1
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Wang Q, Liu X, Zhang H, Chu H, Shi C, Zhang L, Bai J, Liu P, Li J, Zhu X, Liu Y, Chen Z, Huang R, Chang H, Liu T, Chang Z, Cheng J, Jiang H. Cytochrome P450 Enzyme Design by Constraining the Catalytic Pocket in a Diffusion Model. RESEARCH (WASHINGTON, D.C.) 2024; 7:0413. [PMID: 38979516 PMCID: PMC11227911 DOI: 10.34133/research.0413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 05/27/2024] [Indexed: 07/10/2024]
Abstract
Although cytochrome P450 enzymes are the most versatile biocatalysts in nature, there is insufficient comprehension of the molecular mechanism underlying their functional innovation process. Here, by combining ancestral sequence reconstruction, reverse mutation assay, and progressive forward accumulation, we identified 5 founder residues in the catalytic pocket of flavone 6-hydroxylase (F6H) and proposed a "3-point fixation" model to elucidate the functional innovation mechanisms of P450s in nature. According to this design principle of catalytic pocket, we further developed a de novo diffusion model (P450Diffusion) to generate artificial P450s. Ultimately, among the 17 non-natural P450s we generated, 10 designs exhibited significant F6H activity and 6 exhibited a 1.3- to 3.5-fold increase in catalytic capacity compared to the natural CYP706X1. This work not only explores the design principle of catalytic pockets of P450s, but also provides an insight into the artificial design of P450 enzymes with desired functions.
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Affiliation(s)
- Qian Wang
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology,
Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Xiaonan Liu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology,
Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Hejian Zhang
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology,
Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- College of Biotechnology,
Tianjin University of Science and Technology, Tianjin 300457, China
| | - Huanyu Chu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology,
Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Shi
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences,
Peking University, Beijing 100191, China
| | - Lei Zhang
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology,
Chinese Academy of Sciences, Tianjin 300308, China
- College of Life Science and Technology,
Wuhan Polytechnic University, Wuhan, Hubei 430023, China
| | - Jie Bai
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology,
Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Pi Liu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology,
Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Jing Li
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology,
Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry,
Nankai University, Tianjin 300071, China
- College of Life Science,
Nankai University, Tianjin 300071, China
| | - Xiaoxi Zhu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology,
Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Yuwan Liu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology,
Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Zhangxin Chen
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences,
Peking University, Beijing 100191, China
| | - Rong Huang
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology,
Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Hong Chang
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology,
Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Tian Liu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology,
Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Zhenzhan Chang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences,
Peking University, Beijing 100191, China
| | - Jian Cheng
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology,
Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Huifeng Jiang
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology,
Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
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2
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Ndochinwa OG, Wang QY, Amadi OC, Nwagu TN, Nnamchi CI, Okeke ES, Moneke AN. Current status and emerging frontiers in enzyme engineering: An industrial perspective. Heliyon 2024; 10:e32673. [PMID: 38912509 PMCID: PMC11193041 DOI: 10.1016/j.heliyon.2024.e32673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/25/2024] Open
Abstract
Protein engineering mechanisms can be an efficient approach to enhance the biochemical properties of various biocatalysts. Immobilization of biocatalysts and the introduction of new-to-nature chemical reactivities are also possible through the same mechanism. Discovering new protocols that enhance the catalytic active protein that possesses novelty in terms of being stable, active, and, stereoselectivity with functions could be identified as essential areas in terms of concurrent bioorganic chemistry (synergistic relationship between organic chemistry and biochemistry in the context of enzyme engineering). However, with our current level of knowledge about protein folding and its correlation with protein conformation and activities, it is almost impossible to design proteins with specific biological and physical properties. Hence, contemporary protein engineering typically involves reprogramming existing enzymes by mutagenesis to generate new phenotypes with desired properties. These processes ensure that limitations of naturally occurring enzymes are not encountered. For example, researchers have engineered cellulases and hemicellulases to withstand harsh conditions encountered during biomass pretreatment, such as high temperatures and acidic environments. By enhancing the activity and robustness of these enzymes, biofuel production becomes more economically viable and environmentally sustainable. Recent trends in enzyme engineering have enabled the development of tailored biocatalysts for pharmaceutical applications. For instance, researchers have engineered enzymes such as cytochrome P450s and amine oxidases to catalyze challenging reactions involved in drug synthesis. In addition to conventional methods, there has been an increasing application of machine learning techniques to identify patterns in data. These patterns are then used to predict protein structures, enhance enzyme solubility, stability, and function, forecast substrate specificity, and assist in rational protein design. In this review, we discussed recent trends in enzyme engineering to optimize the biochemical properties of various biocatalysts. Using examples relevant to biotechnology in engineering enzymes, we try to expatiate the significance of enzyme engineering with how these methods could be applied to optimize the biochemical properties of a naturally occurring enzyme.
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Affiliation(s)
- Obinna Giles Ndochinwa
- Department of Microbiology, Faculty of Biological Science, University of Nigeria, Nsukka, Nigeria
| | - Qing-Yan Wang
- State Key Laboratory of Biomass Enzyme Technology, National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi, China
| | - Oyetugo Chioma Amadi
- Department of Microbiology, Faculty of Biological Science, University of Nigeria, Nsukka, Nigeria
| | - Tochukwu Nwamaka Nwagu
- Department of Microbiology, Faculty of Biological Science, University of Nigeria, Nsukka, Nigeria
| | | | - Emmanuel Sunday Okeke
- Department of Biochemistry, Faculty of Biological Sciences & Natural Science Unit, School of General Studies, University of Nigeria, Nsukka, Enugu State, 410001, Nigeria
- Institute of Environmental Health and Ecological Security, School of the Environment and Safety, Jiangsu University, 301 Xuefu Rd., 212013, Zhenjiang, Jiangsu, China
| | - Anene Nwabu Moneke
- Department of Microbiology, Faculty of Biological Science, University of Nigeria, Nsukka, Nigeria
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3
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Chen R, Wang M, Keasling JD, Hu T, Yin X. Expanding the structural diversity of terpenes by synthetic biology approaches. Trends Biotechnol 2024; 42:699-713. [PMID: 38233232 DOI: 10.1016/j.tibtech.2023.12.006] [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: 08/22/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024]
Abstract
Terpenoids display chemical and structural diversities as well as important biological activities. Despite their extreme variability, the range of these structures is limited by the scope of natural products that canonically derive from interconvertible five-carbon (C5) isoprene units. New approaches have recently been developed to expand their structural diversity. This review systematically explores the combinatorial biosynthesis of noncanonical building blocks via the coexpression of the canonical mevalonate (MVA) pathway and C-methyltransferases (C-MTs), or by using the lepidopteran mevalonate (LMVA) pathway. Unnatural terpenoids can be created from farnesyl diphosphate (FPP) analogs by chemobiological synthesis and terpene cyclopropanation by artificial metalloenzymes (ArMs). Advanced technologies to accelerate terpene biosynthesis are discussed. This review provides a valuable reference for increasing the diversity of valuable terpenoids and their derivatives, as well as for expanding their potential applications.
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Affiliation(s)
- Rong Chen
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, School of Pharmacy, School of Public Health, Hangzhou Normal University, Hangzhou 310000, China; Joint BioEnergy Institute, Emeryville, CA 94608, USA.
| | - Ming Wang
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, School of Pharmacy, School of Public Health, Hangzhou Normal University, Hangzhou 310000, China
| | - Jay D Keasling
- Joint BioEnergy Institute, Emeryville, CA 94608, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA; Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Bioengineering, University of California, Berkeley, CA 94720, USA; Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technologies, Shenzhen 518055, China; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Tianyuan Hu
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, School of Pharmacy, School of Public Health, Hangzhou Normal University, Hangzhou 310000, China
| | - Xiaopu Yin
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, School of Pharmacy, School of Public Health, Hangzhou Normal University, Hangzhou 310000, China.
