Native chemical ligation is a technique for constructing a large peptide from two or more smaller peptides, with C-terminal thioesters and N-terminal cysteines. This process was developed by Phillip Dawson and Stephen Kent at The Scripps Research Institute in 1994, about the same time that inteins were discovered, which is nature's analogous reaction.

Peptides synthesized by native chemical ligation must be handled carefully; the thioester piece cannot be synthesized with a nucleophilic base, thus favoring BOC chemistry. FMOC techniques for generating thioesters involving the reduction of a sulfone are known. Protecting groups on the N-terminal piece cannot have constituents which release as aldehydes or ketones since these will cap the n-terminal cysteine. For the same reason, acetone should be avoided in general use, particularly prior to lyophilization and in washing glassware.

The payoff is that coupling long peptides by this technique is in many cases nearly quantitative and provides synthetic access to proteins otherwise impossible to make, due to length or decoration by posttranslational modification.

Access to large proteins (in excess of 300 amino acids or so) is still impossible even with native chemical ligation, although c-terminal thioesters can be reacted with an extein from an intein system to provide semisynthesized proteins.

By exploiting natures inteins it is possible to prepare a recombinant C-terminal thioester. This removes the size restriction of the C-terminal thioester fragment. The recombinant thioester can be ligated to a synthetic peptide bearing an N-terminal cysteine. Native Chemical Ligations of this kind using recombinant C-terminal thioesters is known as Expressed Protein Ligation.