygenases. In this Account, we highlight the emerging strategies we have developed for producing practical P450 peroxizyme biocatalysts. Although the DFSM strategy is primarily applied to P450BM3 to date, both strategies of redox-sensitive residue engineering and H2O2 tunnel engineering show great potential to extend to other P450s. These strategies have expanded the scope of applications of P450 chemistry and catalysis. Additionally, they provide a unique solution to the challenging selective oxidation of inert C-H bonds in synthetic chemistry.
Collapse
Affiliation(s)
- Shengxian Fan
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiqi Cong
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shandong Energy Institute, Qingdao, Shandong 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China
| |
Collapse
|
4
|
Cao T, Bai Y, Buschbeck P, Tan Q, Cantrell MB, Chen Y, Jiang Y, Liu RZ, Ries NK, Shi X, Sun Y, Ware MA, Yang F, Zhang H, Han J, Zhang L, Huang J, Lohr M, Peers G, Li X. An unexpected hydratase synthesizes the green light-absorbing pigment fucoxanthin. THE PLANT CELL 2023; 35:3053-3072. [PMID: 37100425 PMCID: PMC10396388 DOI: 10.1093/plcell/koad116] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 04/05/2023] [Accepted: 04/06/2023] [Indexed: 06/19/2023]
Abstract
The ketocarotenoid fucoxanthin and its derivatives can absorb blue-green light enriched in marine environments. Fucoxanthin is widely adopted by phytoplankton species as a main light-harvesting pigment, in contrast to land plants that primarily employ chlorophylls. Despite its supreme abundance in the oceans, the last steps of fucoxanthin biosynthesis have remained elusive. Here, we identified the carotenoid isomerase-like protein CRTISO5 as the diatom fucoxanthin synthase that is related to the carotenoid cis-trans isomerase CRTISO from land plants but harbors unexpected enzymatic activity. A crtiso5 knockout mutant in the model diatom Phaeodactylum tricornutum completely lacked fucoxanthin and accumulated the acetylenic carotenoid phaneroxanthin. Recombinant CRTISO5 converted phaneroxanthin into fucoxanthin in vitro by hydrating its carbon-carbon triple bond, instead of functioning as an isomerase. Molecular docking and mutational analyses revealed residues essential for this activity. Furthermore, a photophysiological characterization of the crtiso5 mutant revealed a major structural and functional role of fucoxanthin in photosynthetic pigment-protein complexes of diatoms. As CRTISO5 hydrates an internal alkyne physiologically, the enzyme has unique potential for biocatalytic applications. The discovery of CRTISO5 illustrates how neofunctionalization leads to major diversification events in evolution of photosynthetic mechanisms and the prominent brown coloration of most marine photosynthetic eukaryotes.
Collapse
Affiliation(s)
- Tianjun Cao
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Yu Bai
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Paul Buschbeck
- Institut für Molekulare Physiologie, Johannes Gutenberg-University, 55099 Mainz, Germany
| | - Qiaozhu Tan
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Michael B Cantrell
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Yinjuan Chen
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Instrumentation and Service Center for Molecular Sciences, Westlake University, Hangzhou 310024, China
| | - Yanyou Jiang
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Run-Zhou Liu
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, Hangzhou 310024, China
| | - Nana K Ries
- Institut für Molekulare Physiologie, Johannes Gutenberg-University, 55099 Mainz, Germany
| | - Xiaohuo Shi
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Instrumentation and Service Center for Molecular Sciences, Westlake University, Hangzhou 310024, China
| | - Yan Sun
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315211, China
| | - Maxwell A Ware
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Fenghua Yang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Huan Zhang
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Jichang Han
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315211, China
| | - Lihan Zhang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, Hangzhou 310024, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Jing Huang
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China
| | - Martin Lohr
- Institut für Molekulare Physiologie, Johannes Gutenberg-University, 55099 Mainz, Germany
| | - Graham Peers
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Xiaobo Li
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, China
| |
Collapse
|
5
|
Gajdoš M, Wagner J, Ospina F, Köhler A, Engqvist MKM, Hammer SC. Chiral Alcohols from Alkenes and Water: Directed Evolution of a Styrene Hydratase. Angew Chem Int Ed Engl 2023; 62:e202215093. [PMID: 36511829 PMCID: PMC10107627 DOI: 10.1002/anie.202215093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/13/2022] [Accepted: 12/13/2022] [Indexed: 12/15/2022]
Abstract
Enantioselective synthesis of chiral alcohols through asymmetric addition of water across an unactivated alkene is a highly sought-after transformation and a big challenge in catalysis. Herein we report the identification and directed evolution of a fatty acid hydratase from Marinitoga hydrogenitolerans for the highly enantioselective hydration of styrenes to yield chiral 1-arylethanols. While directed evolution for styrene hydration was performed in the presence of heptanoic acid to mimic fatty acid binding, the engineered enzyme displayed remarkable asymmetric styrene hydration activity in the absence of the small molecule activator. The evolved styrene hydratase provided access to chiral alcohols from simple alkenes and water with high enantioselectivity (>99 : 1 e.r.) and could be applied on a preparative scale.
Collapse
Affiliation(s)
- Matúš Gajdoš
- Faculty of Chemistry, Organic Chemistry and Biocatalysis, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Jendrik Wagner
- Faculty of Chemistry, Organic Chemistry and Biocatalysis, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Felipe Ospina
- Faculty of Chemistry, Organic Chemistry and Biocatalysis, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Antonia Köhler
- Faculty of Chemistry, Organic Chemistry and Biocatalysis, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Martin K M Engqvist
- Department of Biology and Biological Engineering., Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Stephan C Hammer
- Faculty of Chemistry, Organic Chemistry and Biocatalysis, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| |
Collapse
|
6
|
Biundo A, Stamm A, Gorgoglione R, Syrén PO, Curia S, Hauer B, Capriati V, Vitale P, Perna F, Agrimi G, Pisano I. REGIO- AND STEREOSELECTIVE BIOCATALYTIC HYDRATION OF FATTY ACIDS FROM WASTE COOKING OILS EN ROUTE TO HYDROXY FATTY ACIDS AND BIO-BASED POLYESTERS. Enzyme Microb Technol 2022; 163:110164. [DOI: 10.1016/j.enzmictec.2022.110164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/17/2022] [Accepted: 11/19/2022] [Indexed: 11/27/2022]
|
7
|
Zhang G, Zeng H, Zheng S, Neary MC, Dub PA. Markovnikov alcohols via epoxide hydroboration by molecular alkali metal catalysts. iScience 2022; 25:105119. [PMID: 36185366 PMCID: PMC9515598 DOI: 10.1016/j.isci.2022.105119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/29/2022] [Accepted: 09/08/2022] [Indexed: 11/28/2022] Open
Affiliation(s)
- Guoqi Zhang
- Department of Sciences, John Jay College and PhD in Chemistry Program, the Graduate Center of City University of New York, New York, NY 10019, USA
- Corresponding author
| | - Haisu Zeng
- Department of Sciences, John Jay College and PhD in Chemistry Program, the Graduate Center of City University of New York, New York, NY 10019, USA
- Department of Chemistry, Hunter College, City University of New York, New York, NY 10065, USA
| | - Shengping Zheng
- Department of Chemistry, Hunter College, City University of New York, New York, NY 10065, USA
| | - Michelle C. Neary
- Department of Chemistry, Hunter College, City University of New York, New York, NY 10065, USA
| | - Pavel A. Dub
- Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- Corresponding author
| |
Collapse
|
8
|
Alcántara AR, Domínguez de María P, Littlechild JA, Schürmann M, Sheldon RA, Wohlgemuth R. Biocatalysis as Key to Sustainable Industrial Chemistry. CHEMSUSCHEM 2022; 15:e202102709. [PMID: 35238475 DOI: 10.1002/cssc.202102709] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/10/2022] [Indexed: 06/14/2023]
Abstract
The role and power of biocatalysis in sustainable chemistry has been continuously brought forward step by step to its present outstanding position. The problem-solving capabilities of biocatalysis have been realized by numerous substantial achievements in biology, chemistry and engineering. Advances and breakthroughs in the life sciences and interdisciplinary cooperation with chemistry have clearly accelerated the implementation of biocatalytic synthesis in modern chemistry. Resource-efficient biocatalytic manufacturing processes have already provided numerous benefits to sustainable chemistry as well as customer-centric value creation in the pharmaceutical, food, flavor, fragrance, vitamin, agrochemical, polymer, specialty, and fine chemical industries. Biocatalysis can make significant contributions not only to manufacturing processes, but also to the design of completely new value-creation chains. Biocatalysis can now be considered as a key enabling technology to implement sustainable chemistry.