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4
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Decembrino D, Cannella D. The thin line between monooxygenases and peroxygenases. P450s, UPOs, MMOs, and LPMOs: A brick to bridge fields of expertise. Biotechnol Adv 2024; 72:108321. [PMID: 38336187 DOI: 10.1016/j.biotechadv.2024.108321] [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: 10/31/2023] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
Many scientific fields, although driven by similar purposes and dealing with similar technologies, often appear so isolated and far from each other that even the vocabularies to describe the very same phenomenon might differ. Concerning the vast field of biocatalysis, a special role is played by those redox enzymes that employ oxygen-based chemistry to unlock transformations otherwise possible only with metal-based catalysts. As such, greener chemical synthesis methods and environmentally-driven biotechnological approaches were enabled over the last decades by the use of several enzymes and ultimately resulted in the first industrial applications. Among what can be called today the environmental biorefinery sector, biomass transformation, greenhouse gas reduction, bio-gas/fuels production, bioremediation, as well as bulk or fine chemicals and even pharmaceuticals manufacturing are all examples of fields in which successful prototypes have been demonstrated employing redox enzymes. In this review we decided to focus on the most prominent enzymes (MMOs, LPMO, P450 and UPO) capable of overcoming the ∼100 kcal mol-1 barrier of inactivated CH bonds for the oxyfunctionalization of organic compounds. Harnessing the enormous potential that lies within these enzymes is of extreme value to develop sustainable industrial schemes and it is still deeply coveted by many within the aforementioned fields of application. Hence, the ambitious scope of this account is to bridge the current cutting-edge knowledge gathered upon each enzyme. By creating a broad comparison, scientists belonging to the different fields may find inspiration and might overcome obstacles already solved by the others. This work is organised in three major parts: a first section will be serving as an introduction to each one of the enzymes regarding their structural and activity diversity, whereas a second one will be encompassing the mechanistic aspects of their catalysis. In this regard, the machineries that lead to analogous catalytic outcomes are depicted, highlighting the major differences and similarities. Finally, a third section will be focusing on the elements that allow the oxyfunctionalization chemistry to occur by delivering redox equivalents to the enzyme by the action of diverse redox partners. Redox partners are often overlooked in comparison to the catalytic counterparts, yet they represent fundamental elements to better understand and further develop practical applications based on mono- and peroxygenases.
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Affiliation(s)
- Davide Decembrino
- Photobiocatalysis Unit - Crop Production and Biostimulation Lab (CPBL), and Biomass Transformation Lab (BTL), École Interfacultaire de Bioingénieurs, Université Libre de Bruxelles, Belgium.
| | - David Cannella
- Photobiocatalysis Unit - Crop Production and Biostimulation Lab (CPBL), and Biomass Transformation Lab (BTL), École Interfacultaire de Bioingénieurs, Université Libre de Bruxelles, Belgium.
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5
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Vargas DA, Ren X, Sengupta A, Zhu L, Roy S, Garcia-Borràs M, Houk KN, Fasan R. Biocatalytic strategy for the construction of sp 3-rich polycyclic compounds from directed evolution and computational modelling. Nat Chem 2024; 16:817-826. [PMID: 38351380 PMCID: PMC11088497 DOI: 10.1038/s41557-023-01435-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 12/20/2023] [Indexed: 02/17/2024]
Abstract
Catalysis with engineered enzymes has provided more efficient routes for the production of active pharmaceutical agents. However, the potential of biocatalysis to assist in early-stage drug discovery campaigns remains largely untapped. In this study, we have developed a biocatalytic strategy for the construction of sp3-rich polycyclic compounds via the intramolecular cyclopropanation of benzothiophenes and related heterocycles. Two carbene transferases with complementary regioisomer selectivity were evolved to catalyse the stereoselective cyclization of benzothiophene substrates bearing diazo ester groups at the C2 or C3 position of the heterocycle. The detailed mechanisms of these reactions were elucidated by a combination of crystallographic and computational analyses. Leveraging these insights, the substrate scope of one of the biocatalysts could be expanded to include previously unreactive substrates, highlighting the value of integrating evolutionary and rational strategies to develop enzymes for new-to-nature transformations. The molecular scaffolds accessed here feature a combination of three-dimensional and stereochemical complexity with 'rule-of-three' properties, which should make them highly valuable for fragment-based drug discovery campaigns.
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Affiliation(s)
- David A Vargas
- Process Research and Development, Merck, Rahway, NJ, USA
| | - Xinkun Ren
- College of Engineering and Applied Sciences, Nanjing University, Nanjing, China
| | - Arkajyoti Sengupta
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Ledong Zhu
- Environment Research Institute, Shandong University, Qingdao, People's Republic of China
| | - Satyajit Roy
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX, USA
| | - Marc Garcia-Borràs
- Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Girona, Spain
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA.
| | - Rudi Fasan
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX, USA.
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6
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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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7
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Edholm F, Nandy A, Reinhardt CR, Kastner DW, Kulik HJ. Protein3D: Enabling analysis and extraction of metal-containing sites from the Protein Data Bank with molSimplify. J Comput Chem 2024; 45:352-361. [PMID: 37873926 DOI: 10.1002/jcc.27242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/27/2023] [Accepted: 10/03/2023] [Indexed: 10/25/2023]
Abstract
Metalloenzymes catalyze a wide range of chemical transformations, with the active site residues playing a key role in modulating chemical reactivity and selectivity. Unlike smaller synthetic catalysts, a metalloenzyme active site is embedded in a larger protein, which makes interrogation of electronic properties and geometric features with quantum mechanical calculations challenging. Here we implement the ability to fetch crystallographic structures from the Protein Data Bank and analyze the metal binding sites in the program molSimplify. We show the usefulness of the newly created protein3D class to extract the local environment around non-heme iron enzymes containing a two histidine motif and prepare 372 structures for quantum mechanical calculations. Our implementation of protein3D serves to expand the range of systems molSimplify can be used to analyze and will enable high-throughput study of metal-containing active sites in proteins.
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Affiliation(s)
- Freya Edholm
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Aditya Nandy
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Clorice R Reinhardt
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - David W Kastner
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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8
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Schulz-Mirbach H, Dronsella B, He H, Erb TJ. Creating new-to-nature carbon fixation: A guide. Metab Eng 2024; 82:12-28. [PMID: 38160747 DOI: 10.1016/j.ymben.2023.12.012] [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: 10/10/2023] [Revised: 12/23/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024]
Abstract
Synthetic biology aims at designing new biological functions from first principles. These new designs allow to expand the natural solution space and overcome the limitations of naturally evolved systems. One example is synthetic CO2-fixation pathways that promise to provide more efficient ways for the capture and conversion of CO2 than natural pathways, such as the Calvin Benson Bassham (CBB) cycle of photosynthesis. In this review, we provide a practical guideline for the design and realization of such new-to-nature CO2-fixation pathways. We introduce the concept of "synthetic CO2-fixation", and give a general overview over the enzymology and topology of synthetic pathways, before we derive general principles for their design from their eight naturally evolved analogs. We provide a comprehensive summary of synthetic carbon-assimilation pathways and derive a step-by-step, practical guide from the theoretical design to their practical implementation, before ending with an outlook on new developments in the field.
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Affiliation(s)
- Helena Schulz-Mirbach
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Beau Dronsella
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany; Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Hai He
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Tobias J Erb
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany; Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch-Str. 16, D-35043, Marburg, Germany.
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9
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Naeem Y, Matsuo BT, Davies HML. Enantioselective Intermolecular C-H Functionalization of Primary Benzylic C-H Bonds Using ((Aryl)(diazo)methyl)phosphonates. ACS Catal 2024; 14:124-130. [PMID: 38205024 PMCID: PMC10775147 DOI: 10.1021/acscatal.3c04661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 01/12/2024]
Abstract
Catalyst-controlled C-H functionalization using donor/acceptor carbenes has been shown to be an efficient process capable of high levels of site control and stereocontrol. This study demonstrated that the scope of the donor/acceptor carbene C-H functionalization can be extended to systems where the acceptor group is a phosphonate. When using the optimized dirhodium catalyst, Rh2(S-di-(4-Br)TPPTTL)4, ((aryl)(diazo)methyl)phosphonates undergo highly enantioselective (84-99% ee) and site-selective (>30:1 r.r.) benzylic C-H functionalization. The phosphonate group is much more sterically demanding than the previously studied carboxylate ester group, leading to much higher selectivity for a primary site versus more sterically crowded positions. The effectiveness of this methodology has been demonstrated by the late-stage primary C-H functionalization of estrone, adapalene, (S)-naproxen, clofibrate, and gemfibrozil derivatives.
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Affiliation(s)
- Yasir Naeem
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Bianca T. Matsuo
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Huw M. L. Davies
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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10
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Simões MMQ, Cavaleiro JAS, Ferreira VF. Recent Synthetic Advances on the Use of Diazo Compounds Catalyzed by Metalloporphyrins. Molecules 2023; 28:6683. [PMID: 37764459 PMCID: PMC10537418 DOI: 10.3390/molecules28186683] [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: 07/21/2023] [Revised: 09/12/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Diazo compounds are organic substances that are often used as precursors in organic synthesis like cyclization reactions, olefinations, cyclopropanations, cyclopropenations, rearrangements, and carbene or metallocarbene insertions into C-H, N-H, O-H, S-H, and Si-H bonds. Typically, reactions from diazo compounds are catalyzed by transition metals with various ligands that modulate the capacity and selectivity of the catalyst. These ligands can modify and enhance chemoselectivity in the substrate, regioselectivity and enantioselectivity by reflecting these preferences in the products. Porphyrins have been used as catalysts in several important reactions for organic synthesis and also in several medicinal applications. In the chemistry of diazo compounds, porphyrins are very efficient as catalysts when complexed with low-cost metals (e.g., Fe and Co) and, therefore, in recent years, this has been the subject of significant research. This review will summarize the advances in the studies involving the field of diazo compounds catalyzed by metalloporphyrins (M-Porph, M = Fe, Ru, Os, Co, Rh, Ir) in the last five years to provide a clear overview and possible opportunities for future applications. Also, at the end of this review, the properties of artificial metalloenzymes and hemoproteins as biocatalysts for a broad range of applications, namely those concerning carbene-transfer reactions, will be considered.
