1
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Huang A, Zhang X, Yang Y, Shi C, Zhang B, Tuo X, Shen P, Jiao X, Zhang N. Biocatalytic Synthesis of Ruxolitinib Intermediate via Engineered Imine Reductase. J Org Chem 2024; 89:11446-11454. [PMID: 39113180 DOI: 10.1021/acs.joc.4c01119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
An enzyme catalyzed strategy for the synthesis of a chiral hydrazine from 3-cyclopentyl-3-oxopropanenitrile 5 and hydrazine hydrate 2 is presented. An imine reductase (IRED) from Streptosporangium roseum was identified to catalyze the reaction between 3-cyclopentyl-3-oxopropanenitrile 5 and hydrazine hydrate 2 to produce trace amounts of (R)-3-cyclopentyl-3-hydrazineylpropanenitrile 4. We employed a 2-fold approach to optimize the catalytic performance of this enzyme. First, a transition state analogue (TSA) model was constructed to illuminate the enzyme-substrate interactions. Subsequently, the Enzyme_design and Funclib methods were utilized to predict mutants for experimental evaluation. Through three rounds of site-directed mutagenesis, site saturation mutagenesis, and combinatorial mutagenesis, we obtained mutant M6 with a yield of 98% and an enantiomeric excess (ee) of 99%. This study presents an effective method for constructing a hydrazine derivative via IRED-catalyzed reductive amination of ketone and hydrazine. Furthermore, it provides a general approach for constructing suitable enzymes, starting from nonreactive enzymes and gradually enhancing their catalytic activity through active site modifications.
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Affiliation(s)
- Aiping Huang
- Center of Biosynthesis Technology, Asymchem Life Science (Tianjin) Co, Ltd, Tianjin 300457, P.R. China
| | - Xuewen Zhang
- Center of Biosynthesis Technology, Asymchem Life Science (Tianjin) Co, Ltd, Tianjin 300457, P.R. China
| | - Yiming Yang
- Center of Biosynthesis Technology, Asymchem Life Science (Tianjin) Co, Ltd, Tianjin 300457, P.R. China
| | - Chengcheng Shi
- Center of Biosynthesis Technology, Asymchem Life Science (Tianjin) Co, Ltd, Tianjin 300457, P.R. China
| | - Bifei Zhang
- Center of Biosynthesis Technology, Asymchem Life Science (Tianjin) Co, Ltd, Tianjin 300457, P.R. China
| | - Xinkun Tuo
- Center of Biosynthesis Technology, Asymchem Life Science (Tianjin) Co, Ltd, Tianjin 300457, P.R. China
| | - Peili Shen
- Center of Biosynthesis Technology, Asymchem Life Science (Tianjin) Co, Ltd, Tianjin 300457, P.R. China
| | - Xuecheng Jiao
- Center of Biosynthesis Technology, Asymchem Life Science (Tianjin) Co, Ltd, Tianjin 300457, P.R. China
| | - Na Zhang
- Center of Biosynthesis Technology, Asymchem Life Science (Tianjin) Co, Ltd, Tianjin 300457, P.R. China
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2
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Roth S, Niese R, Müller M, Hall M. Redox Out of the Box: Catalytic Versatility Across NAD(P)H-Dependent Oxidoreductases. Angew Chem Int Ed Engl 2024; 63:e202314740. [PMID: 37924279 DOI: 10.1002/anie.202314740] [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: 10/01/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/06/2023]
Abstract
The asymmetric reduction of double bonds using NAD(P)H-dependent oxidoreductases has proven to be an efficient tool for the synthesis of important chiral molecules in research and on industrial scale. These enzymes are commercially available in screening kits for the reduction of C=O (ketones), C=C (activated alkenes), or C=N bonds (imines). Recent reports, however, indicate that the ability to accommodate multiple reductase activities on distinct C=X bonds occurs in different enzyme classes, either natively or after mutagenesis. This challenges the common perception of highly selective oxidoreductases for one type of electrophilic substrate. Consideration of this underexplored potential in enzyme screenings and protein engineering campaigns may contribute to the identification of complementary biocatalytic processes for the synthesis of chiral compounds. This review will contribute to a global understanding of the promiscuous behavior of NAD(P)H-dependent oxidoreductases on C=X bond reduction and inspire future discoveries with respect to unconventional biocatalytic routes in asymmetric synthesis.
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Affiliation(s)
- Sebastian Roth
- Institute of Chemistry, University of Graz, Heinrichstrasse 28, 8010, Graz, Austria
| | - Richard Niese
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Michael Müller
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Mélanie Hall
- Institute of Chemistry, University of Graz, Heinrichstrasse 28, 8010, Graz, Austria
- BioHealth, Field of Excellence, University of Graz, 8010, Graz, Austria
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3
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Daniel-Ivad P, Ryan KS. An imine reductase that captures reactive intermediates in the biosynthesis of the indolocarbazole reductasporine. J Biol Chem 2024; 300:105642. [PMID: 38199566 PMCID: PMC10851217 DOI: 10.1016/j.jbc.2024.105642] [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: 09/11/2023] [Revised: 12/21/2023] [Accepted: 12/31/2023] [Indexed: 01/12/2024] Open
Abstract
Imine reductases (IREDs) and reductive aminases have been used in the synthesis of chiral amine products for drug manufacturing; however, little is known about their biological contexts. Here we employ structural studies and site-directed mutagenesis to interrogate the mechanism of the IRED RedE from the biosynthetic pathway to the indolocarbazole natural product reductasporine. Cocrystal structures with the substrate-mimic arcyriaflavin A reveal an extended active site cleft capable of binding two indolocarbazole molecules. Site-directed mutagenesis of a conserved aspartate in the primary binding site reveals a new role for this residue in anchoring the substrate above the NADPH cofactor. Variants targeting the secondary binding site greatly reduce catalytic efficiency, while accumulating oxidized side-products. As indolocarbazole biosynthetic intermediates are susceptible to spontaneous oxidation, we propose the secondary site acts to protect against autooxidation, and the primary site drives catalysis through precise substrate orientation and desolvation effects. The structure of RedE with its extended active site can be the starting point as a new scaffold for engineering IREDs and reductive aminases to intercept large substrates relevant to industrial applications.
