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Screening and characterization of a diverse panel of metagenomic imine reductases for biocatalytic reductive amination

Abstract

Finding faster and simpler ways to screen protein sequence space to enable the identification of new biocatalysts for asymmetric synthesis remains both a challenge and a rate-limiting step in enzyme discovery. Biocatalytic strategies for the synthesis of chiral amines are increasingly attractive and include enzymatic asymmetric reductive amination, which offers an efficient route to many of these high-value compounds. Here we report the discovery of over 300 new imine reductases and the production of a large (384 enzymes) and sequence-diverse panel of imine reductases available for screening. We also report the development of a facile high-throughput screen to interrogate their activity. Through this approach we identified imine reductase biocatalysts capable of accepting structurally demanding ketones and amines, which include the preparative synthesis of N-substituted β-amino ester derivatives via a dynamic kinetic resolution process, with excellent yields and stereochemical purities.

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Fig. 1: A workflow and approximate time frame for generating a metagenomic library with examples of how this platform was used to expand the biocatalytic toolbox as applied to IREDs.
Fig. 2: 384 IREDy-to-go screening of amine 2b combined with biotransformation data for the reductive amination of 2 with b mapped phylogenetically to show the overall distribution of activity.
Fig. 3: High-throughput characterization employing the colorimetric screen, a chart showing the substrates presented to the colorimetric screen alongside the number of definitive enzyme hits; the method for the number of hits calculated is given in Supplementary Section 4.5.
Fig. 4: Analytical scale reductive aminations.
Fig. 5: Preparative-scale asymmetric reductive aminations of β-keto esters.

Data availability

Data supporting the results and conclusions are available within this paper and the Supplementary Information. Both the IREDy-to-go screen and a duplication of the screening plate without the colorimetric screening components containing 0.5 mg of crude lysate of each IRED in each well are freely available through Prozomix Ltd.

References

  1. 1.

    Kan, S. B. J., Lewis, R. D., Chen, K. & Arnold, F. H. Directed evolution of cytochrome C for carbon–silicon bond formation: bringing silicon to life. Science 354, 1048–1051 (2016).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  2. 2.

    Wijma, H. J. et al. Enantioselective enzymes by computational design and in silico screening. Angew. Chem. Int. Ed. 54, 3726–3730 (2015).

    CAS  Article  Google Scholar 

  3. 3.

    Burke, A. J. et al. Design and evolution of an enzyme with a non-canonical organocatalytic mechanism. Nature 570, 219–223 (2019).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  4. 4.

    Zeymer, C., Zschoche, R. & Hilvert, D. Optimization of enzyme mechanism along the evolutionary trajectory of a computationally designed (retro-)aldolase. J. Am. Chem. Soc. 139, 12541–12549 (2017).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  5. 5.

    Sandoval, B. A., Meichan, A. J. & Hyster, T. K. Enantioselective hydrogen atom transfer: discovery of catalytic promiscuity in flavin-dependent ‘ene’-reductases. J. Am. Chem. Soc. 139, 11313–11316 (2017).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  6. 6.

    Sandoval, B. A. & Hyster, T. K. Emerging strategies for expanding the toolbox of enzymes in biocatalysis. Curr. Opin. Chem. Biol. 55, 45–51 (2020).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  7. 7.

    Devine, P. N. et al. Extending the application of biocatalysis to meet the challenges of drug development. Nat. Rev. Chem. 2, 409–421 (2018).

    Article  Google Scholar 

  8. 8.

    Xiao, H., Bao, Z. & Zhao, H. High throughput screening and selection methods for directed enzyme evolution. Ind. Eng. Chem. Res. 54, 4011–4020 (2015).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  9. 9.

    Robbins, D. W. & Hartwig, J. F. A simple, multidimensional approach to high-throughput discovery of catalytic reactions. Science 333, 1423–1427 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  10. 10.

    Friedfeld, M. R. et al. Cobalt precursors for high-throughput discovery of base metal asymmetric alkene hydrogenation catalysts. Science 342, 1076 (2013).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  11. 11.

    Collins, K. D., Gensch, T. & Glorius, F. Contemporary screening approaches to reaction discovery and development. Nat. Chem. 6, 859–871 (2014).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  12. 12.

    Cabrera-Pardo, J., Chai, D. I., Liu, S., Mrksich, M. & A. Kozmin, S. Label-assisted mass spectrometry for the acceleration of reaction discovery and optimization. Nat. Chem. 5, 423–427 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  13. 13.

