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Elisée E, Ducrot L, Méheust R, Bastard K, Fossey-Jouenne A, Grogan G, Pelletier E, Petit JL, Stam M, de Berardinis V, Zaparucha A, Vallenet D, Vergne-Vaxelaire C. A refined picture of the native amine dehydrogenase family revealed by extensive biodiversity screening. Nat Commun 2024; 15:4933. [PMID: 38858403 PMCID: PMC11164908 DOI: 10.1038/s41467-024-49009-2] [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: 09/21/2023] [Accepted: 05/20/2024] [Indexed: 06/12/2024] Open
Abstract
Native amine dehydrogenases offer sustainable access to chiral amines, so the search for scaffolds capable of converting more diverse carbonyl compounds is required to reach the full potential of this alternative to conventional synthetic reductive aminations. Here we report a multidisciplinary strategy combining bioinformatics, chemoinformatics and biocatalysis to extensively screen billions of sequences in silico and to efficiently find native amine dehydrogenases features using computational approaches. In this way, we achieve a comprehensive overview of the initial native amine dehydrogenase family, extending it from 2,011 to 17,959 sequences, and identify native amine dehydrogenases with non-reported substrate spectra, including hindered carbonyls and ethyl ketones, and accepting methylamine and cyclopropylamine as amine donor. We also present preliminary model-based structural information to inform the design of potential (R)-selective amine dehydrogenases, as native amine dehydrogenases are mostly (S)-selective. This integrated strategy paves the way for expanding the resource of other enzyme families and in highlighting enzymes with original features.
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Affiliation(s)
- Eddy Elisée
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Laurine Ducrot
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Raphaël Méheust
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Karine Bastard
- School of Pharmacy, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, 2006, Australia
| | - Aurélie Fossey-Jouenne
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Gideon Grogan
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Jean-Louis Petit
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Mark Stam
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Véronique de Berardinis
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Anne Zaparucha
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - David Vallenet
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France.
| | - Carine Vergne-Vaxelaire
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France.
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2
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Emmanuel MA, Bender SG, Bilodeau C, Carceller JM, DeHovitz JS, Fu H, Liu Y, Nicholls BT, Ouyang Y, Page CG, Qiao T, Raps FC, Sorigué DR, Sun SZ, Turek-Herman J, Ye Y, Rivas-Souchet A, Cao J, Hyster TK. Photobiocatalytic Strategies for Organic Synthesis. Chem Rev 2023; 123:5459-5520. [PMID: 37115521 PMCID: PMC10905417 DOI: 10.1021/acs.chemrev.2c00767] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Biocatalysis has revolutionized chemical synthesis, providing sustainable methods for preparing various organic molecules. In enzyme-mediated organic synthesis, most reactions involve molecules operating from their ground states. Over the past 25 years, there has been an increased interest in enzymatic processes that utilize electronically excited states accessed through photoexcitation. These photobiocatalytic processes involve a diverse array of reaction mechanisms that are complementary to one another. This comprehensive review will describe the state-of-the-art strategies in photobiocatalysis for organic synthesis until December 2022. Apart from reviewing the relevant literature, a central goal of this review is to delineate the mechanistic differences between the general strategies employed in the field. We will organize this review based on the relationship between the photochemical step and the enzymatic transformations. The review will include mechanistic studies, substrate scopes, and protein optimization strategies. By clearly defining mechanistically-distinct strategies in photobiocatalytic chemistry, we hope to illuminate future synthetic opportunities in the area.
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Affiliation(s)
- Megan A Emmanuel
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Sophie G Bender
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Catherine Bilodeau
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Jose M Carceller
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Institute of Chemical Technology (ITQ), Universitat Politècnica de València, València 46022,Spain
| | - Jacob S DeHovitz
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Haigen Fu
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Yi Liu
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Bryce T Nicholls
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Yao Ouyang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Claire G Page
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Tianzhang Qiao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Felix C Raps
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Damien R Sorigué
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - Shang-Zheng Sun
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Joshua Turek-Herman
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Yuxuan Ye
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Ariadna Rivas-Souchet
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Jingzhe Cao
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Todd K Hyster
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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4
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Cohen B, Lehnherr D, Sezen-Edmonds M, Forstater JH, Frederick MO, Deng L, Ferretti AC, Harper K, Diwan M. Emerging Reaction Technologies in Pharmaceutical Development: Challenges and Opportunities in Electrochemistry, Photochemistry, and Biocatalysis. Chem Eng Res Des 2023. [DOI: 10.1016/j.cherd.2023.02.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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5
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Meyer LE, Hobisch M, Kara S. Process intensification in continuous flow biocatalysis by up and downstream processing strategies. Curr Opin Biotechnol 2022; 78:102835. [PMID: 36332339 DOI: 10.1016/j.copbio.2022.102835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 10/01/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022]
Abstract
In this review, we focus on the holistic continuous enzymatic production and put special emphasis on process intensification by up- and downstream processing in continuous flow biocatalysis. After a brief introduction, we provide an overview of current examples of enzyme immobilization as an upstream process for flow biocatalysis. Thereafter, we provide an overview of unit operations as downstream processing strategies, namely continuous (i) liquid-liquid extraction, (ii) adsorptive downstream processing, and (iii) crystallization and precipitation. Eventually, we present our perspectives on future trends in this research field.
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Affiliation(s)
- Lars-Erik Meyer
- Biocatalysis and Bioprocessing Group, Department of Biological and Chemical Engineering, Aarhus University, Gustav Wieds Vej 10, 8000 Aarhus, Denmark
| | - Markus Hobisch
- Biocatalysis and Bioprocessing Group, Department of Biological and Chemical Engineering, Aarhus University, Gustav Wieds Vej 10, 8000 Aarhus, Denmark
| | - Selin Kara
- Biocatalysis and Bioprocessing Group, Department of Biological and Chemical Engineering, Aarhus University, Gustav Wieds Vej 10, 8000 Aarhus, Denmark; Institute of Technical Chemistry, Leibniz University Hannover, Callinstr. 5, 30167 Hannover, Germany.
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