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Affiliation(s)
- Phillip Daniel-Ivad
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Katherine S Ryan
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia, Canada.
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4
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Wu K, Yan J, Liu Q, Wang X, Wu P, Cao Y, Lu X, Xu Y, Huang J, Shao L. Computational design of an imine reductase: mechanism-guided stereoselectivity reversion and interface stabilization. Chem Sci 2024; 15:1431-1440. [PMID: 38274081 PMCID: PMC10806680 DOI: 10.1039/d3sc04636b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 12/12/2023] [Indexed: 01/27/2024] Open
Abstract
Imine reductases (IREDs) are important biocatalysts in the asymmetric synthesis of chiral amines. However, a detailed understanding of the stereocontrol mechanism of IRED remains incomplete, making the design of IRED for producing the desired amine enantiomers challenging. In this study, we investigated the stereoselective catalytic mechanism and designed an (R)-stereoselective IRED from Paenibacillus mucilaginosus (PmIR) using pharmaceutically relevant 2-aryl-substituted pyrrolines as substrates. A putative mechanism for controlling stereoselectivity was proposed based on the crucial role of electrostatic interactions in controlling iminium cation orientation and employed to achieve complete inversion of stereoselectivity in PmIR using computational design. The variant PmIR-Re (Q138M/P140M/Y187E/Q190A/D250M/R251N) exhibited opposite (S)-stereoselectivity, with >96% enantiomeric excess (ee) towards tested 2-aryl-substituted pyrrolines. Computational tools were employed to identify stabilizing mutations at the interface between the two subunits. The variant PmIR-6P (P140A/Q190S/R251N/Q217E/A257R/T277M) showed a nearly 5-fold increase in activity and a 12 °C increase in melting temperature. The PmIR-6P successfully produced (R)-2-(2,5-difluorophenyl)-pyrrolidine, a key chiral pharmaceutical intermediate, at a concentration of 400 mM with an ee exceeding 99%. This study provides insight into the stereocontrol elements of IREDs and demonstrates the potential of computational design for tailored stereoselectivity and thermal stability.
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Affiliation(s)
- Kai Wu
- School of Pharmacy, Shanghai University of Medicine & Health Sciences 279 Zhouzhu Highway, Pudong New Area Shanghai 201318 China
| | - Jinrong Yan
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science 333 Longteng Road Shanghai 201620 China
- State Key Laboratory of New Drug and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry 285 Gebaini Rd. Shanghai 200040 China
| | - Qinde Liu
- School of Pharmacy, Shanghai University of Medicine & Health Sciences 279 Zhouzhu Highway, Pudong New Area Shanghai 201318 China
- Shanghai University of Traditional Chinese Medicine 1200 Cailun Road Shanghai 201203 China
| | - Xiaojing Wang
- School of Pharmacy, Shanghai University of Medicine & Health Sciences 279 Zhouzhu Highway, Pudong New Area Shanghai 201318 China
| | - Piaoru Wu
- School of Pharmacy, Shanghai University of Medicine & Health Sciences 279 Zhouzhu Highway, Pudong New Area Shanghai 201318 China
| | - Yiyang Cao
- School of Pharmacy, Shanghai University of Medicine & Health Sciences 279 Zhouzhu Highway, Pudong New Area Shanghai 201318 China
| | - Xiuhong Lu
- School of Pharmacy, Shanghai University of Medicine & Health Sciences 279 Zhouzhu Highway, Pudong New Area Shanghai 201318 China
| | - Yixin Xu
- School of Pharmacy, Shanghai University of Medicine & Health Sciences 279 Zhouzhu Highway, Pudong New Area Shanghai 201318 China
| | - Junhai Huang
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science 333 Longteng Road Shanghai 201620 China
- State Key Laboratory of New Drug and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry 285 Gebaini Rd. Shanghai 200040 China
| | - Lei Shao
- School of Pharmacy, Shanghai University of Medicine & Health Sciences 279 Zhouzhu Highway, Pudong New Area Shanghai 201318 China
- State Key Laboratory of New Drug and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry 285 Gebaini Rd. Shanghai 200040 China
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5
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Yu Y, Rué Casamajo A, Finnigan W, Schnepel C, Barker R, Morrill C, Heath RS, De Maria L, Turner NJ, Scrutton NS. Structure-Based Design of Small Imine Reductase Panels for Target Substrates. ACS Catal 2023; 13:12310-12321. [PMID: 37736118 PMCID: PMC10510103 DOI: 10.1021/acscatal.3c02278] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/20/2023] [Indexed: 09/23/2023]
Abstract
Biocatalysis is important in the discovery, development, and manufacture of pharmaceuticals. However, the identification of enzymes for target transformations of interest requires major screening efforts. Here, we report a structure-based computational workflow to prioritize protein sequences by a score based on predicted activities on substrates, thereby reducing a resource-intensive laboratory-based biocatalyst screening. We selected imine reductases (IREDs) as a class of biocatalysts to illustrate the application of the computational workflow termed IREDFisher. Validation by using published data showed that IREDFisher can retrieve the best enzymes and increase the hit rate by identifying the top 20 ranked sequences. The power of IREDFisher is confirmed by computationally screening 1400 sequences for chosen reductive amination reactions with different levels of complexity. Highly active IREDs were identified by only testing 20 samples in vitro. Our speed test shows that it only takes 90 min to rank 85 sequences from user input and 30 min for the established IREDFisher database containing 591 IRED sequences. IREDFisher is available as a user-friendly web interface (https://enzymeevolver.com/IREDFisher). IREDFisher enables the rapid discovery of IREDs for applications in synthesis and directed evolution studies, with minimal time and resource expenditure. Future use of the workflow with other enzyme families could be implemented following the modification of the workflow scoring function.
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Affiliation(s)
- Yuqi Yu
- Department
of Chemistry, The University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, U.K.