Collapse
Affiliation(s)
- Andrés R Alcántara
- Department of Chemistry in Pharmaceutical Sciences (QUICIFARM), Complutense University of Madrid (UCM), 28040-, Madrid, Spain
| | - Pablo Domínguez de María
- Sustainable Momentum, SL, Av. Ansite 3, 4-6, 35011, Las Palmas de Gran Canaria, Canary Is., Spain
| | - Jennifer A Littlechild
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, United Kingdom
| | | | - Roger A Sheldon
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Braamfontein, Johannesburg, South Africa
| | - Roland Wohlgemuth
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, 90-537, Lodz, Poland
- Swiss Coordination Committee for Biotechnology, 8021, Zurich, Switzerland
| |
Collapse
|
9
|
Yang X, Li X, Chen P, Liu G. Palladium(II)-Catalyzed Enantioselective Hydrooxygenation of Unactivated Terminal Alkenes. J Am Chem Soc 2022; 144:7972-7977. [PMID: 35468295 DOI: 10.1021/jacs.2c02753] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A novel Pd(II)-catalyzed enantioselective Markovnikov hydrooxygenation of unactivated terminal alkenes using a substituted pyridinyl oxazoline (Pyox) ligand has been developed. Herein it was discovered that the (EtO)2MeSiH/BQ redox system is vital for the highly selective and efficient hydrooxygenation, where the alkylpalladium(II) species generated from enantioselective oxypalladation step is reduced by silane. This method provides efficient access to optically pure alcohol esters from easily available alkenes with excellent enantioselectivities and features a broad substrate scope.
Collapse
Affiliation(s)
- Xintuo Yang
- State Key Laboratory of Organometallic Chemistry and Shanghai Hong Kong Joint Laboratory in Chemical Synthesis, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Xiang Li
- State Key Laboratory of Organometallic Chemistry and Shanghai Hong Kong Joint Laboratory in Chemical Synthesis, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Pinhong Chen
- State Key Laboratory of Organometallic Chemistry and Shanghai Hong Kong Joint Laboratory in Chemical Synthesis, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Guosheng Liu
- State Key Laboratory of Organometallic Chemistry and Shanghai Hong Kong Joint Laboratory in Chemical Synthesis, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.,Chang-Kung Chuang Institute, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China
| |
Collapse
|
10
|
Prem S, Helmer CPO, Dimos N, Himpich S, Brück T, Garbe D, Loll B. Towards an understanding of oleate hydratases and their application in industrial processes. Microb Cell Fact 2022; 21:58. [PMID: 35397585 PMCID: PMC8994360 DOI: 10.1186/s12934-022-01777-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/18/2022] [Indexed: 11/21/2022] Open
Abstract
Fatty acid hydratases are unique to microorganisms. Their native function is the oxidation of unsaturated C–C bonds to enable detoxification of environmental toxins. Within this enzyme family, the oleate hydratases (Ohys), which catalyze the hydroxylation of oleic acid to 10-(R)-hydroxy stearic acid (10-HSA) have recently gained particular industrial interest. 10-HSA is considered to be a replacement for 12-(R)-hydroxy stearic acid (12-HSA), which has a broad application in the chemical and pharmaceutical industry. As 12-HSA is obtained through an energy consuming synthesis process, the biotechnological route for sustainable 10-HSA production is of significant industrial interest. All Ohys identified to date have a non-redox active FAD bound in their active site. Ohys can be divided in several subfamilies, that differ in their oligomerization state and the decoration with amino acids in their active sites. The latter observation indicates a different reaction mechanism across those subfamilies. Despite intensive biotechnological, biochemical and structural investigations, surprising little is known about substrate binding and the reaction mechanism of this enzyme family. This review, summarizes our current understanding of Ohys with a focus on sustainable biotransformation.
Collapse
|
11
|
Le CC, Bae M, Kiamehr S, Balskus EP. Emerging Chemical Diversity and Potential Applications of Enzymes in the DMSO Reductase Superfamily. Annu Rev Biochem 2022; 91:475-504. [PMID: 35320685 DOI: 10.1146/annurev-biochem-032620-110804] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Molybdenum- and tungsten-dependent proteins catalyze essential processes in living organisms and biogeochemical cycles. Among these enzymes, members of the dimethyl sulfoxide (DMSO) reductase superfamily are considered the most diverse, facilitating a wide range of chemical transformations that can be categorized as oxygen atom installation, removal, and transfer. Importantly, DMSO reductase enzymes provide high efficiency and excellent selectivity while operating under mild conditions without conventional oxidants such as oxygen or peroxides. Despite the potential utility of these enzymes as biocatalysts, such applications have not been fully explored. In addition, the vast majority of DMSO reductase enzymes still remain uncharacterized. In this review, we describe the reactivities, proposed mechanisms, and potential synthetic applications of selected enzymes in the DMSO reductase superfamily. We also highlight emerging opportunities to discover new chemical activity and current challenges in studying and engineering proteins in the DMSO reductase superfamily. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Chi Chip Le
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA;
| | - Minwoo Bae
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA;
| | - Sina Kiamehr
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA;
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA;
| |
Collapse
|
12
|
Kennemur J, Maji R, Scharf MJ, List B. Catalytic Asymmetric Hydroalkoxylation of C-C Multiple Bonds. Chem Rev 2021; 121:14649-14681. [PMID: 34860509 PMCID: PMC8704240 DOI: 10.1021/acs.chemrev.1c00620] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Indexed: 01/30/2023]
Abstract
Asymmetric hydroalkoxylation of alkenes constitutes a redox-neutral and 100% atom-economical strategy toward enantioenriched oxygenated building blocks from readily available starting materials. Despite their great potential, catalytic enantioselective additions of alcohols across a C-C multiple bond are particularly underdeveloped, especially compared to other hydrofunctionalization methods such as hydroamination. However, driven by some recent innovations, e.g., asymmetric MHAT methods, asymmetric photocatalytic methods, and the development of extremely strong chiral Brønsted acids, there has been a gratifying surge of reports in this burgeoning field. The goal of this review is to survey the growing landscape of asymmetric hydroalkoxylation by highlighting exciting new advances, deconstructing mechanistic underpinnings, and drawing insight from related asymmetric hydroacyloxylation and hydration. A deep appreciation of the underlying principles informs an understanding of the various selectivity parameters and activation modes in the realm of asymmetric alkene hydrofunctionalization while simultaneously evoking the outstanding challenges to the field moving forward. Overall, we aim to lay a foundation for cross-fertilization among various catalytic fields and spur further innovation in asymmetric hydroalkoxylations of C-C multiple bonds.
