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Enantiodivergent synthesis of isoindolones catalysed by a Rh(III)-based artificial metalloenzyme

Nature Synthesis (2024)Cite this article

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Abstract

Combining enzyme and transition-metal catalysis within artificial metalloenzymes has broadened the scope of new-to-nature reactions and efficiently solved several problems in asymmetric organometallic catalysis through compartmentalization of the catalytic centre within a protein active site and by providing easy access to cooperative catalysis and unparalleled selectivity via protein engineering. Streptavidin, a homotetrameric protein, along with a biotinylated metal complex is a promising artificial metalloenzyme for its application in diverse non-natural reactions. However, the use of engineered streptavidin-based artificial metalloenzymes for the synthesis of enantioenriched isoindolones has remained elusive. Here we report a streptavidin–biotin–Rh(III) system to synthesize chiral isoindolones from N-(pivaloyloxy)benzamides and aromatic diazoesters with up to 95:5 e.r. This hybrid catalytic platform can accommodate a diverse range of diazoesters and yields chiral isoindolones with several useful functionalities such as biphenyl, thioether, selenoether, amine, olefin and alkyne. Mechanistic studies reveal that the process involves a directed inner-sphere C–H activation followed by diazo insertion. A high-resolution crystal structure of streptavidin with the biotinylated Rh(III) cofactor allowed us to rationally engineer mutants at the N49 position for enantiodivergence.

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Fig. 1: Metalloenzyme-catalysed asymmetric synthesis of isoindolones.
Fig. 2: Reaction substrate scope.
Fig. 3: Additional reaction substrate scope.
Fig. 4: Rational engineering of tSav for enantiodivergence.
Fig. 5: Mechanistic studies.

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Data availability

All the data related to this work are available in the main text or the Supplementary Information. Crystallographic data for the structures reported in this Article have been deposited at the Cambridge Crystallographic Data Centre, under deposition numbers CCDC 2189656 ((R)-3e, from a sample with e.r. 86:14), 2313156 ((R)-3e, pure enantiomer obtained through preparative chiral HPLC), 2299915 ((S)-3e, pure enantiomer obtained through preparative chiral HPLC) and 2168680 ((±)-3ad). The atomic coordinates of the streptavidin–ligand complex have been deposited in the Protein Data Bank (PDB) with the accession code 8GOG.

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Acknowledgements

D.M. thanks T. R. Ward (University of Basel) for his generous offering of Sav plasmids and kind help in setting up our facilities. We thank the SERB for financial support. H.J.D. thanks the PMRF for financial support. The Protein Crystallography Facility at IIT Bombay is also acknowledged. We thank Syngenta Biosciences Pvt Ltd Goa for their generous help with chiral preparatory HPLC to determine the absolute configuration of the major isomer.

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Author notes

  1. These authors contributed equally: Prasun Mukherjee, Anjali Sairaman.

Authors and Affiliations

  1. Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India

    Prasun Mukherjee, Hirak Jyoti Deka, Shubhanshu Jain, Sandip Kumar Mishra, Sayan Roy & Debabrata Maiti

  2. Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India

    Anjali Sairaman & Prasenjit Bhaumik

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Contributions

P.M. and D.M. conceived the initial idea. P.M., A.S., P.B. and D.M. designed the overall project. P.M. synthesized the starting materials, cofactor, iminobiotin Sepharose resin and racemic standards. P.M. investigated the optimization of reaction conditions and substrate scope, and performed the mechanistic study. A.S. and P.B. designed the mutants for enantiodivergence. A.S. performed site-directed mutagenesis, and expression and purification of all the streptavidin mutants. A.S. optimized the crystallization conditions, collected the diffraction data and solved the protein crystal structure under the supervision of P.B. H.J.D. performed the replica reactions and contributed to synthesizing the starting materials and determining the substrate scope. S.J. and S.K.M. contributed to the optimization study, substrate scope and synthesis of racemic standards. S.R. helped with synthesis of the starting materials. P.M., A.S., P.B. and D.M. wrote the manuscript. P.B. and D.M. supervised the entire study.

Corresponding authors

Correspondence to Prasenjit Bhaumik or Debabrata Maiti.

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Nature Synthesis thanks Takashi Hayashi and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Primary Handling Editor: Thomas West, in collaboration with the Nature Synthesis team.

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Supplementary information

Supplementary Information

Supplementary Figs. 1–13, Tables 1–8, experimental procedures and X-ray crystallographic analysis.

Reporting Summary

Supplementary Data 1

Crystallographic data for compound (R)-3e, from a sample with e.r. 86:14. CCDC 2189656.

Supplementary Data 2

Crystallographic data for compound (R)-3e, pure enantiomer obtained through preparative chiral HPLC. CCDC 2313156.

Supplementary Data 3

Crystallographic data for compound (S)-3e, pure enantiomer obtained through preparative chiral HPLC. CCDC 2299915.

Supplementary Data 4

Crystallographic data for compound (±)-3ad, CCDC 2168680.

Supplementary Data 5

Crystallographic data for the streptavidin–ligand complex [PDB:8GOG].

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Mukherjee, P., Sairaman, A., Deka, H.J. et al. Enantiodivergent synthesis of isoindolones catalysed by a Rh(III)-based artificial metalloenzyme. Nat. Synth (2024). https://doi.org/10.1038/s44160-024-00533-5

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