- Augmented
Biologics Discovery & Design, Department of Biologics Engineering, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB21 6GH, U.K.
| | - Arnau Rué Casamajo
- Department
of Chemistry, The University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, U.K.
| | - William Finnigan
- Department
of Chemistry, The University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Christian Schnepel
- Department
of Chemistry, The University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Rhys Barker
- Department
of Chemistry, The University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Charlotte Morrill
- Department
of Chemistry, The University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Rachel S. Heath
- Department
of Chemistry, The University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Leonardo De Maria
- Medicinal
Chemistry, Research and Early Development, Respiratory and Immunology
(RI), BioPharmaceuticals R&D, AstraZeneca, Gothenburg 43150, Sweden
| | - Nicholas J. Turner
- Department
of Chemistry, The University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Nigel S. Scrutton
- Department
of Chemistry, The University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, U.K.
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6
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Li Y, Yue X, Li Z, Huang Z, Chen F. Asymmetric Synthesis of Sterically Hindered 1-Substituted Tetrahydro-β-carbolines Enabled by Imine Reductase: Enzyme Discovery, Protein Engineering, and Reaction Development. Org Lett 2023; 25:1285-1289. [PMID: 36802632 DOI: 10.1021/acs.orglett.3c00147] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
We report the discovery of a new imine reductase (IRED), named AtIRED, by genome mining. Site-saturation mutagenesis on AtIRED generated two single mutants M118'L and P120'G and the double mutant M118'L/P120'G with improved specific activity toward sterically hindered 1-substituted dihydro-β-carbolines. The synthetic potential of these engineered IREDs was showcased by the preparative-scale synthesis of nine chiral 1-substituted tetrahydro-β-carbolines (THβCs), including (S)-1-t-butyl-THβC and (S)-1-t-pentyl-THβC, in 30-87% isolated yields with excellent optical purities (98-99% ee).
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Affiliation(s)
- Yitong Li
- Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, P.R. China
| | - Xiaoping Yue
- Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, P.R. China
| | - Zhining Li
- Department of Chemistry, Engineering Center of Catalysis and Synthesis for Chiral Molecules, Fudan University, Shanghai Engineering Research Center of Industrial Asymmetric Cataly sis of Chiral Drugs, 220 Handan Road, Shanghai 200433, P.R. China
| | - Zedu Huang
- Department of Chemistry, Engineering Center of Catalysis and Synthesis for Chiral Molecules, Fudan University, Shanghai Engineering Research Center of Industrial Asymmetric Cataly sis of Chiral Drugs, 220 Handan Road, Shanghai 200433, P.R. China
| | - Fener Chen
- Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, P.R. China.,Department of Chemistry, Engineering Center of Catalysis and Synthesis for Chiral Molecules, Fudan University, Shanghai Engineering Research Center of Industrial Asymmetric Cataly sis of Chiral Drugs, 220 Handan Road, Shanghai 200433, P.R. China
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7
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Cárdenas‐Fernández M, Roddan R, Carter EM, Hailes HC, Ward JM. The Discovery of Imine Reductases and their Utilisation for the Synthesis of Tetrahydroisoquinolines. ChemCatChem 2023; 15:e202201126. [PMID: 37081856 PMCID: PMC10107726 DOI: 10.1002/cctc.202201126] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/13/2022] [Indexed: 01/13/2023]
Abstract
Imine reductases (IREDs) are NADPH-dependent enzymes with significant biocatalytic potential for the synthesis of primary, secondary, and tertiary chiral amines. Their applications include the reduction of cyclic imines and the reductive amination of prochiral ketones. In this study, twenty-nine novel IREDs were revealed through genome mining. Imine reductase activities were screened at pH 7 and 9 and in presence of either NADPH or NADH; some IREDs showed good activities at both pHs and were able to accept both cofactors. IREDs with Asn and Glu at the key 187 residue showed preference for NADH. IREDs were also screened against a series of dihydroisoquinolines to synthesise tetrahydroisoquinolines (THIQs), bioactive alkaloids with a wide range of therapeutic properties. Selected IREDs showed high stereoselectivity, as well high THIQ yields (>90 %) when coupled to a glucose-6-phosphate dehydrogenase for NADPH cofactor recycling.
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Affiliation(s)
- Max Cárdenas‐Fernández
- Department of Biochemical Engineering University College London Gower Street, Bernard Katz Building London WC1E 6BT UK
- School of Biosciences University of Kent K ent CT2 7NJ UK
| | - Rebecca Roddan
- Department of Chemistry University College London 20 Gordon Street London WC1H 0AJ UK
| | - Eve M. Carter
- Department of Chemistry University College London 20 Gordon Street London WC1H 0AJ UK
| | - Helen C. Hailes
- Department of Chemistry University College London 20 Gordon Street London WC1H 0AJ UK
| | - John M. Ward
- Department of Biochemical Engineering University College London Gower Street, Bernard Katz Building London WC1E 6BT UK
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8
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Hughes DL. Highlights of the Recent Patent Literature─Focus on Biocatalysis Innovation. Org Process Res Dev 2022. [DOI: 10.1021/acs.oprd.1c00417] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- David L. Hughes
- Private location: 6755 Mira Mesa Boulevard, Suite 123-217, San Diego, California 92121, United States
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9
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Stockinger P, Borlinghaus N, Sharma M, Aberle B, Grogan G, Pleiss J, Nestl BM. Inverting the Stereoselectivity of an NADH-Dependent Imine-Reductase Variant. ChemCatChem 2021; 13:5210-5215. [PMID: 35873105 PMCID: PMC9297850 DOI: 10.1002/cctc.202101057] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/12/2021] [Indexed: 12/31/2022]
Abstract
Imine reductases (IREDs) offer biocatalytic routes to chiral amines and have a natural preference for the NADPH cofactor. In previous work, we reported enzyme engineering of the (R)-selective IRED from Myxococcus stipitatus (NADH-IRED-Ms) yielding a NADH-dependent variant with high catalytic efficiency. However, no IRED with NADH specificity and (S)-selectivity in asymmetric reductions has yet been reported. Herein, we applied semi-rational enzyme engineering to switch the selectivity of NADH-IRED-Ms. The quintuple variant A241V/H242Y/N243D/V244Y/A245L showed reverse stereopreference in the reduction of the cyclic imine 2-methylpyrroline compared to the wild-type and afforded the (S)-amine product with >99 % conversion and 91 % enantiomeric excess. We also report the crystal-structures of the NADPH-dependent (R)-IRED-Ms wild-type enzyme and the NADH-dependent NADH-IRED-Ms variant and molecular dynamics (MD) simulations to rationalize the inverted stereoselectivity of the quintuple variant.