Collapse
Affiliation(s)
| | | | - Manuel J. Scharf
- Max-Planck-Institut für
Kohlenforschung, Kaiser Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Benjamin List
- Max-Planck-Institut für
Kohlenforschung, Kaiser Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| |
Collapse
|
13
|
Zhang Y, Breum NMD, Schubert S, Hashemi N, Kyhnau R, Knauf MS, Mathialakan M, Takeuchi M, Kishino S, Ogawa J, Kristensen P, Guo Z, Eser BE. Semi-rational Engineering of a Promiscuous Fatty Acid Hydratase for Alteration of Regioselectivity. Chembiochem 2021; 23:e202100606. [PMID: 34929055 DOI: 10.1002/cbic.202100606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/14/2021] [Indexed: 11/12/2022]
Abstract
Fatty acid hydratases (FAHs) catalyze regio- and stereo-selective hydration of unsaturated fatty acids to produce hydroxy fatty acids. Fatty acid hydratase-1 (FA-HY1) from Lactobacillus Acidophilus is the most promiscuous and regiodiverse FAH identified so far. Here, we engineered binding site residues of FA-HY1 (S393, S395, S218 and P380) by semi-rational protein engineering to alter regioselectivity. Although it was not possible to obtain a completely new type of regioselectivity with our mutant libraries, a significant shift of regioselectivity was observed towards cis-5, cis-8, cis-11, cis-14, cis-17-eicosapentaenoic acid (EPA). We identified mutants (S393/S395 mutants) with excellent regioselectivity, generating a single hydroxy fatty acid product from EPA (15-OH product), which is advantageous from application perspective. This result is impressive given that wild-type FA-HY1 produces a mixture of 12-OH and 15-OH products at 63 : 37 ratio (12-OH : 15-OH). Moreover, our results indicate that native FA-HY1 is at its limit in terms of promiscuity and regiospecificity, thus it may not be possible to diversify its product portfolio with active site engineering. This behavior of FA-HY1 is unlike its orthologue, fatty acid hydratase-2 (FA-HY2; 58 % sequence identity to FA-HY1), which has been shown earlier to exhibit significant promiscuity and regioselectivity changes by a few active site mutations. Our reverse engineering from FA-HY1 to FA-HY2 further demonstrates this conclusion.
Collapse
Affiliation(s)
- Yan Zhang
- Department of Biological and Chemical Engineering, Aarhus University, 8000, Aarhus, Denmark
| | | | - Sune Schubert
- Department of Biological and Chemical Engineering, Aarhus University, 8000, Aarhus, Denmark
| | - Negin Hashemi
- Department of Biological and Chemical Engineering, Aarhus University, 8000, Aarhus, Denmark
| | - Rikke Kyhnau
- Department of Biological and Chemical Engineering, Aarhus University, 8000, Aarhus, Denmark
| | - Marius Sandholt Knauf
- Department of Biological and Chemical Engineering, Aarhus University, 8000, Aarhus, Denmark
| | - Masuthan Mathialakan
- Department of Biological and Chemical Engineering, Aarhus University, 8000, Aarhus, Denmark
| | - Michiki Takeuchi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Shigenobu Kishino
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Jun Ogawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Peter Kristensen
- Faculty of Engineering and Science, Department of Chemistry and Bioscience, Aalborg University, 9220, Aalborg, Denmark
| | - Zheng Guo
- Department of Biological and Chemical Engineering, Aarhus University, 8000, Aarhus, Denmark
| | - Bekir Engin Eser
- Department of Biological and Chemical Engineering, Aarhus University, 8000, Aarhus, Denmark
| |
Collapse
|
14
|
Biermann U, Bornscheuer UT, Feussner I, Meier MAR, Metzger JO. Fatty Acids and their Derivatives as Renewable Platform Molecules for the Chemical Industry. Angew Chem Int Ed Engl 2021; 60:20144-20165. [PMID: 33617111 PMCID: PMC8453566 DOI: 10.1002/anie.202100778] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Indexed: 12/13/2022]
Abstract
Oils and fats of vegetable and animal origin remain an important renewable feedstock for the chemical industry. Their industrial use has increased during the last 10 years from 31 to 51 million tonnes annually. Remarkable achievements made in the field of oleochemistry in this timeframe are summarized herein, including the reduction of fatty esters to ethers, the selective oxidation and oxidative cleavage of C-C double bonds, the synthesis of alkyl-branched fatty compounds, the isomerizing hydroformylation and alkoxycarbonylation, and olefin metathesis. The use of oleochemicals for the synthesis of a great variety of polymeric materials has increased tremendously, too. In addition to lipases and phospholipases, other enzymes have found their way into biocatalytic oleochemistry. Important achievements have also generated new oil qualities in existing crop plants or by using microorganisms optimized by metabolic engineering.
Collapse
Affiliation(s)
- Ursula Biermann
- Institute of ChemistryUniversity of Oldenburg26111OldenburgGermany
- abiosuse.V.Bloherfelder Straße 23926129OldenburgGermany
| | - Uwe T. Bornscheuer
- Institute of BiochemistryDept. of Biotechnology & Enzyme CatalysisGreifswald UniversityFelix-Hausdorff-Strasse 417487GreifswaldGermany
| | - Ivo Feussner
- University of GoettingenAlbrecht-von-Haller Institute for Plant SciencesInternational Center for Advanced Studies of Energy Conversion (ICASEC) and Goettingen Center of Molecular Biosciences (GZMB)Dept. of Plant BiochemistryJustus-von-Liebig-Weg 1137077GoettingenGermany
| | - Michael A. R. Meier
- Laboratory of Applied ChemistryInstitute of Organic Chemistry (IOC)Karlsruhe Institute of Technology (KIT)Straße am Forum 776131KarlsruheGermany
- Laboratory of Applied ChemistryInstitute of Biological and Chemical Systems—Functional Molecular Systems (IBCS-FMS)Karlsruhe Institute of Technology (KIT)Hermann-von-Helmholtz-Platz 176344Eggenstein-LeopoldshafenGermany
| | - Jürgen O. Metzger
- Institute of ChemistryUniversity of Oldenburg26111OldenburgGermany
- abiosuse.V.Bloherfelder Straße 23926129OldenburgGermany
| |
Collapse
|
15
|
Biermann U, Bornscheuer UT, Feussner I, Meier MAR, Metzger JO. Fettsäuren und Fettsäurederivate als nachwachsende Plattformmoleküle für die chemische Industrie. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100778] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ursula Biermann
- Institut für Chemie Universität Oldenburg 26111 Oldenburg Deutschland
- abiosuse.V. Bloherfelder Straße 239 26129 Oldenburg Deutschland
| | - Uwe T. Bornscheuer
- Institut für Biochemie Abt. Biotechnologie & Enzymkatalyse Universität Greifswald Felix-Hausdorff-Straße 4 17487 Greifswald Deutschland
| | - Ivo Feussner
- Universität Göttingen Albrecht-von-Haller Institut für Pflanzenwissenschaften International Center for Advanced Studies of Energy Conversion (ICASEC) und Göttinger Zentrum für Molekulare Biowissenschaften (GZMB) Abt. für die Biochemie der Pflanze Justus-von-Liebig-Weg 11 37077 Göttingen Deutschland
| | - Michael A. R. Meier
- Labor für Angewandte Chemie Institut für Organische Chemie (IOC) Karlsruher Institut für Technology (KIT) Straße am Forum 7 76131 Karlsruhe Deutschland
- Labor für Angewandte Chemie Institut für biologische und chemische Systeme –, Funktionale Molekülsysteme (IBCS-FMS) Karlsruher Institut für Technologie (KIT) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Deutschland