    Vanacek, P. et al. Exploration of enzyme diversity by integrating bioinformatics with expression analysis and biochemical characterization. ACS Catal. 8, 2402–2412 (2018).

    CAS  Article  Google Scholar 

  14. 14.

    Yan, C. et al. Real-time screening of biocatalysts in live bacterial colonies. J. Am. Chem. Soc. 139, 1408–1411 (2017).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  15. 15.

    Vallejo, D., Nikoomanzar, A., Paegel, B. M. & Chaput, J. C. Fluorescence-activated droplet sorting for single-cell directed evolution. ACS Synth. Biol. 8, 1430–1440 (2019).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  16. 16.

    Gielen, F. et al. Ultrahigh-throughput-directed enzyme evolution by absorbance-activated droplet sorting (AADS). Proc. Natl Acad. Sci. USA 113, E7383–E7389 (2016).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  17. 17.

    Davids, T., Schmidt, M., Böttcher, D. & Bornscheuer, U. T. Strategies for the discovery and engineering of enzymes for biocatalysis. Curr. Opin. Chem. Biol. 17, 215–220 (2013).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  18. 18.

    Bunzel, H. A., Garrabou, X., Pott, M. & Hilvert, D. Speeding up enzyme discovery and engineering with ultrahigh-throughput methods. Curr. Opin. Struct. Biol. 48, 149–156 (2018).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  19. 19.

    Ghislieri, D. & Turner, N. J. Biocatalytic approaches to the synthesis of enantiomerically pure chiral amines. Top. Catal. 57, 284–300 (2014).

    CAS  Article  Google Scholar 

  20. 20.

    Weise, N., Parmeggiani, F., Ahmed, S. & Turner, N. J. Discovery and investigation of mutase-like activity in a phenylalanine ammonia lyase from Anabaena variabilis. Top. Catal. 61, 288–295 (2018).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  21. 21.

    Grogan, G. Synthesis of chiral amines using redox biocatalysis. Curr. Opin. Chem. Biol. 43, 15–22 (2018).

    CAS  PubMed  Article  Google Scholar 

  22. 22.

    Turner, N. J. Enantioselective oxidation of C–O and C–N bonds using oxidases. Chem. Rev. 111, 4073–4087 (2011).

    CAS  PubMed  Article  Google Scholar 

  23. 23.

    Jia, Z.-J., Gao, S. & Arnold, F. H. Enzymatic primary amination of benzylic and allylic C(sp3)-H bonds. J. Am. Chem. Soc. 142, 10279–10283 (2020).

    CAS  PubMed  Article  Google Scholar 

  24. 24.

    Schrittwieser, J. H., Velikogne, S. & Kroutil, W. Biocatalytic imine reduction and reductive amination of ketones. Adv. Synth. Catal. 357, 1665–1685 (2015).

    Google Scholar 

  25. 25.

    Hyslop, J. F. et al. Biocatalytic synthesis of chiral N-functionalized amino acids. Angew. Chem. Int. Ed. 57, 13821–13824 (2018).

    CAS  Article  Google Scholar 

  26. 26.

    Stahl, L. The Handbook of Homogeneous Hydrogenation, Volumes 1−3 Edited by Johannes G. de Vries (DSM Pharmaceutical Products, Geleen, The Netherlands) and Cornelis J. Elsevier (Universiteit van Amsterdam, The Netherlands). Wiley-VCH Verlag GmbH & Co. KGaA: Weinheim. 2007. 1632 pp. $625.00. ISBN 978-3-527-31161-3. J. Am. Chem. Soc. 129, 10297–10298 (2007).

    CAS  Article  Google Scholar 

  27. 27.

    Li, W. Stereoselective Formation of Amines (Springer, 2014).

  28. 28.

    Roughley, S. D. & Jordan, A. M. The medicinal chemist’s toolbox: an analysis of reactions used in the pursuit of drug candidates. J. Med. Chem. 54, 3451–3479 (2011).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  29. 29.

    Wang, L. & Xiao, J. Hydrogen-atom transfer reactions. Top. Curr. Chem. 374, 1–55 (2016).

    Article  CAS  Google Scholar 

  30. 30.

    Hou, G. et al. Enantioselective hydrogenation of N–H imines. J. Am. Chem. Soc. 131, 9882–9883 (2009).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  31. 31.

    Aurelio, L., Brownlee, R. & Hughes, A. B. Synthetic preparation of N-methyl-ɑ-amino acids. Chem. Rev. 104, 5823–5846 (2004).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  32. 32.