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Affiliation(s)
- Peter Stockinger
- Institute of Biochemistry and Technical Biochemistry Department of Technical Biochemistry Universitaet Stuttgart Allmandring 31 70569 Stuttgart Germany
| | - Niels Borlinghaus
- Institute of Biochemistry and Technical Biochemistry Department of Technical Biochemistry Universitaet Stuttgart Allmandring 31 70569 Stuttgart Germany
| | - Mahima Sharma
- York Structural Biology Laboratory Department of Chemistry University of York YO10 5DD York UK
| | - Benjamin Aberle
- Institute of Biochemistry and Technical Biochemistry Department of Technical Biochemistry Universitaet Stuttgart Allmandring 31 70569 Stuttgart Germany
| | - Gideon Grogan
- York Structural Biology Laboratory Department of Chemistry University of York YO10 5DD York UK
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry Department of Technical Biochemistry Universitaet Stuttgart Allmandring 31 70569 Stuttgart Germany
| | - Bettina M Nestl
- Institute of Biochemistry and Technical Biochemistry Department of Technical Biochemistry Universitaet Stuttgart Allmandring 31 70569 Stuttgart Germany
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10
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Ma EJ, Siirola E, Moore C, Kummer A, Stoeckli M, Faller M, Bouquet C, Eggimann F, Ligibel M, Huynh D, Cutler G, Siegrist L, Lewis RA, Acker AC, Freund E, Koch E, Vogel M, Schlingensiepen H, Oakeley EJ, Snajdrova R. Machine-Directed Evolution of an Imine Reductase for Activity and Stereoselectivity. ACS Catal 2021. [DOI: 10.1021/acscatal.1c02786] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Eric J. Ma
- NIBR Informatics, Novartis Institutes for BioMedical Research (NIBR), 181 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Elina Siirola
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
| | - Charles Moore
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
| | - Arkadij Kummer
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
| | - Markus Stoeckli
- Analytical Sciences and Imaging, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
| | - Michael Faller
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
| | - Caroline Bouquet
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
| | - Fabian Eggimann
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
| | - Mathieu Ligibel
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
| | - Dan Huynh
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
| | - Geoffrey Cutler
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
| | - Luca Siegrist
- NIBR Biologics Center, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
| | - Richard A. Lewis
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
| | - Anne-Christine Acker
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
| | - Ernst Freund
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
| | - Elke Koch
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
| | - Markus Vogel
- NIBR Biologics Center, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
| | - Holger Schlingensiepen
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
| | - Edward J. Oakeley
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
| | - Radka Snajdrova
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
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11
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Hall M. Enzymatic strategies for asymmetric synthesis. RSC Chem Biol 2021; 2:958-989. [PMID: 34458820 PMCID: PMC8341948 DOI: 10.1039/d1cb00080b] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 05/28/2021] [Indexed: 12/13/2022] Open
Abstract
Enzymes, at the turn of the 21st century, are gaining a momentum. Especially in the field of synthetic organic chemistry, a broad variety of biocatalysts are being applied in an increasing number of processes running at up to industrial scale. In addition to the advantages of employing enzymes under environmentally friendly reaction conditions, synthetic chemists are recognizing the value of enzymes connected to the exquisite selectivity of these natural (or engineered) catalysts. The use of hydrolases in enantioselective protocols paved the way to the application of enzymes in asymmetric synthesis, in particular in the context of biocatalytic (dynamic) kinetic resolutions. After two decades of impressive development, the field is now mature to propose a panel of catalytically diverse enzymes for (i) stereoselective reactions with prochiral compounds, such as double bond reduction and bond forming reactions, (ii) formal enantioselective replacement of one of two enantiotopic groups of prochiral substrates, as well as (iii) atroposelective reactions with noncentrally chiral compounds. In this review, the major enzymatic strategies broadly applicable in the asymmetric synthesis of optically pure chiral compounds are presented, with a focus on the reactions developed within the past decade.
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Affiliation(s)
- Mélanie Hall
- Institute of Chemistry, University of Graz Heinrichstrasse 28 8010 Graz Austria
- Field of Excellence BioHealth - University of Graz Austria
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12
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Stockinger P, Schelle L, Schober B, Buchholz PCF, Pleiss J, Nestl BM. Engineering of Thermostable β-Hydroxyacid Dehydrogenase for the Asymmetric Reduction of Imines. Chembiochem 2020; 21:3511-3514. [PMID: 32939899 PMCID: PMC7756219 DOI: 10.1002/cbic.202000526] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Indexed: 01/08/2023]
Abstract
The β-hydroxyacid dehydrogenase from Thermocrinus albus (Ta-βHAD), which catalyzes the NADP+ -dependent oxidation of β-hydroxyacids, was engineered to accept imines as substrates. The catalytic activity of the proton-donor variant K189D was further increased by the introduction of two nonpolar flanking residues (N192 L, N193 L). Engineering the putative alternative proton donor (D258S) and the gate-keeping residue (F250 A) led to a switched substrate specificity as compared to the single and triple variants. The two most active Ta-βHAD variants were applied to biocatalytic asymmetric reductions of imines at elevated temperatures and enabled enhanced product formation at a reaction temperature of 50 °C.