| | - Jürgen O. Metzger
- Institut für Chemie Universität Oldenburg 26111 Oldenburg Deutschland
- abiosuse.V. Bloherfelder Straße 239 26129 Oldenburg Deutschland
| |
Collapse
|
16
|
Song J, Baeg Y, Jeong H, Lee J, Oh D, Hollmann F, Park J. Bacterial Outer Membrane Vesicles as Nano‐Scale Bioreactors: A Fatty Acid Conversion Case Study. ChemCatChem 2021. [DOI: 10.1002/cctc.202100778] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ji‐Won Song
- Department of Food Science & Engineering Ewha Womans University Seoul 03760 Republic of Korea
| | - Yoonjin Baeg
- Department of Food Science & Engineering Ewha Womans University Seoul 03760 Republic of Korea
| | - Ha‐Yeon Jeong
- Department of Food Science & Engineering Ewha Womans University Seoul 03760 Republic of Korea
| | - Jinwon Lee
- Department of Chemical and Biomolecular Engineering Sogang University Seoul 04107 Republic of Korea
| | - Deok‐Kun Oh
- Department of Bioscience and Biotechnology Konkuk University Seoul 05029 Republic of Korea
| | - Frank Hollmann
- Department of Biotechnology Delft University of Technology Van der Maasweg 9 2629HZ Delft The Netherlands
| | - Jin‐Byung Park
- Department of Food Science & Engineering Ewha Womans University Seoul 03760 Republic of Korea
| |
Collapse
|
17
|
Hall M. Enzymatic strategies for asymmetric synthesis. RSC Chem Biol 2021; 2:958-989. [PMID: 34458820 PMCID: PMC8341948 DOI: 10.1039/d1cb00080b] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 05/28/2021] [Indexed: 12/13/2022] Open
Abstract
Enzymes, at the turn of the 21st century, are gaining a momentum. Especially in the field of synthetic organic chemistry, a broad variety of biocatalysts are being applied in an increasing number of processes running at up to industrial scale. In addition to the advantages of employing enzymes under environmentally friendly reaction conditions, synthetic chemists are recognizing the value of enzymes connected to the exquisite selectivity of these natural (or engineered) catalysts. The use of hydrolases in enantioselective protocols paved the way to the application of enzymes in asymmetric synthesis, in particular in the context of biocatalytic (dynamic) kinetic resolutions. After two decades of impressive development, the field is now mature to propose a panel of catalytically diverse enzymes for (i) stereoselective reactions with prochiral compounds, such as double bond reduction and bond forming reactions, (ii) formal enantioselective replacement of one of two enantiotopic groups of prochiral substrates, as well as (iii) atroposelective reactions with noncentrally chiral compounds. In this review, the major enzymatic strategies broadly applicable in the asymmetric synthesis of optically pure chiral compounds are presented, with a focus on the reactions developed within the past decade.
Collapse
Affiliation(s)
- Mélanie Hall
- Institute of Chemistry, University of Graz Heinrichstrasse 28 8010 Graz Austria
- Field of Excellence BioHealth - University of Graz Austria
| |
Collapse
|
18
|
Hagedoorn PL, Hollmann F, Hanefeld U. Novel oleate hydratases and potential biotechnological applications. Appl Microbiol Biotechnol 2021; 105:6159-6172. [PMID: 34350478 PMCID: PMC8403116 DOI: 10.1007/s00253-021-11465-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 07/19/2021] [Accepted: 07/19/2021] [Indexed: 11/29/2022]
Abstract
Abstract Oleate hydratase catalyses the addition of water to the CC double bond of oleic acid to produce (R)-10-hydroxystearic acid. The enzyme requires an FAD cofactor that functions to optimise the active site structure. A wide range of unsaturated fatty acids can be hydrated at the C10 and in some cases the C13 position. The substrate scope can be expanded using ‘decoy’ small carboxylic acids to convert small chain alkenes to secondary alcohols, albeit at low conversion rates. Systematic protein engineering and directed evolution to widen the substrate scope and increase the conversion rate is possible, supported by new high throughput screening assays that have been developed. Multi-enzyme cascades allow the formation of a wide range of products including keto-fatty acids, secondary alcohols, secondary amines and α,ω-dicarboxylic acids. Key points • Phylogenetically distinct oleate hydratases may exhibit mechanistic differences. • Protein engineering to improve productivity and substrate scope is possible. • Multi-enzymatic cascades greatly widen the product portfolio.
Collapse
Affiliation(s)
- Peter Leon Hagedoorn
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, The Netherlands.
| | - Frank Hollmann
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, The Netherlands
| | - Ulf Hanefeld
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, The Netherlands
| |
Collapse
|
19
|
Zhang Y, Eser BE, Kougioumtzoglou G, Eser Z, Poborsky M, Kishino S, Takeuchi M, Ogawa J, Kristensen P, Guo Z. Effects of the engineering of a single binding pocket residue on specificity and regioselectivity of hydratases from Lactobacillus Acidophilus. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
20
|
Timonina D, Sharapova Y, Švedas V, Suplatov D. Bioinformatic analysis of subfamily-specific regions in 3D-structures of homologs to study functional diversity and conformational plasticity in protein superfamilies. Comput Struct Biotechnol J 2021; 19:1302-1311. [PMID: 33738079 PMCID: PMC7933735 DOI: 10.1016/j.csbj.2021.02.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 02/07/2023] Open
Abstract
Local 3D-structural differences in homologous proteins contribute to functional diversity observed in a superfamily, but so far received little attention as bioinformatic analysis was usually carried out at the level of amino acid sequences. We have developed Zebra3D - the first-of-its-kind bioinformatic software for systematic analysis of 3D-alignments of protein families using machine learning. The new tool identifies subfamily-specific regions (SSRs) - patterns of local 3D-structure (i.e. single residues, loops, or secondary structure fragments) that are spatially equivalent within families/subfamilies, but are different among them, and thus can be associated with functional diversity and function-related conformational plasticity. Bioinformatic analysis of protein superfamilies by Zebra3D can be used to study 3D-determinants of catalytic activity and specific accommodation of ligands, help to prepare focused libraries for directed evolution or assist development of chimeric enzymes with novel properties by exchange of equivalent regions between homologs, and to characterize plasticity in binding sites. A companion Mustguseal web-server is available to automatically construct a 3D-alignment of functionally diverse proteins, thus reducing the minimal input required to operate Zebra3D to a single PDB code. The Zebra3D + Mustguseal combined approach provides the opportunity to systematically explore the value of SSRs in superfamilies and to use this information for protein design and drug discovery. The software is available open-access at https://biokinet.belozersky.msu.ru/Zebra3D.