    Aleku, A. G. et al. A reductive aminase from Aspergillus oryzae. Nat. Chem. 9, 961–969 (2017).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  33. 33.

    Tobias, H. et al. Direct reductive amination of ketones: structure and activity of S‐selective imine reductases from Streptomyces. ChemCatChem 6, 2248–2252 (2014).

    Article  CAS  Google Scholar 

  34. 34.

    Scheller, P. N., Lenz, M., Hammer, S. C., Hauer, B. & Nestl, B. M. Imine reductase‐catalyzed intermolecular reductive amination of aldehydes and ketones. ChemCatChem 7, 3239–3242 (2015).

    CAS  Article  Google Scholar 

  35. 35.

    Wetzl, D. et al. Asymmetric reductive amination of ketones catalyzed by imine reductases. ChemCatChem 8, 2023–2026 (2016).

    CAS  Article  Google Scholar 

  36. 36.

    Maugeri, Z. & Rother, D. Reductive amination of ketones catalyzed by whole cell biocatalysts containing imine reductases (IREDs). J. Biotechnol. 258, 167–170 (2017).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  37. 37.

    Roiban, G. D. et al. Efficient biocatalytic reductive aminations by extending the imine reductase toolbox. ChemCatChem 9, 4475–4479 (2017).

    CAS  Article  Google Scholar 

  38. 38.

    Sharma, M. et al. A mechanism for reductive amination catalyzed by fungal reductive aminases. ACS Catal. 8, 11534–11541 (2018).

    CAS  Article  Google Scholar 

  39. 39.

    Mitsukura, K., Suzuki, M., Tada, K., Yoshida, T. & Nagasawa, T. Asymmetric synthesis of chiral cyclic amine from cyclic imine by bacterial whole-cell catalyst of enantioselective imine reductase. Org. Biomol. Chem. 8, 4533–4535 (2010).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  40. 40.

    Mitsukura, K. et al. Purification and characterization of a novel (R)-imine reductase from Streptomyces sp. GF3587. Biosci. Biotechnol. Biochem. 75, 1778–1782 (2011).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  41. 41.

    Slabu, I., Galman, J. L., Lloyd, R. C. & Turner, N. J. Discovery, engineering, and synthetic application of transaminase biocatalysts. ACS Catal. 7, 8263–8284 (2017).

    CAS  Article  Google Scholar 

  42. 42.

    Mangas-Sanchez, J. et al. Imine reductases (IREDs). Curr. Opin. Chem. Biol. 37, 19–25 (2017).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  43. 43.

    Lenz, M., Borlinghaus, N., Weinmann, L. & Nestl, B. M. Recent advances in imine reductase-catalyzed reactions. World J. Microbiol. Biotechnol. 33, 199 (2017).

    PubMed  Article  CAS  PubMed Central  Google Scholar 

  44. 44.

    Schober, M. et al. Chiral synthesis of LSD1 inhibitor GSK2879552 enabled by directed evolution of an imine reductase. Nat. Catal. 2, 909–915 (2019).

    CAS  Article  Google Scholar 

  45. 45.

    Wetzl, D. et al. Expanding the imine reductase toolbox by exploring the bacterial protein‐sequence space. ChemBioChem 16, 1749–1756 (2015).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  46. 46.

    France, S. P. et al. Identification of novel bacterial members of the imine reductase enzyme family that perform reductive amination. ChemCatChem 10, 510–514 (2018).

    CAS  Article  Google Scholar 

  47. 47.

    Gheorghe‐Doru, R. et al. Efficient biocatalytic reductive aminations by extending the imine reductase toolbox. ChemCatChem 9, 4475–4479 (2017).

    Article  CAS  Google Scholar 

  48. 48.

    Zhu, J. et al. Enantioselective synthesis of 1-aryl-substituted tetrahydroisoquinolines employing imine reductase. ACS Catal. 7, 7003–7007 (2017).

    CAS  Article  Google Scholar 

  49. 49.

    Li, H., Luan, Z. J., Zheng, G. W. & Xu, J. H. Efficient synthesis of chiral indolines using an imine reductase from Paenibacillus lactis. Adv. Synth. Catal. 357, 1692–1696 (2015).

    CAS  Article  Google Scholar 

  50. 50.

    Nugent, T. C. & El‐Shazly, M. Chiral amine synthesis—recent developments and trends for enamide reduction, reductive amination, and imine reduction. Adv. Synth. Catal. 352, 753–819 (2010).

