Kinetic and Mechanistic Studies of Native Chemical Ligation with Phenyl Α-Selenoester Peptides

Native chemical ligation (NCL) ligates two unprotected peptides in an aqueous buffer. One of the fragments features a C-terminal alpha-thioester functional group, and the second bears an N-terminal cysteine. The reaction mechanism depicts two steps: an intermolecular thiol-thioester exchange resulting in a transient thioester, followed by an intramolecular S-to-N acyl shift to yield the final native peptide bond. Although this mechanism is well established, the direct observation of the transient thioester has been elusive because the fast intramolecular rearrangement prevents its accumulation. Here, the use of alpha-selenoester peptides allows a faster first reaction and an early buildup of the intermediate, enabling its quantification and the kinetic monitoring of the first and second steps. The results show a correlation between the steric hindrance in the alpha-thioester residue and the rearrangement rate. In bulky residues, the S-to-N acyl shift has a significant contribution to the overall reaction rate. This is particularly notable for valine and likely for other similar beta-branched amino acids.