Peptide (revision 35)

A peptide is a molecule composed of amino acid residues joined by amide bonds formed between the carboxyl group of one residue and the amino group of the next. The boundary with protein is conventional rather than physical; a common cut is around fifty residues, and regulatory definitions differ from chemical usage.^[1]

Peptides are directional. By convention a sequence is written from the free amino terminus to the free carboxyl terminus, and the direction is not arbitrary: the same residues in reverse order are a different molecule with different properties. This is the reason a sequence given without its direction is ambiguous.^[1]

Almost everything else on this wiki is a peptide or is about peptides — their synthesis, their analysis, their handling and their supply. Peptides sold for laboratory research are not approved for human use, whatever their sequence resembles; see Research use only.

The amide bond has partial double-bond character, which restricts rotation and makes the six atoms of the peptide unit approximately planar. Conformational freedom therefore resides in the two dihedral angles either side of each α-carbon, and it is the accessible combinations of these that give rise to the α-helix, the β-sheet and the turn.^[1]

Peptides of fewer than about fifteen residues are usually conformationally disordered in solution, sampling many states; longer chains can adopt a persistent fold. Several of the therapeutic peptides discussed on this wiki are helical over part of their length when bound to their receptor but substantially disordered when free, which matters for how they are analysed and stored.

Side chains determine chemistry. Charged residues set the isoelectric point and therefore the pH of minimum solubility; hydrophobic residues drive aggregation; asparagine, glutamine and methionine introduce the specific chemical liabilities discussed at Deamidation and Methionine oxidation.

Numbering is a frequent source of confusion in the incretin literature, because GLP-1 is numbered from the N-terminus of proglucagon-derived GLP-1(1–37) while its active form begins at residue 7. The same substitution is therefore described as being at position 2 or position 8 depending on convention, which is why semaglutide is described both as having Aib at position 8 and as having a substitution at the second residue of the active peptide.^[1]

Non-proteinogenic residues are common in engineered peptides and are the main reason a peptide drug cannot generally be produced by biological expression. See Solid-phase peptide synthesis.

Peptides occupy a middle ground between small molecules and proteins. They bind large, flat protein-protein interfaces that small molecules bind poorly, while remaining accessible to chemical synthesis, which proteins are not.^[2]

Their liabilities are equally characteristic. Oral bioavailability is negligible without a formulation strategy, because gastrointestinal proteases and the intestinal barrier remove them. Circulating half-life is short unless engineered — see Albumin binding half-life extension. They are chemically labile in solution in ways small molecules are not, which drives the reliance on lyophilised presentations and a cold chain.

Because they are made by stepwise chemical synthesis, the impurity profile of a peptide is distinctive: deletion sequences missing one residue, truncated sequences, and modified side chains, all structurally close to the intended molecule and often chromatographically close as well. This is why method specificity against process-related impurities carries the weight it does in peptide analysis, and why a specification is judged by which attributes it covers rather than by the number it reports.^[2][3]

A large market exists in peptides supplied for laboratory research. Material in that market is not manufactured under a marketing authorisation, is not released against a pharmacopoeial monograph, and is described by whatever documentation the supplier chooses to provide.^[4]

The documentation most often supplied is a certificate of analysis. What such a document establishes depends entirely on which determinations it reports: an area percent figure without peptide content and water does not establish how much peptide is present, and a purity figure without an identity determination does not establish what the peptide is.^[2]

This wiki documents these instruments and their limits. It sells nothing, is independent of every supplier named in it, and does not represent research-use material as suitable for human administration.

• Peptide synthesis
• Solid-phase peptide synthesis
• Research use only
• Certificate of analysis
• Peptide aggregation
• Glossary of peptide terminology