    CAS  Article  Google Scholar 

  51. 51.

    Baud, D., Jeffries, J. W. E., Moody, T. S., Ward, J. M. & Hailes, H. C. A metagenomics approach for new biocatalyst discovery: application to transaminases and the synthesis of allylic amines. Green Chem. 19, 1134–1143 (2017).

    CAS  Article  Google Scholar 

  52. 52.

    Hernández, K., Szekrenyi, A. & Clapés, P. Nucleophile promiscuity of natural and engineered aldolases. ChemBioChem 19, 1353–1358 (2018).

    PubMed  Article  CAS  PubMed Central  Google Scholar 

  53. 53.

    Leipold, L. et al. The identification and use of robust transaminases from a domestic drain metagenome. Green Chem. 21, 75–86 (2019).

    CAS  PubMed  Article  Google Scholar 

  54. 54.

    Caparco, A. et al. Metagenomic mining for amine dehydrogenase discovery. Adv. Synth. Catal. 362, 2427 (2020).

    CAS  Article  Google Scholar 

  55. 55.

    Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization to the Convention on Biological Diversity Treaty (UK Parliament Foreign And Commonwealth Office, 2010).

  56. 56.

    Zawodny, W. et al. Chemoenzymatic synthesis of substituted azepanes by sequential biocatalytic reduction and organolithium-mediated rearrangement. J. Am. Chem. Sci. 140, 17872–17877 (2018).

    CAS  Article  Google Scholar 

  57. 57.

    Montgomery, S. L. et al. Characterization of imine reductases in reductive amination for the exploration of structure–activity relationships. Sci. Adv. 6, eaay9320 (2020).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  58. 58.

    Mayer, K. M. & Arnold, F. H. A colorimetric assay to quantify dehydrogenase activity in crude cell lysates. J. Biomol. Screen 7, 135–140 (2002).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  59. 59.

    Peng, H. et al. Deciphering piperidine formation in polyketide-derived indolizidines reveals a thioester reduction, transamination, and unusual imine reduction process. ACS Chem. Biol. 11, 3278–3283 (2016).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  60. 60.

    Ye, S. et al. Identification by genome mining of a type I polyketide gene cluster from Streptomyces argillaceus involved in the biosynthesis of pyridine and piperidine alkaloids argimycins P. Front. Microbiol. 8, 194 (2017).

    PubMed  PubMed Central  Google Scholar 

  61. 61.

    Lenz, M. et al. Asymmetric ketone reduction by imine reductases. ChemBioChem 18, 253–256 (2017).

    CAS  PubMed  Article  Google Scholar 

  62. 62.

    González-Martínez, D. et al. Asymmetric synthesis of primary and secondary β-fluoro-arylamines using reductive aminases from fungi. ChemCatChem 12, 2421 (2020).

    Article  CAS  Google Scholar 

  63. 63.

    Smith, J. A. et al. in A101 Advances in Cough, Dyspnea, and Interventional Pulmonary A2672–A2672 (American Thoracic Society, 2017).

  64. 64.

    Darcsi, A., Tóth, G., Kökösi, J. & Béni, S. Structure elucidation of a process-related impurity of dapoxetine. J. Pharm. Biomed. Anal. 96, 272–277 (2014).

    CAS  PubMed  Article  Google Scholar 

  65. 65.

    Fuchs, M., Koszelewski, D., Tauber, K., Kroutil, W. & Faber, K. Chemoenzymatic asymmetric total synthesis of (S)-rivastigmine using omega-transaminases. Chemic. Commun. 46, 5500–5502 (2010).

    CAS  Article  Google Scholar 

  66. 66.

    Zhang, D. et al. Development of β-amino acid dehydrogenase for the synthesis of β-amino acids via reductive amination of β-keto acids. ACS Catal. 5, 2220–2224 (2015).

    CAS  Article  Google Scholar 

  67. 67.

    Midelfort, K. et al. Redesigning and characterizing the substrate specificity and activity of Vibrio fluvialis aminotransferase for the synthesis of imagabalin. Protein Eng. Des. Sel. 26, 25–33 (2013).

    CAS  PubMed  Article  Google Scholar 

  68. 68.

    Juraisti, E. & Soloshonok, V. Enantioselective Synthesis of β-Amino Acids 2nd edn (Wiley, 2005).

  69. 69.