Collapse
Affiliation(s)
- Daria Timonina
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Lenin Hills 1-73, Moscow 119234, Russia
| | - Yana Sharapova
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Lenin Hills 1-73, Moscow 119234, Russia
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Lenin Hills 1-73, Moscow 119234, Russia
| | - Vytas Švedas
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Lenin Hills 1-73, Moscow 119234, Russia
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Lenin Hills 1-73, Moscow 119234, Russia
| | - Dmitry Suplatov
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Lenin Hills 1-73, Moscow 119234, Russia
- Corresponding author.
| |
Collapse
|
21
|
Marshall JR, Mangas-Sanchez J, Turner NJ. Expanding the synthetic scope of biocatalysis by enzyme discovery and protein engineering. Tetrahedron 2021. [DOI: 10.1016/j.tet.2021.131926] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
22
|
Wu S, Snajdrova R, Moore JC, Baldenius K, Bornscheuer UT. Biocatalysis: Enzymatic Synthesis for Industrial Applications. Angew Chem Int Ed Engl 2021; 60:88-119. [PMID: 32558088 PMCID: PMC7818486 DOI: 10.1002/anie.202006648] [Citation(s) in RCA: 522] [Impact Index Per Article: 174.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Indexed: 12/12/2022]
Abstract
Biocatalysis has found numerous applications in various fields as an alternative to chemical catalysis. The use of enzymes in organic synthesis, especially to make chiral compounds for pharmaceuticals as well for the flavors and fragrance industry, are the most prominent examples. In addition, biocatalysts are used on a large scale to make specialty and even bulk chemicals. This review intends to give illustrative examples in this field with a special focus on scalable chemical production using enzymes. It also discusses the opportunities and limitations of enzymatic syntheses using distinct examples and provides an outlook on emerging enzyme classes.
Collapse
Affiliation(s)
- Shuke Wu
- Institute of BiochemistryDept. of Biotechnology & Enzyme CatalysisGreifswald UniversityFelix-Hausdorff-Strasse 417487GreifswaldGermany
| | - Radka Snajdrova
- Novartis Institutes for BioMedical ResearchGlobal Discovery Chemistry4056BaselSwitzerland
| | - Jeffrey C. Moore
- Process Research and DevelopmentMerck & Co., Inc.126 E. Lincoln AveRahwayNJ07065USA
| | - Kai Baldenius
- Baldenius Biotech ConsultingHafenstr. 3168159MannheimGermany
| | - Uwe T. Bornscheuer
- Institute of BiochemistryDept. of Biotechnology & Enzyme CatalysisGreifswald UniversityFelix-Hausdorff-Strasse 417487GreifswaldGermany
| |
Collapse
|
23
|
Wohlgemuth R. Biocatalysis - Key enabling tools from biocatalytic one-step and multi-step reactions to biocatalytic total synthesis. N Biotechnol 2020; 60:113-123. [PMID: 33045418 DOI: 10.1016/j.nbt.2020.08.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 07/07/2020] [Accepted: 08/31/2020] [Indexed: 12/20/2022]
Abstract
In the area of human-made innovations to improve the quality of life, biocatalysis has already had a great impact and contributed enormously to a growing number of catalytic transformations aimed at the detection and analysis of compounds, the bioconversion of starting materials and the preparation of target compounds at any scale, from laboratory small scale to industrial large scale. The key enabling tools which have been developed in biocatalysis over the last decades also provide great opportunities for further development and numerous applications in various sectors of the global bioeconomy. Systems biocatalysis is a modular, bottom-up approach to designing the architecture of enzyme-catalyzed reaction steps in a synthetic route from starting materials to target molecules. The integration of biocatalysis and sustainable chemistry in vitro aims at ideal conversions with high molecular economy and their intensification. Retrosynthetic analysis in the chemical and biological domain has been a valuable tool for target-oriented synthesis while, on the other hand, diversity-oriented synthesis builds on forward-looking analysis. Bioinformatic tools for rapid identification of the required enzyme functions, efficient enzyme production systems, as well as generalized bioprocess design tools, are important for rapid prototyping of the biocatalytic reactions. The tools for enzyme engineering and the reaction engineering of each enzyme-catalyzed one-step reaction are also valuable for coupling reactions. The tools to overcome interaction issues with other components or enzymes are of great interest in designing multi-step reactions as well as in biocatalytic total synthesis.
Collapse
Affiliation(s)
- Roland Wohlgemuth
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Lodz, Poland; Swiss Coordination Committee on Biotechnology (SKB), Nordstrasse 15, 8021 Zürich, Switzerland.
| |
Collapse
|
24
|
Suplatov D, Sharapova Y, Geraseva E, Švedas V. Zebra2: advanced and easy-to-use web-server for bioinformatic analysis of subfamily-specific and conserved positions in diverse protein superfamilies. Nucleic Acids Res 2020; 48:W65-W71. [PMID: 32313959 PMCID: PMC7319439 DOI: 10.1093/nar/gkaa276] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 03/29/2020] [Accepted: 04/08/2020] [Indexed: 12/17/2022] Open
Abstract
Zebra2 is a highly automated web-tool to search for subfamily-specific and conserved positions (i.e. the determinants of functional diversity as well as the key catalytic and structural residues) in protein superfamilies. The bioinformatic analysis is facilitated by Mustguseal—a companion web-server to automatically collect and superimpose a large representative set of functionally diverse homologs with high structure similarity but low sequence identity to the selected query protein. The results are automatically prioritized and provided at four information levels to facilitate the knowledge-driven expert selection of the most promising positions on-line: as a sequence similarity network; interfaces to sequence-based and 3D-structure-based analysis of conservation and variability; and accompanied by the detailed annotation of proteins accumulated from the integrated databases with links to the external resources. The integration of Zebra2 and Mustguseal web-tools provides the first of its kind out-of-the-box open-access solution to conduct a systematic analysis of evolutionarily related proteins implementing different functions within a shared 3D-structure of the superfamily, determine common and specific patterns of function-associated local structural elements, assist to select hot-spots for rational design and to prepare focused libraries for directed evolution. The web-servers are free and open to all users at https://biokinet.belozersky.msu.ru/zebra2, no login required.
Collapse
Affiliation(s)
- Dmitry Suplatov
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology and Faculty of Bioengineering and Bioinformatics, Lenin Hills 1-73, Moscow 119234, Russia
| | - Yana Sharapova
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology and Faculty of Bioengineering and Bioinformatics, Lenin Hills 1-73, Moscow 119234, Russia
| | - Elizaveta Geraseva
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology and Faculty of Bioengineering and Bioinformatics, Lenin Hills 1-73, Moscow 119234, Russia
| | - Vytas Švedas
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology and Faculty of Bioengineering and Bioinformatics, Lenin Hills 1-73, Moscow 119234, Russia
| |
Collapse
|
25
|
Schober L, Sako M, Takizawa S, Gröger H, Sasai H. Catalytic and enantioselective oxa-Piancatelli reaction using a chiral vanadium complex. Chem Commun (Camb) 2020; 56:10151-10154. [PMID: 32735309 DOI: 10.1039/d0cc02621b] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
An enantioselective oxa-Piancatelli reaction was established for the first time using a chiral vanadium(v) catalyst. The dual Brønsted and Lewis acid properties of the vanadium catalyst afforded 4-hydroxycyclopent-2-enone derivatives in up to 90% yields and with 93 : 7 enantiomeric ratios, as well as >20 : 1 diastereomeric ratios.
