Peptoids

Peptoids are peptidomimetic polymers comprised of glycine subunits, where the side‐chains are located on the nitrogen atom of the amide backbone rather than the α‐carbon as is the case in peptides. Peptoids lack conformational rigidity in comparison to α-peptides and placement of the monomer side chains on the amide nitrogen makes the peptoid backbone achiral. The amide bonds are now tertiary and the absence of amide protons means secondary structure cannot be stabilized by hydrogen bonding in the same manner as in peptides. These characteristics make peptoids highly flexible, with properties dominated by the side-chain identity and monomer sequence.

There is as yet no universally accepted convention for the naming or abbreviation of peptoid monomers. Throughout the Isca website and literature the following nomenclature is used: a capital “N” to indicate the side chain is on the glycine nitrogen atom, followed by two or three characters. For side chains representing naturally occurring peptides we use the standard three digit amino acid abbreviation following the “N”, with the first letter capitalised (for example NAla, NMet, NSer). For side chains representing non naturally occurring peptides a similar system is used but with a two or three letter code, now in lower case. For example, the amine building block (S)-(1-phenylethyl)amine is abbreviated spe, and the peptoid monomer N-(S)-(1-phenylethyl)glycine is abbreviated Nspe. Usually, the three-letter codes refer to the α-chiral side chains, and the first letter designates stereochemistry (r or s for R or S). For achiral side chains, two-letter codes are used, for example Nme for N-(2-methoxyethyl)glycine.

Below are some of the abbreviations for peptoid monomers used throughout our website.

Abbreviation                                                                                         Peptoid monomer

Nae                                                                                                        N-(2-aminoethyl)glycine

Nah                                                                                                       N-(2-aminohexyl)glycine

Nfur                                                                                                       N-(2-furfuryl)glycine

NGlu                                                                                                      N-(2-carboxyethyl)glycine

NHis                                                                                                      N-(methylimidazole)glycine

NLeu                                                                                                     N-substituted leucine

NLys                                                                                                     N-(4-aminobutyl)glycine

NLys(Me)3                                                                                           N-(4-(Nε,Nε,Nε-trimethylammonium)butyl)glycine

Nme                                                                                                      N-(2-methoxyethyl)glycine

NPhe                                                                                                    N-(phenylmethyl)glycine

Nrpe                                                                                                      N-(R)-(1-phenylethyl)glycine

Nsmb                                                                                                     N-(S)-(1-methylbutyl)glycine

Nsna                                                                                                      N-(S)-(1-naphthylethyl)glycine

Nspe                                                                                                      N-(S)-(1-phenylethyl)glycine

Nssb                                                                                                      N-(S)-(sec-butyl)glycine

Ntma                                                                                                      N-(2-thiophenemethyl)glycine

Ntri                                                                                                         N-(tridecyl)glycine

Peptoid Calculator

Peptoid calculator is a peptoid chemical formula and molecular weight calculator and MS peak assignment tool.

Peptoid sequences can be entered using multiple-letter building block codes.  N- and C-termini can be selected from the predefined lists or as custom termini entered as chemical formulae.

Further information on peptoids

Chongsiriwatana et al (2008) Peptoids that mimic the structure, function, and mechanism of helical antimicrobial peptides. Proc. Natl. Acad. Sci 105(8) 2794 PMID: 18287037

Fowler and Blackwell (2009) Structure-function relationships in peptoids: recent advances toward deciphering the structural requirements for biological function. Org. Biomol. Chem. 7(8):1508 PMID: 19343235

Zuckermann (2011) Peptoid origins. Biopolymers, 96 545 PMID: 21184486