C-to-N atom swapping and skeletal editing in indoles and benzofurans

Zhe Wang, Pengwei Xu, Shu-Min Guo, Constantin G. Daniliuc and Armido Studer ()
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Zhe Wang: Universität Münster
Pengwei Xu: Universität Münster
Shu-Min Guo: Universität Münster
Constantin G. Daniliuc: Universität Münster
Armido Studer: Universität Münster

Nature, 2025, vol. 642, issue 8066, 92-98

Abstract: Abstract Skeletal editing comprises the structural reorganization of compounds. Such editing can be achieved through atom swapping, atom insertion, atom deletion or reorganization of the compound’s backbone structure1,2. Conducted at a late stage in drug development campaigns, skeletal editing enables diversification of an existing pharmacophore, enhancing the efficiency of drug development. Instead of constructing a heteroarene classically from basic building blocks, structural variants are readily accessible directly starting from a lead compound or approved pharmacophore. Here we present C to N atom swapping in indoles at the C2 position to give indazoles through oxidative cleavage of the indole heteroarene core and subsequent ring closure. Reactions proceed through ring-opened oximes as intermediates. These ring deconstructed intermediates can also be diverted into benzimidazoles resulting in an overall C to N atom swapping with concomitant skeletal reorganization. The same structural diverting strategies are equally well applicable to benzofurans leading to either benzisoxazoles or benzoxazoles. The compound classes obtained through these methods—indazoles3,4, benzisoxazoles5, benzimidazoles6,7 and benzoxazoles8—are biologically relevant moieties found as substructures in natural products and pharmaceuticals. The procedures introduced substantially enlarge the methods portfolio in the emerging field of skeletal editing.

Date: 2025
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DOI: 10.1038/s41586-025-09019-6

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