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Computational redesign of enzymes for regio- and enantioselective hydroamination

Abstract

Introduction of innovative biocatalytic processes offers great promise for applications in green chemistry. However, owing to limited catalytic performance, the enzymes harvested from nature's biodiversity often need to be improved for their desired functions by time-consuming iterative rounds of laboratory evolution. Here we describe the use of structure-based computational enzyme design to convert Bacillus sp. YM55-1 aspartase, an enzyme with a very narrow substrate scope, to a set of complementary hydroamination biocatalysts. The redesigned enzymes catalyze asymmetric addition of ammonia to substituted acrylates, affording enantiopure aliphatic, polar and aromatic β-amino acids that are valuable building blocks for the synthesis of pharmaceuticals and bioactive compounds. Without a requirement for further optimization by laboratory evolution, the redesigned enzymes exhibit substrate tolerance up to a concentration of 300 g/L, conversion up to 99%, β-regioselectivity >99% and product enantiomeric excess >99%. The results highlight the use of computational design to rapidly adapt an enzyme to industrially viable reactions.

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Fig. 1: Computational active site redesign of AspB.
Fig. 2: Computational redesign of AspB for (R)-β-aminobutanoic acid synthesis.
Fig. 3: Computational redesign of AspB for (R)-β-aminopentanoic acid synthesis.
Fig. 4: Computational redesign of AspB for (S)-β-asparagine synthesis.
Fig. 5: Computational redesign of AspB for (S)-β-phenylalanine synthesis.

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Acknowledgements

We thank W. Szymanski for discussions. We thank for the 100 Talent Program grant (B.W.) and Biological Resources Service Network Initiative (ZSYS-012; B.W.) and a grant (SKT1604; C.Y.L.) from the Chinese Academy of Sciences, Natural Science Foundation of China grants (31601412 (B.W.), 21603013 (C.Y.L.)), and a BE-Basic grant (H.J.W. and D.B.J.) from the Dutch Ministry of Economic Affairs for the financial support.

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D.B.J. and B.W. initiated the project. B.W., H.J.W. and Y. Cui performed the computational work. L.S., R.L., M.O., Y. Tian, J.D., T.L., D.N., Y. Chen and J.F. performed biocatalytic experiments. J.H., H.C. and Y. Tao developed high-density fermentation methods. R.L. performed preparative-scale synthesis of the amino acids. D.B.J. and B.W. provided supervision and input on experimental design and wrote the manuscript, which was revised and approved by all authors. R.L., H.J.W. and L.S. contributed equally to this work.

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Correspondence to Dick B. Janssen or Bian Wu.

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Li, R., Wijma, H.J., Song, L. et al. Computational redesign of enzymes for regio- and enantioselective hydroamination. Nat Chem Biol 14, 664–670 (2018). https://doi.org/10.1038/s41589-018-0053-0

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