Rational Design of a 310 -Helical PIP-Box Mimetic Targeting PCNA, the Human Sliding Clamp

Chemistry. 2018 Aug 6;24(44):11325-11331. doi: 10.1002/chem.201801734. Epub 2018 Jul 19.


The human sliding clamp (PCNA) controls access to DNA for many proteins involved in DNA replication and repair. Proteins are recruited to the PCNA surface by means of a short, conserved peptide motif known as the PCNA-interacting protein box (PIP-box). Inhibitors of these essential protein-protein interactions may be useful as cancer therapeutics by disrupting DNA replication and repair in these highly proliferative cells. PIP-box peptide mimetics have been identified as a potentially rapid route to potent PCNA inhibitors. Here we describe the rational design and synthesis of the first PCNA peptidomimetic ligands, based on the high affinity PIP-box sequence from the natural PCNA inhibitor p21. These mimetics incorporate covalent i,i+4 side-chain/side-chain lactam linkages of different lengths, designed to constrain the peptides into the 310 -helical structure required for PCNA binding. NMR studies confirmed that while the unmodified p21 peptide had little defined structure in solution, mimetic ACR2 pre-organized into 310 -helical structure prior to interaction with PCNA. ACR2 displayed higher affinity binding than most known PIP-box peptides, and retains the native PCNA binding mode, as observed in the co-crystal structure of ACR2 bound to PCNA. This study offers a promising new strategy for PCNA inhibitor design for use as anti-cancer therapeutics.

Keywords: DNA; NMR spectroscopy; X-ray diffraction; peptidomimetics; protein-protein interactions.

MeSH terms

  • Amino Acid Motifs
  • Binding Sites
  • Biochemical Phenomena
  • Crystallography, X-Ray
  • Cyclin-Dependent Kinase Inhibitor p21 / chemistry*
  • Humans
  • Lactams / chemistry
  • Ligands
  • Magnetic Resonance Spectroscopy
  • Models, Molecular
  • Peptides / chemistry*
  • Peptidomimetics / chemistry
  • Proliferating Cell Nuclear Antigen / chemistry*
  • Protein Conformation, alpha-Helical


  • Cyclin-Dependent Kinase Inhibitor p21
  • Lactams
  • Ligands
  • Peptides
  • Peptidomimetics
  • Proliferating Cell Nuclear Antigen