Collapse
Affiliation(s)
- Lukas Schober
- Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany.
| | | | | | | | | |
Collapse
|
26
|
Cuetos A, Iglesias-Fernández J, Danesh-Azari HR, Zukic E, Dowle A, Osuna S, Grogan G. Mutational Analysis of Linalool Dehydratase Isomerase Suggests That Alcohol and Alkene Transformations Are Catalyzed Using Noncovalent Mechanisms. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anibal Cuetos
- York Structural Biology Laboratory, Department of Chemistry, University of York, YO10 5DD York, U.K
| | - Javier Iglesias-Fernández
- CompBioLab group, Institut de Química Computacional i Catàlisi, Departament de Química, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain
| | - Hamid-Reza Danesh-Azari
- York Structural Biology Laboratory, Department of Chemistry, University of York, YO10 5DD York, U.K
| | - Erna Zukic
- York Structural Biology Laboratory, Department of Chemistry, University of York, YO10 5DD York, U.K
| | - Adam Dowle
- Bioscience Technology Facility, Department of Biology, University of York, YO10 5DD, York, U.K
| | - Sílvia Osuna
- CompBioLab group, Institut de Química Computacional i Catàlisi, Departament de Química, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Gideon Grogan
- York Structural Biology Laboratory, Department of Chemistry, University of York, YO10 5DD York, U.K
| |
Collapse
|
27
|
Wu S, Snajdrova R, Moore JC, Baldenius K, Bornscheuer UT. Biokatalyse: Enzymatische Synthese für industrielle Anwendungen. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006648] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Shuke Wu
- Institut für Biochemie Abt. Biotechnologie & Enzymkatalyse Universität Greifswald Felix-Hausdorff-Straße 4 17487 Greifswald Deutschland
| | - Radka Snajdrova
- Novartis Institutes for BioMedical Research Global Discovery Chemistry 4056 Basel Schweiz
| | - Jeffrey C. Moore
- Process Research and Development Merck & Co., Inc. 126 E. Lincoln Ave Rahway NJ 07065 USA
| | - Kai Baldenius
- Baldenius Biotech Consulting Hafenstraße 31 68159 Mannheim Deutschland
| | - Uwe T. Bornscheuer
- Institut für Biochemie Abt. Biotechnologie & Enzymkatalyse Universität Greifswald Felix-Hausdorff-Straße 4 17487 Greifswald Deutschland
| |
Collapse
|
28
|
Zhang Y, Eser BE, Kristensen P, Guo Z. Fatty acid hydratase for value-added biotransformation: A review. Chin J Chem Eng 2020. [DOI: 10.1016/j.cjche.2020.02.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
29
|
Affiliation(s)
- Bernhard Hauer
- Institute of Biochemistry and Technical Biochemistry, Department of Technical Biochemistry, Universitaet Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| |
Collapse
|
30
|
Fatty Acid Hydratases: Versatile Catalysts to Access Hydroxy Fatty Acids in Efficient Syntheses of Industrial Interest. Catalysts 2020. [DOI: 10.3390/catal10030287] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The utilization of hydroxy fatty acids has gained more and more attention due to its applicability in many industrial building blocks that require it, for example, polymers or fragrances. Furthermore, hydroxy fatty acids are accessible from biorenewables, thus contributing to a more sustainable raw material basis for industrial chemicals. Therefore, a range of investigations were done on fatty acid hydratases (FAHs), since these enzymes catalyze the addition of water to an unsaturated fatty acid, thus providing an elegant route towards hydroxy-substituted fatty acids. Besides the discovery and characterization of fatty acid hydratases (FAHs), the design and optimization of syntheses with these enzymes, the implementation in elaborate cascades, and the improvement of these biocatalysts, by way of mutation in terms of the substrate scope, has been investigated. This mini-review focuses on the research done on process development using fatty acid hydratases as a catalyst. It is notable that biotransformations, running at impressive substrate loadings of up to 280 g L−1, have been realized. A further topic of this mini-review is the implementation of fatty acid hydratases in cascade reactions. In such cascades, fatty acid hydratases were, in particular, combined with alcohol dehydrogenases (ADH), Baeyer-Villiger monooxygenases (BVMO), transaminases (TA) and hydrolases, thus enabling access to a broad variety of molecules that are of industrial interest.
Collapse
|
31
|
Jung J, Braun J, Czabany T, Nidetzky B. Unexpected NADPH Hydratase Activity in the Nitrile Reductase QueF from Escherichia coli. Chembiochem 2020; 21:1534-1543. [PMID: 31850614 PMCID: PMC7317782 DOI: 10.1002/cbic.201900679] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Indexed: 11/09/2022]
Abstract
The nitrile reductase QueF catalyzes NADPH-dependent reduction of the nitrile group of preQ0 (7-cyano-7-deazaguanine) into the primary amine of preQ1 (7-aminomethyl-7-deazaguanine), a biologically unique reaction important in bacterial nucleoside biosynthesis. Here we have discovered that the QueF from Escherichia coli-its D197A and E89L variants in particular (apparent kcat ≈10-2 min-1 )-also catalyze the slow hydration of the C5=C6 double bond of the dihydronicotinamide moiety of NADPH. The enzymatically C6-hydrated NADPH is a 3.5:1 mixture of R and S forms and rearranges spontaneously through anomeric epimerization (β→α) and cyclization at the tetrahydronicotinamide C6 and the ribosyl O2. NADH and 1-methyl- or 1-benzyl-1,4-dihydronicotinamide are not substrates of the enzymatic hydration. Mutagenesis results support a QueF hydratase mechanism, in which Cys190-the essential catalytic nucleophile for nitrile reduction-acts as the general acid for protonation at the dihydronicotinamide C5 of NADPH. Thus, the NADPH hydration in the presence of QueF bears mechanistic resemblance to the C=C double bond hydration in natural hydratases.
Collapse
Affiliation(s)
- Jihye Jung
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 10/12, 8010, Graz, Austria.,Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010, Graz, Austria
| | - Jan Braun
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 10/12, 8010, Graz, Austria
| | - Tibor Czabany
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 10/12, 8010, Graz, Austria.,Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010, Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 10/12, 8010, Graz, Austria.,Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010, Graz, Austria
| |
Collapse
|
32
|
Eser BE, Poborsky M, Dai R, Kishino S, Ljubic A, Takeuchi M, Jacobsen C, Ogawa J, Kristensen P, Guo Z. Rational Engineering of Hydratase from
Lactobacillus acidophilus
Reveals Critical Residues Directing Substrate Specificity and Regioselectivity. Chembiochem 2019; 21:550-563. [DOI: 10.1002/cbic.201900389] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Bekir Engin Eser
- Department of EngineeringAarhus University Gustav Wieds Vej 10 8000 Aarhus Denmark
| | - Michal Poborsky
- Department of EngineeringAarhus University Gustav Wieds Vej 10 8000 Aarhus Denmark
| | - Rongrong Dai
- Department of EngineeringAarhus University Gustav Wieds Vej 10 8000 Aarhus Denmark
| | - Shigenobu Kishino
- Division of Applied Life SciencesGraduate School of AgricultureKyoto University Kitashirakawa-oiwakecho Sakyo-ku Kyoto 606-8502 Japan
| | - Anita Ljubic
- Division of Food Technology, National Food InstituteTechnical University of Denmark Kemitorvet, Building 202 2800 Kgs. Lyngby Denmark
| | - Michiki Takeuchi
- Division of Applied Life SciencesGraduate School of AgricultureKyoto University Kitashirakawa-oiwakecho Sakyo-ku Kyoto 606-8502 Japan
| | - Charlotte Jacobsen
- Division of Food Technology, National Food InstituteTechnical University of Denmark Kemitorvet, Building 202 2800 Kgs. Lyngby Denmark
| | - Jun Ogawa
- Division of Applied Life SciencesGraduate School of AgricultureKyoto University Kitashirakawa-oiwakecho Sakyo-ku Kyoto 606-8502 Japan
| | - Peter Kristensen
- Faculty of Engineering and ScienceDepartment of Chemistry and BioscienceAalborg University Frederik Bayers Vej 7H 9220 Aalborg Denmark
| | - Zheng Guo
- Department of EngineeringAarhus University Gustav Wieds Vej 10 8000 Aarhus Denmark
| |
Collapse
|
33
|
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.