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Affiliation(s)
- Mário M. Q. Simões
- Department of Chemistry & LAQV-REQUIMTE, University of Aveiro, 3810-193 Aveiro, Portugal; (M.M.Q.S.); (J.A.S.C.)
| | - José A. S. Cavaleiro
- Department of Chemistry & LAQV-REQUIMTE, University of Aveiro, 3810-193 Aveiro, Portugal; (M.M.Q.S.); (J.A.S.C.)
| | - Vitor F. Ferreira
- Departamento de Tecnologia Farmacêutica Química, Universidade Federal Fluminense, Niterói 24241-002, RJ, Brazil
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11
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Abstract
The ability to site-selectively modify equivalent functional groups in a molecule has the potential to streamline syntheses and increase product yields by lowering step counts. Enzymes catalyze site-selective transformations throughout primary and secondary metabolism, but leveraging this capability for non-native substrates and reactions requires a detailed understanding of the potential and limitations of enzyme catalysis and how these bounds can be extended by protein engineering. In this review, we discuss representative examples of site-selective enzyme catalysis involving functional group manipulation and C-H bond functionalization. We include illustrative examples of native catalysis, but our focus is on cases involving non-native substrates and reactions often using engineered enzymes. We then discuss the use of these enzymes for chemoenzymatic transformations and target-oriented synthesis and conclude with a survey of tools and techniques that could expand the scope of non-native site-selective enzyme catalysis.
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Affiliation(s)
- Dibyendu Mondal
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Harrison M Snodgrass
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Christian A Gomez
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Jared C Lewis
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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12
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Permana D, Kitaoka T, Ichinose H. Conversion and synthesis of chemicals catalyzed by fungal cytochrome P450 monooxygenases: A review. Biotechnol Bioeng 2023. [PMID: 37139574 DOI: 10.1002/bit.28411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/12/2023] [Accepted: 04/17/2023] [Indexed: 05/05/2023]
Abstract
Cytochrome P450s (also called CYPs or P450s) are a superfamily of heme-containing monooxygenases. They are distributed in all biological kingdoms. Most fungi have at least two P450-encoding genes, CYP51 and CYP61, which are housekeeping genes that play important roles in the synthesis of sterols. However, the kingdom fungi is an interesting source of numerous P450s. Here, we review reports on fungal P450s and their applications in the bioconversion and biosynthesis of chemicals. We highlight their history, availability, and versatility. We describe their involvement in hydroxylation, dealkylation, oxygenation, C═C epoxidation, C-C cleavage, C-C ring formation and expansion, C-C ring contraction, and uncommon reactions in bioconversion and/or biosynthesis pathways. The ability of P450s to catalyze these reactions makes them promising enzymes for many applications. Thus, we also discuss future prospects in this field. We hope that this review will stimulate further study and exploitation of fungal P450s for specific reactions and applications.
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Affiliation(s)
- Dani Permana
- Faculty of Agriculture, Kyushu University, Fukuoka, Japan
- Research Center for Environmental and Clean Technology, The National Research and Innovation Agency of the Republic of Indonesia (Badan Riset dan Inovasi Nasional (BRIN)), Bandung Advanced Science and Creative Engineering Space (BASICS), Kawasan Sains dan Teknologi (KST) Prof. Dr. Samaun Samadikun, Bandung, Indonesia
| | - Takuya Kitaoka
- Faculty of Agriculture, Kyushu University, Fukuoka, Japan
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13
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Huang J, Quest A, Cruz-Morales P, Deng K, Pereira JH, Van Cura D, Kakumanu R, Baidoo EEK, Dan Q, Chen Y, Petzold CJ, Northen TR, Adams PD, Clark DS, Balskus EP, Hartwig JF, Mukhopadhyay A, Keasling JD. Complete integration of carbene-transfer chemistry into biosynthesis. Nature 2023; 617:403-408. [PMID: 37138074 PMCID: PMC11334723 DOI: 10.1038/s41586-023-06027-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 03/28/2023] [Indexed: 05/05/2023]
Abstract
Biosynthesis is an environmentally benign and renewable approach that can be used to produce a broad range of natural and, in some cases, new-to-nature products. However, biology lacks many of the reactions that are available to synthetic chemists, resulting in a narrower scope of accessible products when using biosynthesis rather than synthetic chemistry. A prime example of such chemistry is carbene-transfer reactions1. Although it was recently shown that carbene-transfer reactions can be performed in a cell and used for biosynthesis2,3, carbene donors and unnatural cofactors needed to be added exogenously and transported into cells to effect the desired reactions, precluding cost-effective scale-up of the biosynthesis process with these reactions. Here we report the access to a diazo ester carbene precursor by cellular metabolism and a microbial platform for introducing unnatural carbene-transfer reactions into biosynthesis. The α-diazoester azaserine was produced by expressing a biosynthetic gene cluster in Streptomyces albus. The intracellularly produced azaserine was used as a carbene donor to cyclopropanate another intracellularly produced molecule-styrene. The reaction was catalysed by engineered P450 mutants containing a native cofactor with excellent diastereoselectivity and a moderate yield. Our study establishes a scalable, microbial platform for conducting intracellular abiological carbene-transfer reactions to functionalize a range of natural and new-to-nature products and expands the scope of organic products that can be produced by cellular metabolism.
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Affiliation(s)
- Jing Huang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Andrew Quest
- Department of Chemistry, University of California, Berkeley, CA, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Pablo Cruz-Morales
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Kai Deng
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Department of Biomaterials and Biomanufacturing, Sandia National Laboratories, Livermore, CA, USA
| | - Jose Henrique Pereira
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Devon Van Cura
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Ramu Kakumanu
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Edward E K Baidoo
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Qingyun Dan
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Yan Chen
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Christopher J Petzold
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Trent R Northen
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Paul D Adams
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Douglas S Clark
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - John F Hartwig
- Department of Chemistry, University of California, Berkeley, CA, USA.
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA.
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Jay D Keasling
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA.
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA.
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
- Department of Bioengineering, University of California, Berkeley, CA, USA.
- Synthetic Biochemistry Center, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China.
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14
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Gao Q, Ma B, Wang Q, Zhang H, Fushinobu S, Yang J, Lin S, Sun K, Han BN, Xu LH. Improved 2α-Hydroxylation Efficiency of Steroids by CYP154C2 Using Structure-Guided Rational Design. Appl Environ Microbiol 2023; 89:e0218622. [PMID: 36847541 PMCID: PMC10056965 DOI: 10.1128/aem.02186-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/01/2023] [Indexed: 03/01/2023] Open
Abstract
Cytochrome P450 enzymes are promising biocatalysts for industrial use because they catalyze site-selective C-H oxidation and have diverse catalytic reactions and a broad substrate range. In this study, the 2α-hydroxylation activity of CYP154C2 from Streptomyces avermitilis MA-4680T toward androstenedione (ASD) was identified by an in vitro conversion assay. The testosterone (TES)-bound structure of CYP154C2 was solved at 1.42 Å, and this structure was used to design eight mutants, including single, double, and triple mutants, to improve the conversion efficiency. Mutants L88F/M191F and M191F/V285L were found to enhance the conversion rates significantly (i.e., 8.9-fold and 7.4-fold for TES, 46.5-fold and 19.5-fold for ASD, respectively) compared with the wild-type (WT) enzyme while retaining high 2α-position selectivity. The substrate binding affinity of the L88F/M191F mutant toward TES and ASD was enhanced compared with that of WT CYP154C2, supporting the measured increase in the conversion efficiencies. Moreover, the total turnover number and kcat/Km of the L88F/M191F and M191F/V285L mutants increased significantly. Interestingly, all mutants containing L88F generated 16α-hydroxylation products, suggesting that L88 in CYP154C2 plays a vital role in substrate selectivity and that the amino acid corresponding to L88 in the 154C subfamily affects the orientation of steroid binding and substrate selectivity. IMPORTANCE Hydroxylated derivatives of steroids play essential roles in medicine. Cytochrome P450 enzymes selectively hydroxylate methyne groups on steroids, which can dramatically change their polarity, biological activity and toxicity. There is a paucity of reports on the 2α-hydroxylation of steroids, and documented 2α-hydroxylate P450s show extremely low conversion efficiency and/or low regio- and stereoselectivity. This study conducted crystal structure analysis and structure-guided rational engineering of CYP154C2 and efficiently enhanced the conversion efficiency of TES and ASD with high regio- and stereoselectivity. Our results provide an effective strategy and theoretical basis for the 2α-hydroxylation of steroids, and the structure-guided rational design of P450s should facilitate P450 applications in the biosynthesis of steroid drugs.