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Affiliation(s)
- Peter Stockinger
- Institute of Biochemistry and Technical BiochemistryDepartment of Technical BiochemistryUniversity of StuttgartAllmandring 3170569StuttgartGermany
| | - Luca Schelle
- Institute of Biochemistry and Technical BiochemistryDepartment of Technical BiochemistryUniversity of StuttgartAllmandring 3170569StuttgartGermany
| | - Benedikt Schober
- Institute of Biochemistry and Technical BiochemistryDepartment of Technical BiochemistryUniversity of StuttgartAllmandring 3170569StuttgartGermany
| | - Patrick C. F. Buchholz
- Institute of Biochemistry and Technical BiochemistryDepartment of Technical BiochemistryUniversity of StuttgartAllmandring 3170569StuttgartGermany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical BiochemistryDepartment of Technical BiochemistryUniversity of StuttgartAllmandring 3170569StuttgartGermany
| | - Bettina M. Nestl
- Institute of Biochemistry and Technical BiochemistryDepartment of Technical BiochemistryUniversity of StuttgartAllmandring 3170569StuttgartGermany
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13
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Stockinger P, Roth S, Müller M, Pleiss J. Systematic Evaluation of Imine-Reducing Enzymes: Common Principles in Imine Reductases, β-Hydroxy Acid Dehydrogenases, and Short-Chain Dehydrogenases/ Reductases. Chembiochem 2020; 21:2689-2695. [PMID: 32311225 PMCID: PMC7540600 DOI: 10.1002/cbic.202000213] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/16/2020] [Indexed: 12/26/2022]
Abstract
The enzymatic, asymmetric reduction of imines is catalyzed by imine reductases (IREDs), members of the short-chain dehydrogenase/reductase (SDR) family, and β-hydroxy acid dehydrogenase (βHAD) variants. Systematic evaluation of the structures and substrate-binding sites of the three enzyme families has revealed four common principles for imine reduction: structurally conserved cofactor-binding domains; tyrosine, aspartate, or glutamate as proton donor; at least four characteristic flanking residues that adapt the donor's pKa and polarize the substrate; and a negative electrostatic potential in the substrate-binding site to stabilize the transition state. As additional catalytically relevant positions, we propose alternative proton donors in IREDs and βHADs as well as proton relays in IREDs, βHADs, and SDRs. The functional role of flanking residues was experimentally confirmed by alanine scanning of the imine-reducing SDR from Zephyranthes treatiae. Mutating the "gatekeeping" phenylalanine at standard position 200 resulted in a tenfold increase in imine-reducing activity.
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Affiliation(s)
- Peter Stockinger
- Institute of Biochemistry and Technical BiochemistryUniversity of StuttgartAllmandring 3170569StuttgartGermany
| | - Sebastian Roth
- Institute of Pharmaceutical SciencesAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2579104FreiburgGermany
| | - Michael Müller
- Institute of Pharmaceutical SciencesAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2579104FreiburgGermany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical BiochemistryUniversity of StuttgartAllmandring 3170569StuttgartGermany
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14
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Structural Characterization of an S-enantioselective Imine Reductase from Mycobacterium Smegmatis. Biomolecules 2020; 10:biom10081130. [PMID: 32751900 PMCID: PMC7465668 DOI: 10.3390/biom10081130] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/21/2020] [Accepted: 07/27/2020] [Indexed: 11/17/2022] Open
Abstract
NADPH-dependent imine reductases (IREDs) are enzymes capable of enantioselectively reducing imines to chiral secondary amines, which represent important building blocks in the chemical and pharmaceutical industry. Since their discovery in 2011, many previously unknown IREDs have been identified, biochemically and structurally characterized and categorized into families. However, the catalytic mechanism and guiding principles for substrate specificity and stereoselectivity remain disputed. Herein, we describe the crystal structure of S-IRED-Ms from Mycobacterium smegmatis together with its cofactor NADPH. S-IRED-Ms belongs to the S-enantioselective superfamily 3 (SFam3) and is the first IRED from SFam3 to be structurally described. The data presented provide further evidence for the overall high degree of structural conservation between different IREDs of various superfamilies. We discuss the role of Asp170 in catalysis and the importance of hydrophobic amino acids in the active site for stereospecificity. Moreover, a separate entrance to the active site, potentially functioning according to a gatekeeping mechanism regulating access and, therefore, substrate specificity is described.
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15
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Montgomery SL, Pushpanath A, Heath RS, Marshall JR, Klemstein U, Galman JL, Woodlock D, Bisagni S, Taylor CJ, Mangas-Sanchez J, Ramsden JI, Dominguez B, Turner NJ. Characterization of imine reductases in reductive amination for the exploration of structure-activity relationships. SCIENCE ADVANCES 2020; 6:eaay9320. [PMID: 32494734 PMCID: PMC7244260 DOI: 10.1126/sciadv.aay9320] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 02/19/2020] [Indexed: 05/16/2023]
Abstract
Imine reductases (IREDs) have shown great potential as catalysts for the asymmetric synthesis of industrially relevant chiral amines, but a limited understanding of sequence activity relationships makes rational engineering challenging. Here, we describe the characterization of 80 putative and 15 previously described IREDs across 10 different transformations and confirm that reductive amination catalysis is not limited to any particular subgroup or sequence motif. Furthermore, we have identified another dehydrogenase subgroup with chemoselectivity for imine reduction. Enantioselectivities were determined for the reduction of the model substrate 2-phenylpiperideine, and the effect of changing the reaction conditions was also studied for the reductive aminations of 1-indanone, acetophenone, and 4-methoxyphenylacetone. We have performed sequence-structure analysis to help explain clusters in activity across a phylogenetic tree and to inform rational engineering, which, in one case, has conferred a change in chemoselectivity that had not been previously observed.