    Iglesias, E. Ester hydrolysis and enol nitrosation reactions of ethyl cyclohexanone-2-carboxylate inhibited by β-cyclodextrin. J. Org. Chem. 65, 6583–6594 (2000).

    CAS  PubMed  Article  Google Scholar 

  70. 70.

    Bornadel, A. et al. Technical considerations for scale-up of imine-reductase-catalyzed reductive amination: a case study. Org Process. Res. Dev. 23, 1262–1268 (2019).

    CAS  Article  Google Scholar 

  71. 71.

    Mangas-Sanchez, J. et al. Asymmetric synthesis of primary amines catalyzed by fungal reductive aminases. Chem. Sci. 11, 5052–5057 (2020).

    CAS  Article  Google Scholar 

  72. 72.

    Sutin, L. et al. Oxazolones as potent inhibitors of 11β-hydroxysteroid dehydrogenase type 1. Bioorg. Med. Chem. Lett. 17, 4837–4840 (2007).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  73. 73.

    Afanasyev, O. I., Kuchuk, E., Usanov, D. L. & Chusov, D. Reductive amination in the synthesis of pharmaceuticals. Chem. Rev. 119, 11857–11911 (2019).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  74. 74.

    Salzmann, T. N., Ratcliffe, R. W., Christensen, B. G. & Bouffard, F. A. A stereocontrolled synthesis of (+)-thienamycin. J. Am. Chem. Sci. 102, 6161–6163 (1980).

    CAS  Article  Google Scholar 

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Acknowledgements

We thank the Industrial Biotechnology Innovation Centre (IBioIC) and Biotechnology and Biological Sciences Research Council (BBSRC) for awarding the CASE studentship to J.R.M. from Prozomix Ltd. P.Y. was supported by a CSC scholarship and the Youth Innovation Promotion Association of the Chinese Academy of Sciences (Grant no. 2016166). T.W.T. was supported by a BBSRC CASE studentship awarded by Pfizer. S.L.M. was supported by a BBSRC CASE studentship from Johnson Matthey. R.B.P. and R.S.H. were supported by the European Research Council (ERC Grant no. 742987). J.M.-S. was funded by grant BB/M006832/1 from the UK Biotechnology and Biological Sciences Research Council. S.J.C., D.J.C., J.D.F., R.A.M.D. and K.M.G. acknowledge the European Union’s Seventh Framework Programme for research, technological development and demonstration under grant agreement no. 685474 for supporting MetaFluidics. N.J.T. is grateful to the ERC for the award of an Advanced Grant (Grant no. 742987). We thank D. Heyes of the Manchester Institute of Biotechnology (MIB) for assistance in gathering the circular dichroism data. We thank Y. Qi of Prozomix Ltd for screening of the Prozomix diaphorases. Prozomix and J.R.M., P.Y., S.L.M., T.W.T., R.B.P., J.M.-S., R.S.H. and N.J.T. also thank other staff of Prozomix for their support.

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N.J.T. and S.J.C. devised and supervised the project. J.M.-S. and R.S.H. managed the project. J.R.M., J.D.F, K.M.G., S.L.M. and D.J.C. performed the identification, cloning and expression of the enzymes. J.R.M., J.D.F., R.A.M.D. and S.J.C. were involved in the design, development and implementation of the colorimetric screen and 384-well plates. J.R.M. and P.Y. carried out the high-throughput characterization of the enzymes. J.R.M. and P.Y. performed the analytical scale biotransformations. P.Y. conducted the preparative-scale biotransformations. P.Y. and R.B.P. synthesized the chemical standards. J.R.M. and T.W.T. undertook the thermostability studies. N.J.T., S.J.C., J.R.M., P.Y., R.S.H., J.M.-S., J.D.F. and T.W.T. wrote the manuscript and generated the figures.

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Correspondence to Nicholas J. Turner.

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Supplementary Information

Supplementary Sections 1 (1.1–1.4), 2, 3 (3.1, 3.2.1–3.2.7, 3.3.1–3.3.4, 3.4.1 and 3.4.2), 4 (4.1–4.4, 4.4.1-4.4.5, 4.5 and 4.6), 5 (5.1, 5.2, 5.2.1–5.2.4, 5.3–5.5), 6, 7 (7.1–.7.5), 8 and 9.

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Marshall, J.R., Yao, P., Montgomery, S.L. et al. Screening and characterization of a diverse panel of metagenomic imine reductases for biocatalytic reductive amination. Nat. Chem. 13, 140–148 (2021). https://doi.org/10.1038/s41557-020-00606-w

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