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Affiliation(s)
- Qilin Gao
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Bingbing Ma
- Research Center for Clinical Pharmacy, The First Affiliated Hospital & Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Qianwen Wang
- Ocean College, Zhejiang University, Zhoushan, China
| | - Hao Zhang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Shinya Fushinobu
- Department of Biotechnology, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Jian Yang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Susu Lin
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Keke Sun
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Bing-Nan Han
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Lian-Hua Xu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
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15
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Zhang X, Qiu D, Chen J, Zhang Y, Wang J, Chen D, Liu Y, Cheng M, Monchaud D, Mergny JL, Ju H, Zhou J. Chimeric Biocatalyst Combining Peptidic and Nucleic Acid Components Overcomes the Performance and Limitations of the Native Horseradish Peroxidase. J Am Chem Soc 2023; 145:4517-4526. [PMID: 36795970 DOI: 10.1021/jacs.2c11318] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Chimeric peptide-DNAzyme (CPDzyme) is a novel artificial peroxidase that relies on the covalent assembly of DNA, peptides, and an enzyme cofactor in a single scaffold. An accurate control of the assembly of these different partners allows for the design of the CPDzyme prototype G4-Hemin-KHRRH, found to be >2000-fold more active (in terms of conversion number kcat) than the corresponding but non-covalent G4/Hemin complex and, more importantly, >1.5-fold more active than the corresponding native peroxidase (horseradish peroxidase) when considering a single catalytic center. This unique performance originates in a series of gradual improvements, thanks to an accurate selection and arrangement of the different components of the CPDzyme, in order to benefit from synergistic interactions between them. The optimized prototype G4-Hemin-KHRRH is efficient and robust as it can be used under a wide range of non-physiologically relevant conditions [organic solvents, high temperature (95 °C), and in a wide range of pH (from 2 to 10)], thus compensating for the shortcomings of the natural enzymes. Our approach thus opens broad prospects for the design of ever more efficient artificial enzymes.
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Affiliation(s)
- Xiaobo Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Dehui Qiu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jielin Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yue Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jiawei Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China.,Laboratoire d'Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Desheng Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yuan Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Mingpan Cheng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - David Monchaud
- Institut de Chimie Moléculaire (ICMUB), CNRS UMR6302, UBFC, 21078 Dijon, France
| | - Jean-Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China.,Laboratoire d'Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
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16
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Zhang J, Maggiolo AO, Alfonzo E, Mao R, Porter NJ, Abney N, Arnold FH. Chemodivergent C(sp 3)-H and C(sp 2)-H Cyanomethylation Using Engineered Carbene Transferases. Nat Catal 2023; 6:152-160. [PMID: 36875868 PMCID: PMC9983643 DOI: 10.1038/s41929-022-00908-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 12/09/2022] [Indexed: 01/21/2023]
Abstract
The ubiquity of C-H bonds presents an attractive opportunity to elaborate and build complexity in organic molecules. Methods for selective functionalization, however, often must differentiate among multiple chemically similar and, in some cases indistinguishable, C-H bonds. An advantage of enzymes is that they can be finely tuned using directed evolution to achieve control over divergent C-H functionalization pathways. Here, we demonstrate engineered enzymes that effect a new-to-nature C-H alkylation with unparalleled selectivity: two complementary carbene C-H transferases derived from a cytochrome P450 from Bacillus megaterium deliver an α-cyanocarbene into the α-amino C(sp3)-H bonds or the ortho-arene C(sp2)-H bonds of N-substituted arenes. These two transformations proceed via different mechanisms, yet only minimal changes to the protein scaffold (nine mutations, less than 2% of the sequence) were needed to adjust the enzyme's control over the site-selectivity of cyanomethylation. The X-ray crystal structure of the selective C(sp3)-H alkylase, P411-PFA, reveals an unprecedented helical disruption which alters the shape and electrostatics in the enzyme active site. Overall, this work demonstrates the advantages of enzymes as C-H functionalization catalysts for divergent molecular derivatization.
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Affiliation(s)
- Juner Zhang
- Division of Chemistry and Chemical Engineering, California Institute of Technology; Pasadena, California, United States
| | - Ailiena O. Maggiolo
- Division of Chemistry and Chemical Engineering, California Institute of Technology; Pasadena, California, United States
| | - Edwin Alfonzo
- Division of Chemistry and Chemical Engineering, California Institute of Technology; Pasadena, California, United States
| | - Runze Mao
- Division of Chemistry and Chemical Engineering, California Institute of Technology; Pasadena, California, United States
| | - Nicholas J. Porter
- Division of Chemistry and Chemical Engineering, California Institute of Technology; Pasadena, California, United States
| | - Nayla Abney
- Division of Chemistry and Chemical Engineering, California Institute of Technology; Pasadena, California, United States
- Present address: Department of Bioengineering, Stanford University; Stanford, California, United States
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology; Pasadena, California, United States
- Division of Biology and Bioengineering, California Institute of Technology; Pasadena, California, United States
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17
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Zhang Y, Ma L, Su P, Huang L, Gao W. Cytochrome P450s in plant terpenoid biosynthesis: discovery, characterization and metabolic engineering. Crit Rev Biotechnol 2023; 43:1-21. [PMID: 34865579 DOI: 10.1080/07388551.2021.2003292] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
As the largest family of natural products, terpenoids play valuable roles in medicine, agriculture, cosmetics and food. However, the traditional methods that rely on direct extraction from the original plants not only produce low yields, but also result in waste of resources, and are not applicable at all to endangered species. Modern heterologous biosynthesis is considered a promising, efficient, and sustainable production method, but it relies on the premise of a complete analysis of the biosynthetic pathway of terpenoids, especially the functionalization processes involving downstream cytochrome P450s. In this review, we systematically introduce the biotech approaches used to discover and characterize plant terpenoid-related P450s in recent years. In addition, we propose corresponding metabolic engineering approaches to increase the effective expression of P450 and improve the yield of terpenoids, and also elaborate on metabolic engineering strategies and examples of heterologous biosynthesis of terpenoids in Saccharomyces cerevisiae and plant hosts. Finally, we provide perspectives for the biotech approaches to be developed for future research on terpenoid-related P450.
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Affiliation(s)
- Yifeng Zhang
- Beijing Shijitan Hospital, Capital Medical University, Beijing, China.,School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Lin Ma
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Ping Su
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida, USA
| | - Luqi Huang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing, China
| | - Wei Gao
- Beijing Shijitan Hospital, Capital Medical University, Beijing, China.,School of Traditional Chinese Medicine, Capital Medical University, Beijing, China.,Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, China
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18
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Ren Z, Musaev DG, Davies HML. Key Selectivity Controlling Elements in Rhodium-Catalyzed C–H Functionalization with Donor/Acceptor Carbenes. ACS Catal 2022. [DOI: 10.1021/acscatal.2c04490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhi Ren
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
- College of Pharmacy, Shenzhen Technology University, 3002 Lantian Road, Shenzhen, Guangdong, China 518118
| | - Djamaladdin G. Musaev
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
- Cherry L. Emerson Center for Scientific Computation, Emory University, 1521 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Huw M. L. Davies
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
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19
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Nguyen T, Sreekumar S, Wang S, Jiang Q, Montel F, Buono F. Enantioselective Synthesis of trans-Disubstituted Cyclopropyltrifluoroborate Building Blocks through Ru-Catalyzed Cyclopropanation. Org Process Res Dev 2022. [DOI: 10.1021/acs.oprd.2c00265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Thach Nguyen
- Chemical Development, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877-0378, United States
| | - Sanil Sreekumar
- Chemical Development, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877-0378, United States
| | - Shuai Wang
- Chemical Development, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877-0378, United States
| | - Qi Jiang
- Material and Analytical Sciences, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877-0378, United States
| | - Florian Montel
- Discovery Research, Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, 65 Birkendorfer Strasse, Biberach an der Riss 88400, Germany
| | - Frederic Buono
- Chemical Development, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877-0378, United States
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20
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Thomson RES, D'Cunha SA, Hayes MA, Gillam EMJ. Use of engineered cytochromes P450 for accelerating drug discovery and development. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2022; 95:195-252. [PMID: 35953156 DOI: 10.1016/bs.apha.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Numerous steps in drug development, including the generation of authentic metabolites and late-stage functionalization of candidates, necessitate the modification of often complex molecules, such as natural products. While it can be challenging to make the required regio- and stereoselective alterations to a molecule using purely chemical catalysis, enzymes can introduce changes to complex molecules with a high degree of stereo- and regioselectivity. Cytochrome P450 enzymes are biocatalysts of unequalled versatility, capable of regio- and stereoselective functionalization of unactivated CH bonds by monooxygenation. Collectively they catalyze over 60 different biotransformations on structurally and functionally diverse organic molecules, including natural products, drugs, steroids, organic acids and other lipophilic molecules. This catalytic versatility and substrate range makes them likely candidates for application as potential biocatalysts for industrial chemistry. However, several aspects of the P450 catalytic cycle and other characteristics have limited their implementation to date in industry, including: their lability at elevated temperature, in the presence of solvents, and over lengthy incubation times; the typically low efficiency with which they metabolize non-natural substrates; and their lack of specificity for a single metabolic pathway. Protein engineering by rational design or directed evolution provides a way to engineer P450s for industrial use. Here we review the progress made to date toward engineering the properties of P450s, especially eukaryotic forms, for industrial application, and including the recent expansion of their catalytic repertoire to include non-natural reactions.
