Project Details Nomenclature of cyclic peptides

Project No.:
2004-024-1-800
Start Date:
01 June 2004
End Date:

Objective

To extend rule 3AA-19.5 of the Nomenclature and Symbolism for Amino Acids and Peptides (Recommendations 1983) to cover all classes of cyclic peptides.

Description

Cyclic peptides are briefly considered in the Nomenclature and Symbolism for Amino Acids and Peptides (recommendations 1983) [1] in part 2 under symbolism (see 3AA-19.5). There are no recommendations on naming these peptides. This deficiency will be rectified by the proposed recommendations which will be based on the established procedures for naming peptides [1] and recommendation RF-4.3 in Revised Section F: Natural Products and Related Compounds (IUPAC Recommendations 1999) [3], rule C-44.1 and C-212.2 of the IUPAC Nomenclature of Organic Chemistry (1979) [4], R-1.2.6.1 and R-5.5.4.4 of A Guide to IUPAC Nomenclature of Organic Chemistry (1993) [5] and rule 2-Carb-26 of the Nomenclature of Carbohydrate [6].

The recommendations will include rings generated from an acyclic peptide by formation of a peptide or ester bond; by a disulfide link; or by a new carbon-carbon, carbon-nitrogen, nitrogen-oxygen or carbon-sulfur bond (not esters or amides). These new bonds are indicated by the prefix anhydro, cyclo or epoxy, or combinations of them. The inclusion of modified standard amino acids or amino acids not related to standard amino acids will be considered. Any stereochemistry generated by ring formation will be indicated using standard organic conventions.

References

  1. JCBN, Nomenclature and Symbolism for Amino Acids and Peptides, Recommendations 1983, Biochem. J. 219, 345-373 (1984); Eur. J. Biochem. 138, 9-37 (1984) and 152, 1 (1985); Int. J. Pept. Prot. Res. 24, following p. 84 (1984); J. Biol. Chem. 260, 14-42 (1985); Pure Appl. Chem. 56, 595-624 (1984); ‘Amino Acids and Peptides’ (Jones, J.H., ed.) Specialist Periodical Report, The Royal Society of Chemistry, 16, 387-410 (1985), and also on pp. 39-67 in [2].
  2. IUBMB (1992) Biochemical Nomenclature and Related Documents, 2nd edition, Portland Press, London.
  3. IUPAC Commission on the Nomenclature of Organic Chemistry (CNOC), Nomenclature of Organic Chemistry, Revised Section F: Natural Products and Related Compounds, (IUPAC Recommendations 1999), Pure Appl. Chem. 71, 587-643 (1999).
  4. IUPAC (1979) Nomenclature of Organic Chemistry, Sections A, B, C, D, E, F, and H, Pergamon Press, Oxford.
  5. IUPAC (1993) A Guide to IUPAC Nomenclature of Organic Chemistry, Recommendations 1993, Blackwell Scientific Publications, Oxford.
  6. JCBN, Nomenclature of Carbohydrate, Recommendations 1996, Adv. Carbohydr. Chem. Biochem. 52, 43-177 (1997), Carbohydr. Res. 297, 1-90 (1997), J. Carbohydr. Chem. 16, 1191-1280 (1997), Pure Appl. Chem. 68, 1919-2008 (1996).

Progress

In June 2004, a draft arising from the work carried out under the auspices of the IUPAC-IUBMB Joint Commission on Biochemical Nomenclature has been made available to Division VIII for comments. After that initial review period a revised version will be prepared for public review.

A draft document was submitted to public review comments until 31 March 2005. (../reports/provisional/abstract04/moss_310305.html)