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Affiliation(s)
- Sarah L. Montgomery
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK
| | - Ahir Pushpanath
- Johnson Matthey, 28 Cambridge Science Park, Milton Road, Cambridge CB4 0FP, UK
| | - Rachel S. Heath
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK
| | - James R. Marshall
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK
| | - Ulrike Klemstein
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK
| | - James L. Galman
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK
| | - David Woodlock
- Johnson Matthey, 28 Cambridge Science Park, Milton Road, Cambridge CB4 0FP, UK
| | - Serena Bisagni
- Johnson Matthey, 28 Cambridge Science Park, Milton Road, Cambridge CB4 0FP, UK
| | - Christopher J. Taylor
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK
| | - J. Mangas-Sanchez
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK
| | - J. I. Ramsden
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK
| | - Beatriz Dominguez
- Johnson Matthey, 28 Cambridge Science Park, Milton Road, Cambridge CB4 0FP, UK
| | - Nicholas J. Turner
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK
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16
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Bornadel A, Bisagni S, Pushpanath A, Montgomery SL, Turner NJ, Dominguez B. Technical Considerations for Scale-Up of Imine-Reductase-Catalyzed Reductive Amination: A Case Study. Org Process Res Dev 2019. [DOI: 10.1021/acs.oprd.9b00123] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Amin Bornadel
- Johnson Matthey Plc., 28 Cambridge Science Park, Milton Road, Cambridge CB4 0FP, U.K
| | - Serena Bisagni
- Johnson Matthey Plc., 28 Cambridge Science Park, Milton Road, Cambridge CB4 0FP, U.K
| | - Ahir Pushpanath
- Johnson Matthey Plc., 28 Cambridge Science Park, Milton Road, Cambridge CB4 0FP, U.K
| | - Sarah L. Montgomery
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, U.K
| | - Nicholas J. Turner
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, U.K
| | - Beatriz Dominguez
- Johnson Matthey Plc., 28 Cambridge Science Park, Milton Road, Cambridge CB4 0FP, U.K
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17
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Adams JP, Brown MJB, Diaz‐Rodriguez A, Lloyd RC, Roiban G. Biocatalysis: A Pharma Perspective. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201900424] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Joseph P. Adams
- API Chemistry, Medicinal Science and TechnologyPharma R&D, GlaxoSmithKline Medicines Research Centre Gunnels Wood Road, Stevenage SG12NY U.K
| | - Murray J. B. Brown
- Synthetic Biochemistry, Medicinal Science and TechnologyPharma R&D, GlaxoSmithKline Medicines Research Centre Gunnels Wood Road, Stevenage SG12NY U.K
| | - Alba Diaz‐Rodriguez
- API Chemistry, Medicinal Science and TechnologyPharma R&D, GlaxoSmithKline Medicines Research Centre Gunnels Wood Road, Stevenage SG12NY U.K
| | - Richard C. Lloyd
- API Chemistry, Medicinal Science and TechnologyPharma R&D, GlaxoSmithKline Medicines Research Centre Gunnels Wood Road, Stevenage SG12NY U.K
| | - Gheorghe‐Doru Roiban
- Synthetic Biochemistry, Medicinal Science and TechnologyPharma R&D, GlaxoSmithKline Medicines Research Centre Gunnels Wood Road, Stevenage SG12NY U.K
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18
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Lenz M, Fademrecht S, Sharma M, Pleiss J, Grogan G, Nestl BM. New imine-reducing enzymes from β-hydroxyacid dehydrogenases by single amino acid substitutions. Protein Eng Des Sel 2018; 31:109-120. [PMID: 29733377 DOI: 10.1093/protein/gzy006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 04/10/2018] [Indexed: 11/14/2022] Open
Abstract
We report the exploration of the evolutionary relationship between imine reductases (IREDs) and other dehydrogenases. This approach is informed by the sequence similarity between these enzyme families and the recently described promiscuous activity of IREDs for the highly reactive carbonyl compound 2,2,2-trifluoroacetophenone. Using the structure of the R-selective IRED from Streptosporangium roseum (R-IRED-Sr) as a model, β-hydroxyacid dehydrogenases (βHADs) were identified as the dehydrogenases most similar to IREDs. To understand how active site differences in IREDs and βHADs enable the reduction of predominantly C = N or C = O bonds respectively, we substituted amino acid residues in βHADs with the corresponding residues from the R-IRED-Sr and were able to increase the promiscuous activity of βHADs for C = N functions by a single amino acid substitution. Variants βHADAt_K170D and βHADAt_K170F lost mainly their keto acid reduction activity and gained the ability to catalyze the reduction of imines. Moreover, the product enantiomeric purity for a bulky imine substrate could be increased from 23% ee (R-IRED-Sr) to 97% ee (βHADAt_K170D/F_F231A) outcompeting already described IRED selectivity.
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Affiliation(s)
- Maike Lenz
- Institute of Biochemistry and Technical Biochemistry, Department of Chemistry, Universitaet Stuttgart, Allmandring 31, Stuttgart, Germany
| | - Silvia Fademrecht
- Institute of Biochemistry and Technical Biochemistry, Department of Chemistry, Universitaet Stuttgart, Allmandring 31, Stuttgart, Germany
| | - Mahima Sharma
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, UK
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, Department of Chemistry, Universitaet Stuttgart, Allmandring 31, Stuttgart, Germany
| | - Gideon Grogan
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, UK
| | - Bettina M Nestl
- Institute of Biochemistry and Technical Biochemistry, Department of Chemistry, Universitaet Stuttgart, Allmandring 31, Stuttgart, Germany
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19
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Yao P, Xu Z, Yu S, Wu Q, Zhu D. Imine Reductase‐Catalyzed Enantioselective Reduction of Bulky α,β‐Unsaturated Imines en Route to a Pharmaceutically Important Morphinan Skeleton. Adv Synth Catal 2018. [DOI: 10.1002/adsc.201801326] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Peiyuan Yao
- University of Chinese Academy of Sciences 19(A) Yuquan Road, Shijingshan District Beijing 100049 People's Republic of China
- National Engineering Laboratory for Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 People's Republic of China
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme EngineeringSouth China University of Technology Guangzhou 510006 People's Republic of China
| | - Zefei Xu
- University of Chinese Academy of Sciences 19(A) Yuquan Road, Shijingshan District Beijing 100049 People's Republic of China
- National Engineering Laboratory for Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 People's Republic of China
| | - Shanshan Yu
- National Engineering Laboratory for Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 People's Republic of China
| | - Qiaqing Wu
- University of Chinese Academy of Sciences 19(A) Yuquan Road, Shijingshan District Beijing 100049 People's Republic of China
- National Engineering Laboratory for Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 People's Republic of China
| | - Dunming Zhu
- University of Chinese Academy of Sciences 19(A) Yuquan Road, Shijingshan District Beijing 100049 People's Republic of China
- National Engineering Laboratory for Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 People's Republic of China
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20
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Affiliation(s)
- Mahesh D. Patil
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Gideon Grogan
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, United Kingdom
| | - Andreas Bommarius
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, Georgia 30332-2000, United States
| | - Hyungdon Yun
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
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21
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Velikogne S, Resch V, Dertnig C, Schrittwieser JH, Kroutil W. Sequence-Based In-silico Discovery, Characterisation, and Biocatalytic Application of a Set of Imine Reductases. ChemCatChem 2018; 10:3236-3246. [PMID: 30197686 PMCID: PMC6120462 DOI: 10.1002/cctc.201800607] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Indexed: 11/17/2022]
Abstract
Imine reductases (IREDs) have recently become a primary focus of research in biocatalysis, complementing other classes of amine-forming enzymes such as transaminases and amine dehydrogenases. Following in the footsteps of other research groups, we have established a set of IRED biocatalysts by sequence-based in silico enzyme discovery. In this study, we present basic characterisation data for these novel IREDs and explore their activity and stereoselectivity using a panel of structurally diverse cyclic imines as substrates. Specific activities of >1 U/mg and excellent stereoselectivities (ee>99 %) were observed in many cases, and the enzymes proved surprisingly tolerant towards elevated substrate loadings. Co-expression of the IREDs with an alcohol dehydrogenase for cofactor regeneration led to whole-cell biocatalysts capable of efficiently reducing imines at 100 mM initial concentration with no need for the addition of extracellular nicotinamide cofactor. Preparative biotransformations on gram scale using these 'designer cells' afforded chiral amines in good yield and excellent optical purity.
