Mask and Release Strategy-Enabled Diversity-Oriented Synthesis for DNA-Encoded Library

Abstract

An ideal DNA-encoded library (DEL) selection requires the library to consist of diverse core skeletons and cover chemical space as much as possible. However, the lack of efficient on-DNA synthetic approaches toward core skeletons has greatly restricted the diversity of DEL. To mitigate this issue, this work disclosed a "Mask & Release" strategy to streamline the challenging on-DNA core skeleton synthesis. N-phenoxyacetamide is used as a masked phenol and versatile directing group to mediate diversified DNA-compatible C-H functionalization, introducing the 1st-dimensional diversity at a defined site, and simultaneously releasing the phenol functionality, which can facilitate the introduction of the 2nd diversity. This work not only provides a set of efficient syntheses toward DNA-conjugated drug-like core skeletons such as ortho-alkenyl/sulfiliminyl/cyclopropyl phenol, benzofuran, dihydrobenzofuran but also provides a paradigm for on-DNA core skeleton synthetic method development.

Keywords: DNA-encoded library; benzofuran; diversity-oriented synthesis; mask and release; sulfiliminyl phenol.

Figure 1

“Mask & Release” strategy‐enabled diversity‐oriented synthesis of DNA‐encoded core skeletons. a) Synthesis of DEL. b) i) Conventional “protection & deprotection” approach based on‐DNA synthesis of core skeletons. ii) Design concept of “Mask & Release” strategy based on DNA synthesis of core skeletons. c) N‐phenoxyacetamide‐mediated divergent‐oriented on‐DNA synthesis via “Mask & Release” strategy. d) Representative bioactive molecules or drugs.

Figure 2

N‐phenoxyacetamide‐mediated C–H functionalization with alkynes under Rh promotion for the synthesis of DNA‐conjugated ortho‐alkenyl phenols. a) Reaction conditions: (A) (1 equiv, 0.5 mm in ddH₂O), [Cp*RhCl₂]₂ (20 equiv, 10 mm in DMA), CsOAc (200 equiv, 200 mm in ddH₂O), (B) (1000 equiv, 500 mm in DMA) in MeOH‐PBS (1:1, pH 9.4, 20 µL) at room temperature for 17 h without exclusion of air or moisture. b) The reaction was conducted at 60 °C for 8 h. The conversion of (C) was determined by LC‐MS analysis.

Figure 3

N‐phenoxyacetamide mediated on‐DNA synthesis of benzofurans. Reaction conditions: (A) (1 equiv, 0.5 mm in ddH₂O), [Ru(p‐cymene)Cl₂]₂ (20 equiv, 10 mm in DMA), KOPiv (200 equiv, 200 mm in ddH₂O), (B) (1000 equiv, 500 mm in DMA) in MeCN/PBS (1:1, pH 9.4, 20 µL) at room temperature for 17 h without exclusion of air or moisture. The conversion of product (D) was determined by LC‐MS.

Figure 4

N‐phenoxyacetamide‐mediated on‐DNA synthetic application and diversified transformations. a) Metal‐free N‐phenoxyacetamide‐mediated rearrangement for the synthesis of DNA‐conjugated ortho‐sulfiliminyl phenols. b) N‐phenoxyacetamide‐mediated on‐DNA chemodivergent C‐H functionalization reactions & late‐stage functionalization of the released phenol. c) N‐phenoxyacetamide‐mediated on‐DNA synthesis of bioactive benzofuran derivatives in a DEL rehearsal.

Figure 5

Validation of the integrity of the DNA barcode from the samples of enzymatic ligation. a) DNA ligation. b) DNA ligation analysis of the final products C1‐L and D1‐L. c) qPCR analysis of residual amplifiable material of an inhouse DEL after exposure to the reaction conditions of i) on‐DNA ortho‐enamine phenols synthesis and ii) benzofuran synthesis. d) Sanger sequencing results of C1‐L and D1‐L.