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Affiliation(s)
- Raine E S Thomson
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Stephlina A D'Cunha
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Martin A Hayes
- Compound Synthesis and Management, Discovery Sciences, BioPharmaceuticals R&D AstraZeneca, Mölndal, Sweden
| | - Elizabeth M J Gillam
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
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21
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Zhao Q, Yao QY, Zhang YJ, Xu T, Zhang J, Chen X. Selective Cyclopropanation/Aziridination of Olefins Catalyzed by Bis(pyrazolyl)borate Cu(I) Complexes. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Qianyi Zhao
- Henan Normal University School of Chemistry and Chemical Engineering Henan Key Laboratory of Boron Chemistry and Advanced Energy Materials Jianshe Road 453007 Xinxiang CHINA
| | - Qiu-Yue Yao
- Henan Normal University School of Chemistry and Chemical Engineering Henan Key Laboratory of Boron Chemistry and Advanced Energy Materials CHINA
| | - Yan-Jiao Zhang
- Henan Normal University School of Chemistry and Chemical Engineering Henan Key Laboratory of Boron Chemistry and Advanced Energy Materials CHINA
| | - Ting Xu
- Henan Normal University School of Chemistry and Chemical Engineering Henan Key Laboratory of Boron Chemistry and Advanced Energy Materials CHINA
| | - Jie Zhang
- Henan Normal University School of Chemistry and Chemical Engineering Henan Key Laboratory of Boron Chemistry and Advanced Energy Materials CHINA
| | - Xuenian Chen
- Henan Normal University School of Chemistry and Chemical Engineering Henan Key Laboratory of Boron Chemistry and Advanced Energy Materials CHINA
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22
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Gorantla SMNVT, Mondal K. The Labile Nature of Air Stable Ni(II)/Ni(0)-phosphine/Olefin Catalysts/Intermediates: EDA-NOCV Analysis. Chem Asian J 2022; 17:e202200572. [PMID: 35927965 DOI: 10.1002/asia.202200572] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/28/2022] [Indexed: 11/06/2022]
Abstract
Metal ions-based inorganic-organic hybrid composites are often reported acting as good to excellent catalysts with various substrate scopes under milder reaction conditions. The active catalyst of a catalytic cycle is sometimes proposed to be a short-lived reactive intermediate species. A three coordinate (L-Me)Ni(II) intermediate species [L-Me = O 2 N donor dianionic ligand] can bind with short-lived carbene-ester ligands to produce four coordinate Ni(II) species which can act as carbene transfer intermediates under suitable reaction conditions for C-H functionalization or cyclopropanation reactions. The dissociation of phosphine (PPh 3 ) from the Ni(II) centre of (L-Me)Ni(II)(PPh 3 ) ( 1a ) and binding of short lived carbene esters (:CR 1 -CO 2 R 2 ; R 1 = H, Ph; R 2 = aliphatic group; 2-4 and other carbenes; 5-10 ) to Ni(II) rationalize the phenomenon in solution. Air stable Ni(0)-olefin complexes/intermediates ( 12-18 ) have recently been shown to mediate a variety of organic transformations. This analysis will further help organic/organometallic chemists to rationalize the design and synthesis of future catalysts for organic transformation. EDA-NOCV calculations have been performed to shed light on the stability and bonding of those species. Additionally, our analysis provides a proper reason why the analogous (L-Me)Pd-PPh 3 complex ( 1b ) does not dissociate in solution and hence, a similar catalytic product has not been isolated from identical reaction conditions. The stability and the labile nature of Ni(II/0) complexes has been investigated by state-of-the-art EDA-NOCV analyses.
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Affiliation(s)
| | - Kartik Mondal
- Indiana Institute Of Technology Madras, Chemistry, Department of Chemistry, IIT Madras, 600036, Chennai, INDIA
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23
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Hakey BM, Leary DC, Martinez JC, Darmon JM, Akhmedov NG, Petersen JL, Milsmann C. Carbene Transfer from a Pyridine Dipyrrolide Iron–Carbene Complex: Reversible Migration of a Diphenylcarbene Ligand into an Iron–Nitrogen Bond. Organometallics 2022. [DOI: 10.1021/acs.organomet.2c00260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Brett M. Hakey
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Dylan C. Leary
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Jordan C. Martinez
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Jonathan M. Darmon
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Novruz G. Akhmedov
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Jeffrey L. Petersen
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Carsten Milsmann
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
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24
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Van Stappen C, Deng Y, Liu Y, Heidari H, Wang JX, Zhou Y, Ledray AP, Lu Y. Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere. Chem Rev 2022; 122:11974-12045. [PMID: 35816578 DOI: 10.1021/acs.chemrev.2c00106] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.
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Affiliation(s)
- Casey Van Stappen
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yunling Deng
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yiwei Liu
- Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Hirbod Heidari
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Jing-Xiang Wang
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yu Zhou
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Aaron P Ledray
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States.,Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
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25
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Liu Y, Lai KL, Vong K. Transition Metal Scaffolds Used To Bring New‐to‐Nature Reactions into Biological Systems. Eur J Inorg Chem 2022. [DOI: 10.1002/ejic.202200215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yifei Liu
- Department of Chemistry The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon Hong Kong China
| | - Ka Lun Lai
- Department of Chemistry The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon Hong Kong China
| | - Kenward Vong
- Department of Chemistry The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon Hong Kong China
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26
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Balhara R, Jindal G. Does an Enol Pathway Preclude High Stereoselectivity in Iron-Catalyzed Indole C-H Functionalization via Carbene Insertion? J Org Chem 2022; 87:7919-7933. [PMID: 35652604 DOI: 10.1021/acs.joc.2c00573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
C-H functionalization of indoles via Fe carbenoids presents an attractive strategy to obtain biologically important structural motifs. However, obtaining good stereoselectivity with Fe has been a significant challenge. It is unclear whether the low selectivity is due to a radical pathway or an ionic mechanism involving metal-free species. We therefore present a density functional theory (DFT) study of indole alkylation with diazoacetates catalyzed by Fe(ClO4)TMEDA/spirobisoxazoline and myoglobin. We explore three mechanistic pathways: nucleophilic, radical, and oxocarbenium routes. The nucleophilic pathway is the most feasible with the formation of an enol species that tautomerizes to furnish the alkylated indole. While this mechanism is routinely proposed, the stereochemical model has been conspicuously absent until now. We show that the conventionally invoked enol pathway is not responsible for the low enantiomeric excess. The enol intermediate can stay coordinated to the catalyst via different binding sites placing the enol in proximity to the chiral environment and affecting the stereoselective proton transfer. Both the binding strength and the chiral environment are crucial for obtaining high selectivity. Our study provides the much needed insights for the modest-low selectivities of Fe systems and could help in expediting the discovery of an efficient catalytic system. These mechanistic underpinnings could also be applicable to other metal (Rh, Pd, Cu, etc.)-catalyzed X-H insertion reactions.