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Affiliation(s)
- Stefan Velikogne
- University of GrazInstitute of ChemistryNAWI Graz, BioTechMed GrazHeinrichstrasse 288010GrazAustria
| | - Verena Resch
- University of GrazInstitute of ChemistryNAWI Graz, BioTechMed GrazHeinrichstrasse 288010GrazAustria
| | - Carina Dertnig
- University of GrazInstitute of ChemistryNAWI Graz, BioTechMed GrazHeinrichstrasse 288010GrazAustria
| | - Joerg H. Schrittwieser
- University of GrazInstitute of ChemistryNAWI Graz, BioTechMed GrazHeinrichstrasse 288010GrazAustria
| | - Wolfgang Kroutil
- University of GrazInstitute of ChemistryNAWI Graz, BioTechMed GrazHeinrichstrasse 288010GrazAustria
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22
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Hughes DL. Biocatalysis in Drug Development—Highlights of the Recent Patent Literature. Org Process Res Dev 2018. [DOI: 10.1021/acs.oprd.8b00232] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David L. Hughes
- Cidara Therapeutics, Inc., 6310 Nancy Ridge Drive, Suite 101, San Diego, California 92121, United States
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23
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Buchholz PCF, Fademrecht S, Pleiss J. Percolation in protein sequence space. PLoS One 2017; 12:e0189646. [PMID: 29261740 PMCID: PMC5738032 DOI: 10.1371/journal.pone.0189646] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 11/28/2017] [Indexed: 01/08/2023] Open
Abstract
The currently known protein sequences are not distributed equally in sequence space, but cluster into families. Analyzing the cluster size distribution gives a glimpse of the large and unknown extant protein sequence space, which has been explored during evolution. For six protein superfamilies with different fold and function, the cluster size distributions followed a power law with slopes between 2.4 and 3.3, which represent upper limits to the cluster distribution of extant sequences. The power law distribution of cluster sizes is in accordance with percolation theory and strongly supports connectedness of extant sequence space. Percolation of extant sequence space has three major consequences: (1) It transforms our view of sequence space as a highly connected network where each sequence has multiple neighbors, and each pair of sequences is connected by many different paths. A high degree of connectedness is a necessary condition of efficient evolution, because it overcomes the possible blockage by sign epistasis and reciprocal sign epistasis. (2) The Fisher exponent is an indicator of connectedness and saturation of sequence space of each protein superfamily. (3) All clusters are expected to be connected by extant sequences that become apparent as a higher portion of extant sequence space becomes known. Being linked to biochemically distinct homologous families, bridging sequences are promising enzyme candidates for applications in biotechnology because they are expected to have substrate ambiguity or catalytic promiscuity.
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Affiliation(s)
- Patrick C. F. Buchholz
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Silvia Fademrecht
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
- * E-mail:
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24
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Roiban GD, Kern M, Liu Z, Hyslop J, Tey PL, Levine MS, Jordan LS, Brown KK, Hadi T, Ihnken LAF, Brown MJB. Efficient Biocatalytic Reductive Aminations by Extending the Imine Reductase Toolbox. ChemCatChem 2017. [DOI: 10.1002/cctc.201701379] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Gheorghe-Doru Roiban
- Advanced Manufacturing Technologies; GlaxoSmithKline, Medicines Research Centre; Gunnels Wood Road Stevenage SG1 2NY United Kingdom
| | - Marcelo Kern
- Advanced Manufacturing Technologies; GlaxoSmithKline, Medicines Research Centre; Gunnels Wood Road Stevenage SG1 2NY United Kingdom
| | - Zhi Liu
- Advanced Manufacturing Technologies; GlaxoSmithKline; 709 Swedeland Road King of Prussia Pennsylvania 19406 USA
| | - Julia Hyslop
- Advanced Manufacturing Technologies; GlaxoSmithKline, Medicines Research Centre; Gunnels Wood Road Stevenage SG1 2NY United Kingdom
- Department of Pure and Applied Chemistry; University of Strathclyde; Glasgow G1 1XL United Kingdom
| | - Pei Lyn Tey
- Advanced Manufacturing Technologies; GlaxoSmithKline, Medicines Research Centre; Gunnels Wood Road Stevenage SG1 2NY United Kingdom
| | - Matthew S. Levine
- Advanced Manufacturing Technologies; GlaxoSmithKline; 709 Swedeland Road King of Prussia Pennsylvania 19406 USA
| | - Lydia S. Jordan
- Advanced Manufacturing Technologies; GlaxoSmithKline; 709 Swedeland Road King of Prussia Pennsylvania 19406 USA
| | - Kristin K. Brown
- Molecular Design, Computational and Modeling Sciences; GlaxoSmithKline; 1250 S. Collegeville Road Collegeville Pennsylvania 19426 USA
| | - Timin Hadi
- Advanced Manufacturing Technologies; GlaxoSmithKline; 709 Swedeland Road King of Prussia Pennsylvania 19406 USA
| | - Leigh Anne F. Ihnken
- Advanced Manufacturing Technologies; GlaxoSmithKline; 709 Swedeland Road King of Prussia Pennsylvania 19406 USA
| | - Murray J. B. Brown
- Advanced Manufacturing Technologies; GlaxoSmithKline, Medicines Research Centre; Gunnels Wood Road Stevenage SG1 2NY United Kingdom
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25
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First Insights into the Genome Sequence of Pseudomonas oleovorans DSM 1045. GENOME ANNOUNCEMENTS 2017; 5:5/32/e00774-17. [PMID: 28798180 PMCID: PMC5552989 DOI: 10.1128/genomea.00774-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The Gram-negative proteobacterium Pseudomonas oleovorans DSM 1045 is considered a promising source for enzymes of biotechnological interest, e.g., hydrolases and transaminases. Here, we present a draft sequence of its 4.86-Mb genome, enabling the identification of novel biocatalysts.
