Thiophene Backbone Amide Linkers, a New Class of Easily Prepared and Highly Acid-Labile Linkers for Solid-Phase Synthesis

Abstract

Solid-phase synthesis is of tremendous importance for small-molecule and biopolymer synthesis. Linkers (handles) that release amide-containing products after completion of solid-phase synthesis are widely used. Here we present a new class of highly acid-labile backbone amide linkers (BAL handles) based on 3,4-ethylenedioxythiophene (EDOT), which we have termed T-BAL. These thiophene linkers are synthesized in three convenient steps from commercially available EDOT. In the linker design, the spacer was introduced to the EDOT core either via a carbon-carbon bond or via a thioether linkage. Introduction of the spacer via a C-C bond was performed by a chemoselective Negishi coupling without transient protection of the aldehyde group to provide the T-BAL1 handle. Introduction via a thioether linkage was performed by a facile nucleophilic aromatic substitution between the brominated EDOT aldehyde and unprotected mercapto acids to provide T-BAL2 and T-BAL3 handles. The minimal use of protecting groups gave the corresponding linker molecules in few synthetic steps and in good yields. After anchoring of the linker to a polymeric support, introduction of the first amino acid was achieved by reductive amination, giving a secondary amine. A following acylation of the secondary amine with a symmetrical amino acid anhydride resulted in a backbone amide linkage between the handle and the growing substrate (e.g., peptide chain). After solid-phase synthesis, the substrates could be released from the resin by either low acid conditions using 1% TFA in CH2Cl2 or high acid conditions such as 50% TFA in CH2Cl2. Peptide thioesters could be released from the T-BAL1 handle under very mild conditions using aqueous acetic acid. Tert-butyl based protecting groups, tert-butyl esters, tert-butyl ethers, and Boc groups, as well as dimethyl acetals were relatively stable to these mild conditions for release of the peptides.

EDOTn and MIM, new peptide backbone protecting groups

“…MIM and the EDOTn, which are electron-rich systems, have been shown to be acid-labile as amide linkers. 15,16 The backbone-protected derivatives of Gly were easily prepared via reductive amination with the commercially available 1-methylindole-3-carbaldehyde and the 3,4-ethylenedioxythiophene-2-carbaldehyde, which was easily prepared from the heterocycle. 17,18 Finally, Fmoc introduction rendered the appropriate building block for the synthesis (Figure 3).…”

“…The 1-methyl-3-indolylmethyl (MIM) and 3,4-ethylenedioxy-2-thenyl (EDOTn) were inspired by linkers for the SPS of C-terminal-modified peptides. 15,16 FIGURE 1 Mechanism of aspartimide formation with typical side products shown. …”

Sulfonium Ion Derivatization, Isobaric Stable Isotope Labeling and Data Dependent CID- and ETD-MS/MS for Enhanced Phosphopeptide Quantitation, Identification and Phosphorylation Site Characterization

“…Based on the method of Jessing [62], 4-bromobutyric acid (8.35 g, 50.0 mmol) and thiourea (5.70 g, 75.0 mmol) were dissolved in 100 mL of ethanol and refluxed overnight. The solvent was then evaporated under reduced pressure and 65 mL of 7.5 M NaOH (aq) was added.…”

Harnessing “Click”‐Type Chemistry for the Preparation of Novel Electronic Materials

“…2,3‐Dihdro‐thieno[3,4‐b][1,4]dioxine‐5‐carbaldehyde ( 13 ):28 3,4‐Ethyle­nedioxythiophene (2 mL, 18 mmol) was dissolved in dry DMF (10 mL, 126 mmol), the solution was cooled to −10 °C and POCl 3 (1.76 mL, 18 mmol) was added dropwise over 15 min. The mixture was then allowed to reach room temperature then stirred for an additional hour.…”