Collapse
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.
| |
Collapse
|
34
|
Ariyasu S, Kodama Y, Kasai C, Cong Z, Stanfield JK, Aiba Y, Watanabe Y, Shoji O. Development of a High‐Pressure Reactor Based on Liquid‐Flow Pressurisation to Facilitate Enzymatic Hydroxylation of Gaseous Alkanes. ChemCatChem 2019. [DOI: 10.1002/cctc.201901323] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Shinya Ariyasu
- Department of Chemistry Graduate School of ScienceNagoya University Aichi 464-8602 Japan
| | - Yusaku Kodama
- Department of Chemistry Graduate School of ScienceNagoya University Aichi 464-8602 Japan
| | - Chie Kasai
- Department of Chemistry Graduate School of ScienceNagoya University Aichi 464-8602 Japan
| | - Zhiqi Cong
- Department of Chemistry Graduate School of ScienceNagoya University Aichi 464-8602 Japan
| | - Joshua Kyle Stanfield
- Department of Chemistry Graduate School of ScienceNagoya University Aichi 464-8602 Japan
| | - Yuichiro Aiba
- Department of Chemistry Graduate School of ScienceNagoya University Aichi 464-8602 Japan
| | - Yoshihito Watanabe
- Research Center for Material ScienceNagoya University Aichi 464-8602 Japan
| | - Osami Shoji
- Department of Chemistry Graduate School of ScienceNagoya University Aichi 464-8602 Japan
- Core Research for Evolutional Science and TechnologyScience and Technology Agency Tokyo 102-0075 Japan
| |
Collapse
|
35
|
Engleder M, Strohmeier GA, Weber H, Steinkellner G, Leitner E, Müller M, Mink D, Schürmann M, Gruber K, Pichler H. Weiterentwicklung der Substrattoleranz von
Elizabethkingia meningoseptica
Oleathydratase zur regio‐ und stereoselektiven Hydratisierung von Ölsäurederivaten. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901462] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Matthias Engleder
- ACIB GmbH – Austrian Centre of Industrial Biotechnology Petersgasse 14 8010 Graz Österreich
| | - Gernot A. Strohmeier
- ACIB GmbH – Austrian Centre of Industrial Biotechnology Petersgasse 14 8010 Graz Österreich
- Institut für Organische ChemieTechnische Universität Graz, NAWI Graz Stremayrgasse 9 8010 Graz Österreich
| | - Hansjörg Weber
- Institut für Organische ChemieTechnische Universität Graz, NAWI Graz Stremayrgasse 9 8010 Graz Österreich
| | - Georg Steinkellner
- ACIB GmbH – Austrian Centre of Industrial Biotechnology Petersgasse 14 8010 Graz Österreich
- Innophore GmbH Am Eisernen Tor 3 8010 Graz Österreich
| | - Erich Leitner
- Institut für Analytische Chemie und LebensmittelchemieTechnische Universität Graz, NAWI Graz Stremayrgasse 9 8010 Graz Österreich
| | - Monika Müller
- InnoSyn B.V. Urmonderbaan 22 6167 RD Geleen Niederlande
| | - Daniel Mink
- InnoSyn B.V. Urmonderbaan 22 6167 RD Geleen Niederlande
| | | | - Karl Gruber
- ACIB GmbH – Austrian Centre of Industrial Biotechnology Petersgasse 14 8010 Graz Österreich
- Institut für Molekulare BiowissenschaftenUniversität Graz, NAWI Graz, BioTechMed Graz Humboldtstraße 50 8010 Graz Österreich
| | - Harald Pichler
- Institut für Molekulare BiotechnologieTechnische Universität Graz, NAWI Graz, BioTechMed Graz Petersgasse 14 8010 Graz Österreich
- ACIB GmbH – Austrian Centre of Industrial Biotechnology Petersgasse 14 8010 Graz Österreich
| |
Collapse
|
36
|
Engleder M, Strohmeier GA, Weber H, Steinkellner G, Leitner E, Müller M, Mink D, Schürmann M, Gruber K, Pichler H. Evolving the Promiscuity of Elizabethkingia meningoseptica Oleate Hydratase for the Regio- and Stereoselective Hydration of Oleic Acid Derivatives. Angew Chem Int Ed Engl 2019; 58:7480-7484. [PMID: 30848865 PMCID: PMC6563698 DOI: 10.1002/anie.201901462] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Indexed: 12/15/2022]
Abstract
The addition of water to non-activated carbon-carbon double bonds catalyzed by fatty acid hydratases (FAHYs) allows for highly regio- and stereoselective oxyfunctionalization of renewable oil feedstock. So far, the applicability of FAHYs has been limited to free fatty acids, mainly owing to the requirement of a carboxylate function for substrate recognition and binding. Herein, we describe for the first time the hydration of oleic acid (OA) derivatives lacking this free carboxylate by the oleate hydratase from Elizabethkingia meningoseptica (OhyA). Molecular docking of OA to the OhyA 3D-structure and a sequence alignment uncovered conserved amino acid residues at the entrance of the substrate channel as target positions for enzyme engineering. Exchange of selected amino acids gave rise to OhyA variants which showed up to an 18-fold improved conversion of OA derivatives, while retaining the excellent regio- and stereoselectivity in the olefin hydration reaction.
