A dimethyl ketal-protected benzoin-based linker suitable for photolytic release of unprotected peptides.

Nataliya Chumachenko, Yehor Novikov, Richard K Shoemaker, Shelley D Copley

Index: J. Org. Chem. 76(22) , 9409-16, (2011)

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Abstract

Photolabile 3',5'-dimethoxybenzoin-based linkers are advantageous for a variety of solid-phase synthetic procedures and manipulations of biomolecules because UV irradiation in aqueous media provides fast and essentially quantitative release of tethered molecules, while generating unreactive side products. Practical applications of previously reported linkers are compromised to some extent by the 1,3-dithiane protection of the benzoin carbonyl group and the lengthy synthesis. We have extended the group of photocleavable 3',5'-dimethoxybenzoin-based linkers by designing and synthesizing a linker in which the carbonyl group is protected as a dimethyl ketal. This protection is compatible with commonly used esterification and amide bond formation techniques, including the Fmoc/tBu strategy for solid phase peptide synthesis, is stable under mild acidic conditions, and can be quantitatively removed in <5 min by 3% TFA in dichloromethane. Irradiation of beads carrying peptides attached to the linker at 350 nm in aqueous or partially aqueous media affords >90% release after 30 min. The linker was synthesized from commercially available starting materials in five steps with an overall yield of 40% and without any column chromatography purification. Additionally, we developed a route to a dithiane-protected linker that requires only two steps and proceeds in 65% yield, a significant improvement over previous synthetic routes.