Natural peptides are built almost entirely from L-amino acids, and the body's enzymes are tuned to recognise them. Changing the building blocks or the backbone gives chemists powerful ways to control stability, shape and binding. Molecules that imitate peptides with modified chemistry are called peptidomimetics.
Chirality: left- and right-handed amino acids
Every standard amino acid except glycine is chiral: it exists in two mirror-image forms, L and D. Proteins are built from L-forms, but D-amino acids do occur in nature:
- Bacterial cell walls contain D-alanine and D-glutamate.
- Dermorphin, an opioid peptide from frog skin, contains a D-alanine that is essential for its activity.
- The antibiotic gramicidin A alternates L- and D-residues.
Why D-amino acids help
Proteases are themselves chiral and mostly don't recognise D-residues. Swapping a single L-residue at a cleavage site for its D-form can greatly extend a peptide's lifetime in serum. The trade-off is that D-residues change the local shape, so they have to be placed carefully to keep activity.
Mirror-image strategies
- All-D peptides are almost completely protease-resistant, but they fold into the mirror image of the original shape.
- Retro-inverso peptides use D-residues in reversed order, roughly recreating the side-chain layout of the original.
- Mirror-image phage display, first reported in 1996, screens L-peptide libraries against a synthetic D-version of the target. The mirror image of each hit is then a D-peptide that binds the natural target.
Backbone modifications
| Modification | What changes | Effect |
|---|---|---|
| N-methylation | Methyl group on a backbone nitrogen | Protease resistance; can improve membrane permeability (as in cyclosporin) |
| β-amino acids | An extra carbon in the backbone | New folding patterns and strong protease resistance |
| Peptoids | Side chain moved from carbon to nitrogen | Easy to make, very protease-resistant, more flexible |
| Aza-peptides | A backbone carbon replaced by nitrogen | Changes shape and stability locally |
Locking the shape: stapling and cyclisation
Hydrocarbon stapling, developed in the early 2000s, links two side chains one or two helical turns apart with an all-carbon bridge, holding the peptide in a helix. Stapled helices can resist proteases and, in some cases, enter cells. Ring-closing strategies more generally are covered in Cyclic peptides in nature.
Unnatural side chains
Beyond the 20 standard amino acids, chemists can add hundreds of non-canonical ones, such as fluorinated, extended or conformationally locked residues, to fine-tune binding and stability. Modern display methods can even build some of them into huge screening libraries.
Related articles
- How laboratories validate analytical methods
- Why some peptides are hard to make
- Mass spectrometry explained for peptides
Sources and further reading
- Schumacher TNM et al. Identification of D-peptide ligands through mirror-image phage display. Science 1996;271:1854–1857. doi:10.1126/science.271.5257.1854 · PMID: 8596952
- Zuckermann RN et al. Efficient method for the preparation of peptoids [oligo(N-substituted glycines)] by submonomer solid-phase synthesis. J Am Chem Soc 1992;114:10646–10647. doi:10.1021/ja00052a076
- Schafmeister CE, Po J, Verdine GL. An all-hydrocarbon cross-linking system for enhancing the helicity and metabolic stability of peptides. J Am Chem Soc 2000;122:5891–5892. doi:10.1021/ja000563a
- Craik DJ, Fairlie DP, Liras S, Price D. The future of peptide-based drugs. Chem Biol Drug Des 2013;81:136–147. doi:10.1111/cbdd.12055 · PMID: 23253135