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Affiliation(s)
- Reena Balhara
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Garima Jindal
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
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27
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Maity B, Taher M, Mazumdar S, Ueno T. Artificial metalloenzymes based on protein assembly. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2022.214593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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28
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Rocha RA, Speight RE, Scott C. Engineering Enzyme Properties for Improved Biocatalytic Processes in Batch and Continuous Flow. Org Process Res Dev 2022. [DOI: 10.1021/acs.oprd.1c00424] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Raquel A. Rocha
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, Queensland 4000, Australia
- CSIRO Synthetic Biology Future Science Platform, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT 2601, Australia
| | - Robert E. Speight
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, Queensland 4000, Australia
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, Queensland 4000, Australia
| | - Colin Scott
- CSIRO Synthetic Biology Future Science Platform, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT 2601, Australia
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29
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Hakey BM, Leary DC, Xiong J, Harris CF, Darmon JM, Petersen JL, Berry JF, Guo Y, Milsmann C. High Magnetic Anisotropy of a Square-Planar Iron-Carbene Complex. Inorg Chem 2021; 60:18575-18588. [PMID: 34431660 PMCID: PMC9106389 DOI: 10.1021/acs.inorgchem.1c01860] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Among Earth-abundant catalyst systems, iron-carbene intermediates that perform C-C bond forming reactions such as cyclopropanation of olefins and C-H functionalization via carbene insertion are rare. Detailed descriptions of the possible electronic structures for iron-carbene bonds are imperative to obtain better mechanistic insights and enable rational catalyst design. Here, we report the first square-planar iron-carbene complex (MesPDPPh)Fe(CPh2), where [MesPDPPh]2- is the doubly deprotonated form of [2,6-bis(5-(2,4,6-trimethylphenyl)-3-phenyl-1H-pyrrol-2-yl)pyridine]. The compound was prepared via reaction of the disubstituted diazoalkane N2CPh2 with (MesPDPPh)Fe(thf) and represents a rare example of a structurally characterized, paramagnetic iron-carbene complex. Temperature-dependent magnetic susceptibility measurements and applied-field Mössbauer spectroscopic studies revealed an orbitally near-degenerate S = 1 ground state with large unquenched orbital angular momentum resulting in high magnetic anisotropy. Spin-Hamiltonian analysis indicated that this S = 1 spin system has uniaxial magnetic properties arising from a ground MS = ±1 non-Kramers doublet that is well-separated from the MS = 0 sublevel due to very large axial zero-field splitting (D = -195 cm-1, E/D = 0.02 estimated from magnetic susceptibility data). This remarkable electronic structure gives rise to a very large, positive magnetic hyperfine field of more than +60 T for the 57Fe nucleus along the easy magnetization axis observed by Mössbauer spectroscopy. Computational analysis with complete active space self-consistent field (CASSCF) calculations provides a detailed electronic structure analysis and confirms that (MesPDPPh)Fe(CPh2) exhibits a multiconfigurational ground state. The majority contribution originates from a configuration best described as a singlet carbene coordinated to an intermediate-spin FeII center with a (dxy)2{(dxz),(dz2)}3(dyz)1(dx2-y2)0 configuration featuring near-degenerate dxz and dz2 orbitals.
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Affiliation(s)
- Brett M Hakey
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Dylan C Leary
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Jin Xiong
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Caleb F Harris
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Jonathan M Darmon
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Jeffrey L Petersen
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - John F Berry
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Carsten Milsmann
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
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30
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Abstract
Biocatalysis has an enormous impact on chemical synthesis. The waves in which biocatalysis has developed, and in doing so changed our perception of what organic chemistry is, were reviewed 20 and 10 years ago. Here we review the consequences of these waves of development. Nowadays, hydrolases are widely used on an industrial scale for the benign synthesis of commodity and bulk chemicals and are fully developed. In addition, further enzyme classes are gaining ever increasing interest. Particularly, enzymes catalysing selective C-C-bond formation reactions and enzymes catalysing selective oxidation and reduction reactions are solving long-standing synthetic challenges in organic chemistry. Combined efforts from molecular biology, systems biology, organic chemistry and chemical engineering will establish a whole new toolbox for chemistry. Recent developments are critically reviewed.
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Affiliation(s)
- Ulf Hanefeld
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, The Netherlands.
| | - Frank Hollmann
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, The Netherlands.
| | - Caroline E Paul
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, The Netherlands.
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31
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Directed evolution approaches for optogenetic tool development. Biochem Soc Trans 2021; 49:2737-2748. [PMID: 34783342 DOI: 10.1042/bst20210700] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/16/2021] [Accepted: 10/21/2021] [Indexed: 12/30/2022]
Abstract
Photoswitchable proteins enable specific molecular events occurring in complex biological settings to be probed in a rapid and reversible fashion. Recent progress in the development of photoswitchable proteins as components of optogenetic tools has been greatly facilitated by directed evolution approaches in vitro, in bacteria, or in yeast. We review these developments and suggest future directions for this rapidly advancing field.
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32
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Stucki A, Vallapurackal J, Ward TR, Dittrich PS. Droplet Microfluidics and Directed Evolution of Enzymes: An Intertwined Journey. Angew Chem Int Ed Engl 2021; 60:24368-24387. [PMID: 33539653 PMCID: PMC8596820 DOI: 10.1002/anie.202016154] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Indexed: 12/12/2022]
Abstract
Evolution is essential to the generation of complexity and ultimately life. It relies on the propagation of the properties, traits, and characteristics that allow an organism to survive in a challenging environment. It is evolution that shaped our world over about four billion years by slow and iterative adaptation. While natural evolution based on selection is slow and gradual, directed evolution allows the fast and streamlined optimization of a phenotype under selective conditions. The potential of directed evolution for the discovery and optimization of enzymes is mostly limited by the throughput of the tools and methods available for screening. Over the past twenty years, versatile tools based on droplet microfluidics have been developed to address the need for higher throughput. In this Review, we provide a chronological overview of the intertwined development of microfluidics droplet-based compartmentalization methods and in vivo directed evolution of enzymes.
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Affiliation(s)
- Ariane Stucki
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26CH-4058BaselSwitzerland
- National Competence Center in Research (NCCR)Molecular Systems EngineeringBaselSwitzerland
| | - Jaicy Vallapurackal
- Department of ChemistryUniversity of BaselMattenstrasse 24aCH-4058BaselSwitzerland
- National Competence Center in Research (NCCR)Molecular Systems EngineeringBaselSwitzerland
| | - Thomas R. Ward
- Department of ChemistryUniversity of BaselMattenstrasse 24aCH-4058BaselSwitzerland
- National Competence Center in Research (NCCR)Molecular Systems EngineeringBaselSwitzerland
| | - Petra S. Dittrich
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26CH-4058BaselSwitzerland
- National Competence Center in Research (NCCR)Molecular Systems EngineeringBaselSwitzerland
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33
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Ospina F, Schülke KH, Hammer SC. Biocatalytic Alkylation Chemistry: Building Molecular Complexity with High Selectivity. Chempluschem 2021; 87:e202100454. [PMID: 34821073 DOI: 10.1002/cplu.202100454] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/05/2021] [Indexed: 12/28/2022]
Abstract
Biocatalysis has traditionally been viewed as a field that primarily enables access to chiral centers. This includes the synthesis of chiral alcohols, amines and carbonyl compounds, often through functional group interconversion via hydrolytic or oxidation-reduction reactions. This limitation is partly being overcome by the design and evolution of new enzymes. Here, we provide an overview of a recently thriving research field that we summarize as biocatalytic alkylation chemistry. In the past 3-4 years, numerous new enzymes have been developed that catalyze sp3 C-C/N/O/S bond formations. These enzymes utilize different mechanisms to generate molecular complexity by coupling simple fragments with high activity and selectivity. In many cases, the engineered enzymes perform reactions that are difficult or impossible to achieve with current small-molecule catalysts such as organocatalysts and transition-metal complexes. This review further highlights that the design of new enzyme function is particularly successful when off-the-shelf synthetic reagents are utilized to access non-natural reactive intermediates. This underscores how biocatalysis is gradually moving to a field that build molecules through selective bond forming reactions.
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Affiliation(s)
- Felipe Ospina
- Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Kai H Schülke
- Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Stephan C Hammer
- Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
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34
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Dual-function enzyme catalysis for enantioselective carbon-nitrogen bond formation. Nat Chem 2021; 13:1166-1172. [PMID: 34663919 DOI: 10.1038/s41557-021-00794-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 08/23/2021] [Indexed: 12/22/2022]
Abstract
Chiral amines can be made by insertion of a carbene into an N-H bond using two-catalyst systems that combine a transition metal-based carbene-transfer catalyst and a chiral proton-transfer catalyst to enforce stereocontrol. Haem proteins can effect carbene N-H insertion, but asymmetric protonation in an active site replete with proton sources is challenging. Here we describe engineered cytochrome P450 enzymes that catalyse carbene N-H insertion to prepare biologically relevant α-amino lactones with high activity and enantioselectivity (up to 32,100 total turnovers, >99% yield and 98% e.e.). These enzymes serve as dual-function catalysts, inducing carbene transfer and promoting the subsequent proton transfer with excellent stereoselectivity in a single active site. Computational studies uncover the detailed mechanism of this new-to-nature enzymatic reaction and explain how active-site residues accelerate this transformation and provide stereocontrol.
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35
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Ren X, Fasan R. Engineered and Artificial Metalloenzymes for Selective C-H Functionalization. CURRENT OPINION IN GREEN AND SUSTAINABLE CHEMISTRY 2021; 31:100494. [PMID: 34395950 PMCID: PMC8357270 DOI: 10.1016/j.cogsc.2021.100494] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The direct functionalization of C-H bonds constitutes a powerful strategy to construct and diversify organic molecules. However, controlling the chemo- and site-selectivity of this transformation in particularly complex molecular settings represents a significant challenge. Metalloenzymes are ideal platforms for achieving catalyst-controlled selective C-H bond functionalization as their reactivities can be tuned by protein engineering and/or redesign of their cofactor environment. In this review, we highlight recent progress in the development of engineered and artificial metalloenzymes for C-H functionalization, with a focus on biocatalytic strategies for selective C-H oxyfunctionalization and halogenation as well as C-H amination and C-H carbene insertion via abiological nitrene and carbene transfer chemistries. Engineered heme- and non-heme iron dependent enzymes have emerged as promising scaffolds for executing these transformations with high chemo-, regio- and stereocontrol as well as tunable selectivity. These emerging systems and methodologies have expanded the toolbox of sustainable strategies for organic synthesis and created new opportunities for the generation of chiral building blocks, the late-stage C-H functionalization of complex molecules, and the total synthesis of natural products.
