A cyclic peptidic serine protease inhibitor: increasing affinity by increasing peptide flexibility

PLoS One. 2014 Dec 29;9(12):e115872. doi: 10.1371/journal.pone.0115872. eCollection 2014.


Peptides are attracting increasing interest as protease inhibitors. Here, we demonstrate a new inhibitory mechanism and a new type of exosite interactions for a phage-displayed peptide library-derived competitive inhibitor, mupain-1 (CPAYSRYLDC), of the serine protease murine urokinase-type plasminogen activator (uPA). We used X-ray crystal structure analysis, site-directed mutagenesis, liquid state NMR, surface plasmon resonance analysis, and isothermal titration calorimetry and wild type and engineered variants of murine and human uPA. We demonstrate that Arg6 inserts into the S1 specificity pocket, its carbonyl group aligning improperly relative to Ser195 and the oxyanion hole, explaining why the peptide is an inhibitor rather than a substrate. Substitution of the P1 Arg with novel unnatural Arg analogues with aliphatic or aromatic ring structures led to an increased affinity, depending on changes in both P1 - S1 and exosite interactions. Site-directed mutagenesis showed that exosite interactions, while still supporting high affinity binding, differed substantially between different uPA variants. Surprisingly, high affinity binding was facilitated by Ala-substitution of Asp9 of the peptide, in spite of a less favorable binding entropy and loss of a polar interaction. We conclude that increased flexibility of the peptide allows more favorable exosite interactions, which, in combination with the use of novel Arg analogues as P1 residues, can be used to manipulate the affinity and specificity of this peptidic inhibitor, a concept different from conventional attempts at improving inhibitor affinity by reducing the entropic burden.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Binding Sites
  • Calorimetry
  • Crystallography, X-Ray
  • Humans
  • Magnetic Resonance Spectroscopy
  • Mice
  • Molecular Sequence Data
  • Mutagenesis, Site-Directed
  • Mutant Proteins / chemistry
  • Peptides, Cyclic / chemistry
  • Peptides, Cyclic / pharmacology*
  • Protein Binding / drug effects
  • Serine Proteinase Inhibitors / chemistry
  • Serine Proteinase Inhibitors / pharmacology*
  • Surface Plasmon Resonance


  • Mutant Proteins
  • Peptides, Cyclic
  • Serine Proteinase Inhibitors
  • mupain-1

Associated data

  • PDB/4X1N
  • PDB/4X1Q
  • PDB/4X1R
  • PDB/4X1S
  • figshare/10.6084/M9.FIGSHARE.1257686

Grant support

This work was supported by the Danish National Research Foundation (http://dg.dk; grant number 26-331-6 to PAA), the Natural Science Foundation of China (http://en.ustc.edu.cn/dictionary/201105/t20110509_111378.html; grant numbers 31161130356, 31170707, 31370737 to M. Huang), the Natural Science Foundation of the Fujian Province (grant number 2012J05071 to M. Huang), the Lundbeck Foundation (http://www.lundbeckfoundation.com; grant number R83-A7826 to PAA), the Carlsberg Foundation (http://www.carlsbergfondet.dk; grant number 2012_01_0642 to PAA), and the Cancer Research Foundation of 1989 (to PAA). PAA was awarded a Chinese Academy of Sciences visiting professorship for senior international scientists (grant number 2012T1G0023). M. Huang was awarded an Aarhus University Research Foundation visiting professorship (reference number 10). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.