Conformationally homogeneous cyclic tetrapeptides: useful new three-dimensional scaffolds

J Am Chem Soc. 2003 Jan 22;125(3):640-1. doi: 10.1021/ja029205t.

Abstract

The most commonly recognized motifs in protein-protein interactions are gamma and beta turns, which are defined by three to four contiguous amino acids in a peptide sequence. Cyclic tetrapeptides thus represent minimalist turn mimetics, but their usefulness is compromised by strain in their 12-membered rings, making them difficult to cyclize, unstable to hydrolysis/metabolism, and conformationally heterogeneous in polar solvents. Appropriate placement of a beta amino acid in a tetrapeptide creates a 13-membered ring that is shown to be easier to cyclize, hydrolytically more stable, and conformationally homogeneous in polar solvents such as DMSO and water. Three-dimensional structures reveal that these cyclic tetrapeptides are novel rigid scaffolds, their unique side-chain projections matching a structurally diverse range of useful nonpeptidic templates, including sugars and spirocyclic compounds, found as components of natural products. The results provide a potentially useful link between protein architecture and organic natural products. On the basis of protein turn sequences (not protein structures) alone simple cyclic tetrapeptide libraries with a beta amino acid can be rationally designed as conformationally restricted, easily synthesized, and stereochemically controlled screening tools for rapidly identifying pharmacophore space that can then be computer-matched to more complex known natural product templates for drug development.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aminobutyrates / chemistry*
  • Crystallography, X-Ray
  • Models, Molecular
  • Nuclear Magnetic Resonance, Biomolecular
  • Oligopeptides / chemistry*
  • Peptides, Cyclic / chemistry*
  • Protein Structure, Secondary
  • Thermodynamics

Substances

  • Aminobutyrates
  • Oligopeptides
  • Peptides, Cyclic
  • 2-amino-4-phenylbutyric acid