Residue-Based Preorganization of BH3-Derived α/β-Peptides: Modulating Affinity, Selectivity and Proteolytic Susceptibility in α-Helix Mimics

ACS Chem Biol. 2015 Jul 17;10(7):1667-75. doi: 10.1021/acschembio.5b00109. Epub 2015 May 7.

Abstract

We report progress toward a general strategy for mimicking the recognition properties of specific α-helices within natural proteins through the use of oligomers that are less susceptible than conventional peptides to proteolysis. The oligomers contain both α- and β-amino acid residues, with the density of the β subunits low enough that an α-helix-like conformation can be adopted but high enough to interfere with protease activity. Previous studies with a different protein-recognition system that suggested ring-constrained β residues can be superior to flexible β residues in terms of maximizing α/β-peptide affinity for a targeted protein surface. Here, we use mimicry of the 18-residue Bim BH3 domain to expand the scope of this strategy. Two significant advances have been achieved. First, we have developed and validated a new ring-constrained β residue that bears an acidic side chain, which complements previously known analogues that are either hydrophobic or basic. Second, we have discovered that placing cyclic β residues at sites that make direct contact with partner proteins can lead to substantial discrimination between structurally homologous binding partners, the proteins Bcl-xL and Mcl-1. Overall, this study helps to establish that α/β-peptides containing ring-preorganized β residues can reliably provide proteolytically resistant ligands for proteins that naturally evolved to recognize α-helical partners.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Apoptosis
  • Cell Line
  • Humans
  • Mice
  • Molecular Docking Simulation
  • Molecular Sequence Data
  • Myeloid Cell Leukemia Sequence 1 Protein / chemistry
  • Myeloid Cell Leukemia Sequence 1 Protein / metabolism*
  • Peptide Fragments / chemistry*
  • Peptide Fragments / metabolism*
  • Peptides, Cyclic / chemistry
  • Peptides, Cyclic / metabolism
  • Protein Binding
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Proto-Oncogene Proteins / chemistry*
  • Proto-Oncogene Proteins / metabolism*
  • bcl-X Protein / chemistry
  • bcl-X Protein / metabolism*

Substances

  • Bax protein (53-86)
  • Myeloid Cell Leukemia Sequence 1 Protein
  • Peptide Fragments
  • Peptides, Cyclic
  • Proto-Oncogene Proteins
  • bcl-X Protein