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Affiliation(s)
- Xinkun Ren
- Department of Chemistry, University of Rochester, Hutchison Hall, 120 Trustee Rd, Rochester NY 14627, USA
| | - Rudi Fasan
- Department of Chemistry, University of Rochester, Hutchison Hall, 120 Trustee Rd, Rochester NY 14627, USA
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36
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Ma L, Li F, Zhang X, Chen H, Huang Q, Su J, Liu X, Sun T, Fang B, Liu K, Tang D, Wu D, Zhang W, Du L, Li S. Development of MEMS directed evolution strategy for multiplied throughput and convergent evolution of cytochrome P450 enzymes. SCIENCE CHINA-LIFE SCIENCES 2021; 65:550-560. [PMID: 34480693 DOI: 10.1007/s11427-021-1994-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/16/2021] [Indexed: 11/26/2022]
Abstract
Directed evolution (DE) inspired by natural evolution (NE) has been achieving tremendous successes in protein/enzyme engineering. However, the conventional "one-protein-for-one-task" DE cannot match the "multi-proteins-for-multi-tasks" NE in terms of screening throughput and efficiency, thus often failing to meet the fast-growing demands for biocatalysts with desired properties. In this study, we design a novel "multi-enzymes-for-multi-substrates" (MEMS) DE model and establish the proof-of-concept by running a NE-mimicking and higher-throughput screening on the basis of "two-P450s-against-seven-substrates" (2P×7S) in one pot. With the multiplied throughput and improved hit rate, we witness a series of convergent evolution events of the two archetypal cytochrome P450 enzymes (P450 BM3 and P450cam) in laboratory. It is anticipated that the new strategy of MEMS DE will find broader application for a larger repertoire of enzymes in the future. Furthermore, structural and substrate docking analysis of the two functionally convergent P450 variants provide important insights into how distinct P450 active-sites can reach a common catalytic goal.
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Affiliation(s)
- Li Ma
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Fengwei Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xingwang Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Hui Chen
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Qian Huang
- College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Jing Su
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Xiaohui Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Tianjian Sun
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Bo Fang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Kun Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Dandan Tang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Dalei Wu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Wei Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Lei Du
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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37
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Dewey JA, Azizi SA, Lu V, Dickinson BC. A System for the Evolution of Protein-Protein Interaction Inducers. ACS Synth Biol 2021; 10:2096-2110. [PMID: 34319091 DOI: 10.1021/acssynbio.1c00276] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Molecules that induce interactions between proteins, often referred to as "molecular glues", are increasingly recognized as important therapeutic modalities and as entry points for rewiring cellular signaling networks. Here, we report a new PACE-based method to rapidly select and evolve molecules that mediate interactions between otherwise noninteracting proteins: rapid evolution of protein-protein interaction glues (rePPI-G). By leveraging proximity-dependent split RNA polymerase-based biosensors, we developed E. coli-based detection and selection systems that drive gene expression outputs only when interactions between target proteins are induced. We then validated the system using engineered bivalent molecular glues, showing that rePPI-G robustly selects for molecules that induce the target interaction. Proof-of-concept evolutions demonstrated that rePPI-G reduces the "hook effect" of the engineered molecular glues, due at least in part to tuning the interaction affinities of each individual component of the bifunctional molecule. Altogether, this work validates rePPI-G as a continuous, phage-based evolutionary technology for optimizing molecular glues, providing a strategy for developing molecules that reprogram protein-protein interactions.
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Affiliation(s)
- Jeffrey A. Dewey
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60615, United States
| | - Saara-Anne Azizi
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60615, United States
| | - Vivian Lu
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60615, United States
| | - Bryan C. Dickinson
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60615, United States
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38
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Abstract
The Pd-catalyzed carbon-carbon bond formation pioneered by Heck in 1969 has dominated medicinal chemistry development for the ensuing fifty years. As the demand for more complex three-dimensional active pharmaceuticals continues to increase, preparative enzyme-mediated assembly, by virtue of its exquisite selectivity and sustainable nature, is poised to provide a practical and affordable alternative for accessing such compounds. In this minireview, we summarize recent state-of-the-art developments in practical enzyme-mediated assembly of carbocycles. When appropriate, background information on the enzymatic transformation is provided and challenges and/or limitations are also highlighted.
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Affiliation(s)
- Weijin Wang
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Douglass F Taber
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Hans Renata
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
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39
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Wang Y, Xue P, Cao M, Yu T, Lane ST, Zhao H. Directed Evolution: Methodologies and Applications. Chem Rev 2021; 121:12384-12444. [PMID: 34297541 DOI: 10.1021/acs.chemrev.1c00260] [Citation(s) in RCA: 196] [Impact Index Per Article: 65.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Directed evolution aims to expedite the natural evolution process of biological molecules and systems in a test tube through iterative rounds of gene diversifications and library screening/selection. It has become one of the most powerful and widespread tools for engineering improved or novel functions in proteins, metabolic pathways, and even whole genomes. This review describes the commonly used gene diversification strategies, screening/selection methods, and recently developed continuous evolution strategies for directed evolution. Moreover, we highlight some representative applications of directed evolution in engineering nucleic acids, proteins, pathways, genetic circuits, viruses, and whole cells. Finally, we discuss the challenges and future perspectives in directed evolution.
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Affiliation(s)
- Yajie Wang
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Pu Xue
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Mingfeng Cao
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Tianhao Yu
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Stephan T Lane
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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40
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Stucki A, Vallapurackal J, Ward TR, Dittrich PS. Droplet Microfluidics and Directed Evolution of Enzymes: An Intertwined Journey. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016154] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Ariane Stucki
- Department of Biosystems Science and Engineering ETH Zurich Mattenstrasse 26 CH-4058 Basel Switzerland
- National Competence Center in Research (NCCR) Molecular Systems Engineering Basel Switzerland
| | - Jaicy Vallapurackal
- Department of Chemistry University of Basel Mattenstrasse 24a CH-4058 Basel Switzerland
- National Competence Center in Research (NCCR) Molecular Systems Engineering Basel Switzerland
| | - Thomas R. Ward
- Department of Chemistry University of Basel Mattenstrasse 24a CH-4058 Basel Switzerland
- National Competence Center in Research (NCCR) Molecular Systems Engineering Basel Switzerland
| | - Petra S. Dittrich
- Department of Biosystems Science and Engineering ETH Zurich Mattenstrasse 26 CH-4058 Basel Switzerland
- National Competence Center in Research (NCCR) Molecular Systems Engineering Basel Switzerland
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41
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Roelfes G. Repurposed and artificial heme enzymes for cyclopropanation reactions. J Inorg Biochem 2021; 222:111523. [PMID: 34217039 DOI: 10.1016/j.jinorgbio.2021.111523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 06/10/2021] [Accepted: 06/16/2021] [Indexed: 10/21/2022]
Abstract
Heme enzymes are some of the most versatile catalysts in nature. In recent years it has been found that they can also catalyze reactions for which there are no equivalents in nature. This development has been driven by the abiological catalytic reactivity reported for bio-inspired and biomimetic iron porphyrin complexes. This review focuss es on heme enzymes for catalysis of cyclopropanation reactions. The two most important approaches used to create enzymes for cyclopropanation are repurposing of heme enzymes and the various strategies used to improve these enzymes such as mutagenesis and heme replacement, and artificial heme enzymes. These strategies are introduced and compared. Moreover, lessons learned with regard to mechanism and design principles are discussed.
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Affiliation(s)
- Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, the Netherlands.
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42
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Liu Z, Arnold FH. New-to-nature chemistry from old protein machinery: carbene and nitrene transferases. Curr Opin Biotechnol 2021; 69:43-51. [PMID: 33370622 PMCID: PMC8225731 DOI: 10.1016/j.copbio.2020.12.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 11/03/2020] [Accepted: 12/03/2020] [Indexed: 12/19/2022]
Abstract
Hemoprotein-catalyzed carbene and nitrene transformations have emerged as powerful tools for constructing complex molecules; they also nicely illustrate how new protein catalysts can emerge, evolve and diversify. These laboratory-invented enzymes exploit the ability of proteins to tame highly reactive carbene and nitrene species and direct their fates with high selectivity. New-to-nature carbene and nitrene transferases catalyze many useful reactions, including some that have no precedent using chemical methods. Here we cover recent advances in this field, including alkyne cyclopropenation, arene cyclopropanation, carbene CH insertion, intramolecular nitrene CH insertion, alkene aminohydroxylation, and primary amination. For such transformations, biocatalysts have exceeded the performance of reported small-molecule catalysts in terms of selectivity and catalyst turnovers. Finally, we offer our thoughts on using these new enzymatic reactions in chemical synthesis, integrating them into biological pathways and chemo-enzymatic cascades, and on their current limitations.
