DBU as an N alpha-deprotecting reagent for the fluorenylmethoxycarbonyl group in continuous flow solid-phase peptide synthesis.

: The versatility and efficiency of the N alpha-fluorenylmethoxycarbonyl method of solid-phase peptide synthesis have been further enhanced by recent and continuing refinements in side-chain protecting group, linker and amino acid-coupling technology. In contrast, comparatively little work has been carried out on studying and further improving the N alpha-deprotection step. This report demonstrates that, in low concentrations, the non-nucleophilic amidine 1,8-diazabicyclo[5.4.0]undec-7-ene is a preferred alternative to the more commonly employed piperidine for the rapid and efficient cleavage of the N alpha-fluorenylmethoxycarbonyl group in the continuous flow method of solid-phase peptide synthesis. In the cases studied, use of this base did not cause cyclization of Asp(OBut)-Gly or Asn-Gly sequence to succinimide derivatives. At the recommended concentration of 2% 1,8-diazabicyclo[5.4.0]undec-7-ene in dimethylformamide, racemization of resin-bound C-terminal S-trityl cysteine was substantially reduced compared with standard piperidine-mediated deprotection conditions. Additionally, use of the base appears to reduce the extent of broadening of ultraviolet fluorenylmethoxycarbonyl-deprotection peaks occasionally observed when piperidine is employed, indicating that its reaction kinetics and mode of action are different.