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26
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Roth S, Präg A, Wechsler C, Marolt M, Ferlaino S, Lüdeke S, Sandon N, Wetzl D, Iding H, Wirz B, Müller M. Extended Catalytic Scope of a Well-Known Enzyme: Asymmetric Reduction of Iminium Substrates by Glucose Dehydrogenase. Chembiochem 2017; 18:1703-1706. [PMID: 28722796 DOI: 10.1002/cbic.201700261] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Indexed: 11/10/2022]
Abstract
NADP(H)-dependent imine reductases (IREDs) are of interest in biocatalytic research due to their ability to generate chiral amines from imine/iminium substrates. In reaction protocols involving IREDs, glucose dehydrogenase (GDH) is generally used to regenerate the expensive cofactor NADPH by oxidation of d-glucose to gluconolactone. We have characterized different IREDs with regard to reduction of a set of bicyclic iminium compounds and have utilized 1 H NMR and GC analyses to determine degree of substrate conversion and product enantiomeric excess (ee). All IREDs reduced the tested iminium compounds to the corresponding chiral amines. Blank experiments without IREDs also showed substrate conversion, however, thus suggesting an iminium reductase activity of GDH. This unexpected observation was confirmed by additional experiments with GDHs of different origin. The reduction of C=N bonds with good levels of conversion (>50 %) and excellent enantioselectivity (up to >99 % ee) by GDH represents a promiscuous catalytic activity of this enzyme.
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Affiliation(s)
- Sebastian Roth
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Andreas Präg
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Cindy Wechsler
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Marija Marolt
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Sascha Ferlaino
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Steffen Lüdeke
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Nicolas Sandon
- Process Chemistry and Catalysis, F. Hoffmann-La Roche, Ltd., 4070, Basel, Switzerland
| | - Dennis Wetzl
- Process Chemistry and Catalysis, F. Hoffmann-La Roche, Ltd., 4070, Basel, Switzerland
| | - Hans Iding
- Process Chemistry and Catalysis, F. Hoffmann-La Roche, Ltd., 4070, Basel, Switzerland
| | - Beat Wirz
- Process Chemistry and Catalysis, F. Hoffmann-La Roche, Ltd., 4070, Basel, Switzerland
| | - Michael Müller
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
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27
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Li H, Tian P, Xu JH, Zheng GW. Identification of an Imine Reductase for Asymmetric Reduction of Bulky Dihydroisoquinolines. Org Lett 2017; 19:3151-3154. [DOI: 10.1021/acs.orglett.7b01274] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hao Li
- State
Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation
Center for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Ping Tian
- Shanghai
Institute of Organic Chemistry, Chinese Academy of Science, 345
Lingling Road, Shanghai 200032, P. R. China
| | - Jian-He Xu
- State
Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation
Center for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Gao-Wei Zheng
- State
Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation
Center for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
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28
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29
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Krone M, Friess F, Scharnowski K, Reina G, Fademrecht S, Kulschewski T, Pleiss J, Ertl T. Molecular Surface Maps. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2017; 23:701-710. [PMID: 27875185 DOI: 10.1109/tvcg.2016.2598824] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We present Molecular Surface Maps, a novel, view-independent, and concise representation for molecular surfaces. It transfers the well-known world map metaphor to molecular visualization. Our application maps the complex molecular surface to a simple 2D representation through a spherical intermediate, the Molecular Surface Globe. The Molecular Surface Map concisely shows arbitrary attributes of the original molecular surface, such as biochemical properties or geometrical features. This results in an intuitive overview, which allows researchers to assess all molecular surface attributes at a glance. Our representation can be used as a visual summarization of a molecule's interface with its environment. In particular, Molecular Surface Maps simplify the analysis and comparison of different data sets or points in time. Furthermore, the map representation can be used in a Space-time Cube to analyze time-dependent data from molecular simulations without the need for animation. We show the feasibility of Molecular Surface Maps for different typical analysis tasks of biomolecular data.
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Lenz M, Meisner J, Quertinmont L, Lutz S, Kästner J, Nestl BM. Asymmetric Ketone Reduction by Imine Reductases. Chembiochem 2016; 18:253-256. [PMID: 27911981 DOI: 10.1002/cbic.201600647] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Indexed: 11/10/2022]
Abstract
The rapidly growing area of asymmetric imine reduction by imine reductases (IREDs) has provided alternative routes to chiral amines. Here we report the expansion of the reaction scope of IREDs by showing the stereoselective reduction of 2,2,2-trifluoroacetophenone. Assisted by an in silico analysis of energy barriers, we evaluated asymmetric hydrogenations of carbonyls and imines while considering the influence of substrate reactivity on the chemoselectivity of this novel class of reductases. We report the asymmetric reduction of C=N as well as C=O bonds catalysed by members of the IRED enzyme family.
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Affiliation(s)
- Maike Lenz
- Institute of Technical Biochemistry, Universitaet Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Jan Meisner
- Institute for Theoretical Chemistry, Universitaet Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Leann Quertinmont
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia, 30322, USA
| | - Stefan Lutz
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia, 30322, USA
| | - Johannes Kästner
- Institute for Theoretical Chemistry, Universitaet Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Bettina M Nestl
- Institute of Technical Biochemistry, Universitaet Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
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Scheller PN, Nestl BM. The biochemical characterization of three imine-reducing enzymes from Streptosporangium roseum DSM43021, Streptomyces turgidiscabies and Paenibacillus elgii. Appl Microbiol Biotechnol 2016; 100:10509-10520. [DOI: 10.1007/s00253-016-7740-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 07/08/2016] [Accepted: 07/13/2016] [Indexed: 11/28/2022]
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