Stapled Peptides as Potential Therapeutics

Abstract

Stapled peptides are an important class of conformationally constrained, bioactive α‐helical peptides. They have been used extensively as chemical probes for the regulation of protein–protein interactions (PPIs), with one currently progressing through late‐stage clinical trials as a peptide drug candidate. Their ability to interact with shallow protein–protein interfaces, which have previously proven to be challenging to target with small molecules, has led to their rapid uptake by the chemical biology and drug discovery communities. Stapled peptides overcome some of the undesirable physicochemical properties that limit the use of peptides as therapeutics. They generally exhibit good binding affinity and specificity as they aim to accurately reproduce the α‐helix recognition motif from a PPI interface. They are protease resistant and in some instances have shown good cell permeability. The development of stapled peptides has thus resulted in a transformative shift by validating difficult PPIs as therapeutic targets and providing promising drug candidates.

Key Concepts

  • Stapled peptides are conformationally constrained α‐helical peptides.
  • Stapling reduces the entropic penalty of folding to produce the bioactive conformation, thus giving an increase in binding affinity over an unfolded peptide.
  • Through mimicking the interface these compounds have good binding affinity and specificity.
  • Proteolytic stability is enhanced through the induction of secondary structure and the effective shielding of the peptide backbone from recognition by protease enzymes.
  • Cell permeability can be enhanced by peptide stapling as the distribution of lipophilicity compared to the native peptide is altered.
  • Key PPIs implicated in cancer, including p53‐MDM2/MDMX, Aurora‐A/TPX2 and the Bcl family, have been probed using stapled peptides.

Keywords: stapled peptide; protein–protein interaction; α‐helix; chemical probe; therapeutic; peptidomimetic

Figure 1. (a) Crystal structure of MDM2 bound to transactivation domain of p53 showing interfacial residues between peptide and protein (red). Calculated using Pymol Interface Residues, PDB:1YCR. (b) Crystal structure of a small molecule – Nutlin‐3a (green) – bound to MDM2 (PDB:1YCR). Interactions between Nutlin‐3a and the protein (pink). This demonstrates that a small molecule typically binds in a small hydrophobic pocket versus larger surface area covered by a peptide (PDB:1RV1).
Figure 2. Unnatural amino acids incorporated during peptide synthesis for an i,i + 4 hydrocarbon staple (2 × S 5) and for an i,i + 7 staple (R 8 and S 5). The constraint is formed via a ring closing metathesis reaction on resin. Native peptides are susceptible to proteolytic degradation, whereas stapled peptides have been shown to be resistant to protease degradation.
Figure 3. Crystal structure of ATSP‐7041 (green) bound to MDMX (turquoise – PDB:4N5T). Y22 (blue) has water‐mediated hydrogen bond with H68 (blue). Hydrophobic interactions between the staple (red) and MDMX (K47, M50, H51, G54, Q55 and M58) are shown in red. Structures of WT‐p53, SAH‐p53‐8 and ATSP‐7041 are shown for comparison where X = β‐cyclobutyl‐l‐alanine and R 8/S 5 are the unnatural amino acids required for stapling.
Figure 4. Crystal structure of SAH‐MS1‐18 (dark green) bound to human Mcl‐1 (light green – PDB:5W89). Hydrophobic interactions between the staple and Mcl‐1 (V249, M250, H252 and V253) are shown in red. A hydrogen bonding network between D264 of the peptide and Mcl‐1 is shown in orange.
Figure 5. (a) Crystal structure of Aurora‐A (grey) bound to stapled TPX2 (green – PDB:5LXM) with native TPX2 (turquoise – PDB:1OL5) overlaid. (b) Salt bridges between K38 (TPX2) and E183 (Aurora‐A). (c) Salt bridges between E36 (TPX2) and K250 (Aurora‐A).
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Further Reading

Cromm PM , Spiegel J and Grossmann TN (2015) Hydrocarbon stapled peptides as modulators of biological function. ACS Chemical Biology 10: 1362–1375.

Verdine GL and Hilinski GJ (2012) Stapled peptides for intracellular drug targets. Methods in Enzymology 503: 3–33.

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McDougall, Laura, and Jamieson, Andrew G(Mar 2019) Stapled Peptides as Potential Therapeutics. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0028403]