Collapse
Affiliation(s)
- Matthias Engleder
- ACIB GmbH—Austrian Centre of Industrial BiotechnologyPetersgasse 148010GrazAustria
| | - Gernot A. Strohmeier
- ACIB GmbH—Austrian Centre of Industrial BiotechnologyPetersgasse 148010GrazAustria
- Institute of Organic ChemistryGraz University of Technology, NAWI GrazStremayrgasse 98010GrazAustria
| | - Hansjörg Weber
- Institute of Organic ChemistryGraz University of Technology, NAWI GrazStremayrgasse 98010GrazAustria
| | - Georg Steinkellner
- ACIB GmbH—Austrian Centre of Industrial BiotechnologyPetersgasse 148010GrazAustria
- Innophore GmbHAm Eisernen Tor 38010GrazAustria
| | - Erich Leitner
- Institute of Analytical Chemistry and Food ChemistryGraz University of Technology, NAWI GrazStremayrgasse 98010GrazAustria
| | - Monika Müller
- InnoSyn B.V.Urmonderbaan 226167 RDGeleenThe Netherlands
| | - Daniel Mink
- InnoSyn B.V.Urmonderbaan 226167 RDGeleenThe Netherlands
| | | | - Karl Gruber
- ACIB GmbH—Austrian Centre of Industrial BiotechnologyPetersgasse 148010GrazAustria
- Institute of Molecular BiosciencesUniversity of Graz, NAWI Graz, BioTechMed GrazHumboldtstrasse 508010GrazAustria
| | - Harald Pichler
- Institute of Molecular BiotechnologyGraz University of Technology, NAWI Graz, BioTechMed GrazPetersgasse 148010GrazAustria
- ACIB GmbH—Austrian Centre of Industrial BiotechnologyPetersgasse 148010GrazAustria
| |
Collapse
|
37
|
Shoji O, Aiba Y, Watanabe Y. Hoodwinking Cytochrome P450BM3 into Hydroxylating Non-Native Substrates by Exploiting Its Substrate Misrecognition. Acc Chem Res 2019; 52:925-934. [PMID: 30888147 DOI: 10.1021/acs.accounts.8b00651] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Bacterial cytochrome P450s (P450s) are at the focus of attention as potential biocatalysts for applications in green synthetic chemistry, as they possess high activity for the hydroxylation of inert substrate C-H bonds. The high activity of bacterial P450s, such as P450BM3, is chiefly due to their high substrate specificity, and consequently, the catalytic activity of P450BM3 toward non-native substrates is very low, limiting the utility of bacterial P450s as biocatalysts. To enable oxidation of non-native substrates by P450BM3 without any mutagenesis, we have developed a series of "decoy molecules", inert dummy substrates, with structures that resemble those of the native substrates. Decoy molecules fool P450BM3 into generating the active species, so-called Compound I, enabling the catalytic oxidation of non-native substrates other than fatty acids. Perfluorinated carboxylic acids (PFCs) serve as decoy molecules to initiate the activation of molecular oxygen in the same manner as long-alkyl-chain fatty acids, due to their structural similarity, and induce the generation of Compound I, but, unlike the native substrates, PFCs are not oxidizable by Compound I, allowing the hydroxylation of non-native substrates, such as gaseous alkanes and benzene. The catalytic activity for non-native substrate hydroxylation was significantly enhanced by employing second generation decoy molecules, PFCs modified with amino acids (PFC-amino acids). Cocrystals of P450BM3 with PFC9-Trp revealed clear electron density in the fatty-acid-binding channel that was readily assigned to PFC9-Trp. The alkyl chain terminus of PFC9-Trp does not reach the active site owing to multiple hydrogen bonding interactions between the carboxyl and carbonyl groups of PFC9-Trp and amino acids located at the entrance of the substrate binding channel of P450BM3 that fix it in place. The remaining space above the heme after binding of PFC9-Trp can be utilized to accommodate non-native substrates. Further developments revealed that third generation decoy molecules, N-acyl amino acids, such as pelargonoyl-l-phenylalanine (C9-Phe), can serve as decoy molecules, indicating that the rationale "fluorination is required for decoy molecule function" can be safely discarded. Diverse carboxylic acids including dipeptides could now be exploited as building blocks, and a library of decoy molecules possessing diverse structures was prepared. Among the third-generation decoy molecules examined N-enanthyl-l-proline modified with l-phenylalanine (C7-Pro-Phe) afforded the maximum turnover rate for benzene hydroxylation. The structural diversity of third-generation decoy molecules was also utilized to control the stereoselectivity of hydroxylation for the benzylic hydroxylation of Indane, showing that decoy molecules can alter stereoselectivity. As both the catalytic activity and enantioselectivity are dependent upon the structure of the decoy molecules, their design allows us to regulate reactions catalyzed by wild-type enzymes. Furthermore, decoy molecules can also activate intracellular P450BM3, allowing the use of E. coli expressing wild-type P450BM3 as an efficient whole-cell bioreactor. It should be noted that Mn-substituted full-length P450BM3 (Mn-P450BM3) is also active for the hydroxylation of propane in which the regioselectivity diverged from that of Fe-P450BM3. The results summarized in this Account represent good examples of how the reactive properties of P450BM3 can be controlled for the monooxygenation of non-native substrates in vitro as well as in vivo to expand the potential of P450BM3.
Collapse
Affiliation(s)
- Osami Shoji
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, 5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Yuichiro Aiba
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Yoshihito Watanabe
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| |
Collapse
|
38
|
Wu S, Zhou Y, Li Z. Biocatalytic selective functionalisation of alkenes via single-step and one-pot multi-step reactions. Chem Commun (Camb) 2019; 55:883-896. [PMID: 30566124 DOI: 10.1039/c8cc07828a] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Alkenes are excellent starting materials for organic synthesis due to the versatile reactivity of C[double bond, length as m-dash]C bonds and the easy availability of many unfunctionalised alkenes. Direct regio- and/or enantioselective conversion of alkenes into functionalised (chiral) compounds has enormous potential for industrial applications, and thus has attracted the attention of researchers for extensive development using chemo-catalysis over the past few years. On the other hand, many enzymes have also been employed for conversion of alkenes in a highly selective and much greener manner to offer valuable products. Herein, we review recent advances in seven well-known types of biocatalytic conversion of alkenes. Remarkably, recent mechanism-guided directed evolution and enzyme cascades have enabled the development of seven novel types of single-step and one-pot multi-step functionalisation of alkenes, some of which are even unattainable via chemo-catalysis. These new reactions are particularly highlighted in this feature article. Overall, we present an ever-expanding enzyme toolbox for various alkene functionalisations inspiring further research in this fast-developing theme.
Collapse
Affiliation(s)
- Shuke Wu
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585.
| | | | | |
Collapse
|
39
|
Demming RM, Hammer SC, Nestl BM, Gergel S, Fademrecht S, Pleiss J, Hauer B. Asymmetric Enzymatic Hydration of Unactivated, Aliphatic Alkenes. Angew Chem Int Ed Engl 2019; 58:173-177. [PMID: 30256501 PMCID: PMC6471033 DOI: 10.1002/anie.201810005] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Indexed: 11/30/2022]
Abstract
The direct enantioselective addition of water to unactivated alkenes could simplify the synthesis of chiral alcohols and solve a long-standing challenge in catalysis. Here we report that an engineered fatty acid hydratase can catalyze the asymmetric hydration of various terminal and internal alkenes. In the presence of a carboxylic acid decoy molecule for activation of the oleate hydratase from E. meningoseptica, asymmetric hydration of unactivated alkenes was achieved with up to 93 % conversion, excellent selectivity (>99 % ee, >95 % regioselectivity), and on a preparative scale.
Collapse
Affiliation(s)
- Rebecca M. Demming
- Institute of Biochemistry and Technical BiochemistryDepartment of Technical BiochemistryUniversity of StuttgartAllmandring 3170569StuttgartGermany
| | - Stephan C. Hammer
- Institute of Biochemistry and Technical BiochemistryDepartment of Technical BiochemistryUniversity of StuttgartAllmandring 3170569StuttgartGermany
| | - Bettina M. Nestl
- Institute of Biochemistry and Technical BiochemistryDepartment of Technical BiochemistryUniversity of StuttgartAllmandring 3170569StuttgartGermany
| | - Sebastian Gergel
- Institute of Biochemistry and Technical BiochemistryDepartment of Technical BiochemistryUniversity of StuttgartAllmandring 3170569StuttgartGermany
| | - Silvia Fademrecht
- Institute of Biochemistry and Technical BiochemistryDepartment of Technical BiochemistryUniversity of StuttgartAllmandring 3170569StuttgartGermany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical BiochemistryDepartment of Technical BiochemistryUniversity of StuttgartAllmandring 3170569StuttgartGermany
| | - Bernhard Hauer
- Institute of Biochemistry and Technical BiochemistryDepartment of Technical BiochemistryUniversity of StuttgartAllmandring 3170569StuttgartGermany
| |
Collapse
|
40
|
Abstract
A personal selection of 32 recent papers is presented covering various aspects of current developments in bioorganic chemistry and novel natural products such as vlasoulamine A from Vladimiria souliei.
Collapse
|