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Affiliation(s)
- Zhen Liu
- Division of Chemistry and Chemical Engineering, 210-41, California Institute of Technology, 1200 East California Blvd, Pasadena, CA 91125, USA
| | - Frances H Arnold
- Division of Chemistry and Chemical Engineering, 210-41, California Institute of Technology, 1200 East California Blvd, Pasadena, CA 91125, USA.
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43
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Sar S, Das R, Sen S. Blue LED Induced Manganese (I) Catalysed Direct C2−H Activation of Pyrroles with Aryl Diazoesters. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202100305] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Saibal Sar
- Department of Chemistry, School of Natural Sciences Shiv Nadar University, Dadri, Chithera, Gautam Budh Nagar Uttar Pradesh 201314 India
| | - Ranajit Das
- Department of Chemistry, School of Natural Sciences Shiv Nadar University, Dadri, Chithera, Gautam Budh Nagar Uttar Pradesh 201314 India
| | - Subhabrata Sen
- Department of Chemistry, School of Natural Sciences Shiv Nadar University, Dadri, Chithera, Gautam Budh Nagar Uttar Pradesh 201314 India
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44
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Balhara R, Chatterjee R, Jindal G. A computational approach to understand the role of metals and axial ligands in artificial heme enzyme catalyzed C-H insertion. Phys Chem Chem Phys 2021; 23:9500-9511. [PMID: 33885085 DOI: 10.1039/d1cp00412c] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Engineered heme enzymes such as myoglobin and cytochrome P450s metalloproteins are gaining widespread importance due to their efficiency in catalyzing non-natural reactions. In a recent strategy, the naturally occurring Fe metal in the heme unit was replaced with non-native metals such as Ir, Rh, Co, Cu, etc., and axial ligands to generate artificial metalloenzymes. Determining the best metal-ligand for a chemical transformation is not a trivial task. Here we demonstrate how computational approaches can be used in deciding the best metal-ligand combination which would be highly beneficial in designing new enzymes as well as small molecule catalysts. We have used Density Functional Theory (DFT) to shed light on the enhanced reactivity of an Ir system with varying axial ligands. We look at the insertion of a carbene group generated from diazo precursors via N2 extrusion into a C-H bond. For both Ir(Me) and Fe systems, the first step, i.e., N2 extrusion is the rate determining step. Strikingly, neither the better ligand overlap with 5d orbitals on Ir nor the electrophilicity on the carbene centre play a significant role. A comparison of Fe and Ir systems reveals that a lower distortion in the Ir(Me)-porphyrin on moving from the reactant to the transition state renders it catalytically more active. We notice that for both metal porphyrins, the free energy barriers are affected by axial ligand substitution. Further, for Fe porphyrin, the axial ligand also changes the preferred spin state. We show that for the carbene insertion into the C-H bond, Fe porphyrin systems undergo a stepwise HAT (hydrogen atom transfer) instead of a concerted hydride transfer process. Importantly, we find that the substitution of the axial Me ligand on Ir to imidazole or chloride, or without an axial substitution changes the rate determining step of the reaction. Therefore, an optimum ligand that can balance the barriers for both steps of the catalytic cycle is essential. We subsequently used the QM cluster approach to delineate the protein environment's role and mutations in improving the catalytic activity of the Ir(Me) system.
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Affiliation(s)
- Reena Balhara
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India.
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45
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Yang Y, Arnold FH. Navigating the Unnatural Reaction Space: Directed Evolution of Heme Proteins for Selective Carbene and Nitrene Transfer. Acc Chem Res 2021; 54:1209-1225. [PMID: 33491448 PMCID: PMC7931446 DOI: 10.1021/acs.accounts.0c00591] [Citation(s) in RCA: 119] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Despite the astonishing diversity of naturally
occurring biocatalytic
processes, enzymes do not catalyze many of the transformations favored
by synthetic chemists. Either nature does not care about the specific
products, or if she does, she has adopted a different synthetic strategy.
In many cases, the appropriate reagents used by synthetic chemists
are not readily accessible to biological systems. Here, we discuss
our efforts to expand the catalytic repertoire of enzymes to encompass
powerful reactions previously known only in small-molecule catalysis:
formation and transfer of reactive carbene and nitrene intermediates
leading to a broad range of products, including products with bonds
not known in biology. In light of the structural similarity of iron
carbene (Fe=C(R1)(R2)) and iron nitrene
(Fe=NR) to the iron oxo (Fe=O) intermediate involved
in cytochrome P450-catalyzed oxidation, we have used synthetic carbene
and nitrene precursors that biological systems have not encountered
and repurposed P450s to catalyze reactions that are not known in the
natural world. The resulting protein catalysts are fully genetically
encoded and function in intact microbial cells or cell-free lysates,
where their performance can be improved and optimized by directed
evolution. By leveraging the catalytic promiscuity of P450 enzymes,
we evolved a range of carbene and nitrene transferases exhibiting
excellent activity toward these new-to-nature reactions. Since our
initial report in 2012, a number of other heme proteins including
myoglobins, protoglobins, and cytochromes c have
also been found and engineered to promote unnatural carbene and nitrene
transfer. Due to the altered active-site environments, these heme
proteins often displayed complementary activities and selectivities
to P450s. Using wild-type and engineered heme proteins, we and
others have
described a range of selective carbene transfer reactions, including
cyclopropanation, cyclopropenation, Si–H insertion, B–H
insertion, and C–H insertion. Similarly, a variety of asymmetric
nitrene transfer processes including aziridination, sulfide imidation,
C–H amidation, and, most recently, C–H amination have
been demonstrated. The scopes of these biocatalytic carbene and nitrene
transfer reactions are often complementary to the state-of-the-art
processes based on small-molecule transition-metal catalysts, making
engineered biocatalysts a valuable addition to the synthetic chemist’s
toolbox. Moreover, enabled by the exquisite regio- and stereocontrol
imposed by the enzyme catalyst, this biocatalytic platform provides
an exciting opportunity to address challenging problems in modern
synthetic chemistry and selective catalysis, including ones that have
eluded synthetic chemists for decades.
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Affiliation(s)
- Yang Yang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 210-41, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 210-41, 1200 East California Boulevard, Pasadena, California 91125, United States
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46
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Bahukhandi SB, Jana S, Koenigs RM. Brønsted acid‐catalyzed Reactions of Unprotected
N
‐heterocycles with Aryl/Aryl Diazoalkanes. ASIAN J ORG CHEM 2021. [DOI: 10.1002/ajoc.202000709] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | - Sripati Jana
- Institute of Organic Chemistry RWTH Aachen University Landoltweg 1 D-52074 Aachen Germany
| | - Rene M. Koenigs
- Institute of Organic Chemistry RWTH Aachen University Landoltweg 1 D-52074 Aachen Germany
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47
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Vong K, Nasibullin I, Tanaka K. Exploring and Adapting the Molecular Selectivity of Artificial Metalloenzymes. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200316] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Kenward Vong
- Biofunctional Synthetic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
- GlycoTargeting Research Laboratory, RIKEN Baton Zone Program, Wako, Saitama 351-0198, Japan
| | - Igor Nasibullin
- Biofunctional Synthetic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
- Biofunctional Chemistry Laboratory, A. Butlerov Institute of Chemistry, Kazan Federal University, Kazan 420008, Russia
| | - Katsunori Tanaka
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8552, Japan
- Biofunctional Synthetic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
- Biofunctional Chemistry Laboratory, A. Butlerov Institute of Chemistry, Kazan Federal University, Kazan 420008, Russia
- GlycoTargeting Research Laboratory, RIKEN Baton Zone Program, Wako, Saitama 351-0198, Japan
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48
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Erfani A, Zarrintaj P, Seaberg J, Ramsey JD, Aichele CP. Zwitterionic poly(carboxybetaine) microgels for enzyme (chymotrypsin) covalent immobilization with extended stability and activity. J Appl Polym Sci 2021. [DOI: 10.1002/app.50545] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Amir Erfani
- School of Chemical Engineering Oklahoma State University Stillwater Oklahoma USA
| | - Payam Zarrintaj
- School of Chemical Engineering Oklahoma State University Stillwater Oklahoma USA
| | - Joshua Seaberg
- School of Chemical Engineering Oklahoma State University Stillwater Oklahoma USA
| | - Joshua D. Ramsey
- School of Chemical Engineering Oklahoma State University Stillwater Oklahoma USA
| | - Clint P. Aichele
- School of Chemical Engineering Oklahoma State University Stillwater Oklahoma USA
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49
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Li W, Sun W, Li C. Engineered microorganisms and enzymes for efficiently synthesizing plant natural products. Chin J Chem Eng 2021. [DOI: 10.1016/j.cjche.2020.12.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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50
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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]
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