Countering cooperative effects in protease inhibitors using constrained beta-strand-mimicking templates in focused combinatorial libraries

J Med Chem. 2004 Mar 25;47(7):1641-51. doi: 10.1021/jm030337m.


A major problem in de novo design of enzyme inhibitors is the unpredictability of the induced fit, with the shape of both ligand and enzyme changing cooperatively and unpredictably in response to subtle structural changes within a ligand. We have investigated the possibility of dampening the induced fit by using a constrained template as a replacement for adjoining segments of a ligand. The template preorganizes the ligand structure, thereby organizing the local enzyme environment. To test this approach, we used templates consisting of constrained cyclic tripeptides, formed through side chain to main chain linkages, as structural mimics of the protease-bound extended beta-strand conformation of three adjoining amino acid residues at the N- or C-terminal sides of the scissile bond of substrates. The macrocyclic templates were derivatized to a range of 30 structurally diverse molecules via focused combinatorial variation of nonpeptidic appendages incorporating a hydroxyethylamine transition-state isostere. Most compounds in the library were potent inhibitors of the test protease (HIV-1 protease). Comparison of crystal structures for five protease-inhibitor complexes containing an N-terminal macrocycle and three protease-inhibitor complexes containing a C-terminal macrocycle establishes that the macrocycles fix their surrounding enzyme environment, thereby permitting independent variation of acyclic inhibitor components with only local disturbances to the protease. In this way, the location in the protease of various acyclic fragments on either side of the macrocyclic template can be accurately predicted. This type of templating strategy minimizes the problem of induced fit, reducing unpredictable cooperative effects in one inhibitor region caused by changes to adjacent enzyme-inhibitor interactions. This idea might be exploited in template-based approaches to inhibitors of other proteases, where a beta-strand mimetic is also required for recognition, and also other protein-binding ligands where different templates may be more appropriate.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Combinatorial Chemistry Techniques
  • Crystallography, X-Ray
  • Databases, Factual*
  • Drug Design*
  • HIV Protease / chemistry
  • Ligands
  • Models, Molecular
  • Molecular Conformation
  • Molecular Mimicry
  • Oligopeptides / chemical synthesis
  • Oligopeptides / chemistry
  • Protease Inhibitors / chemical synthesis
  • Protease Inhibitors / chemistry*
  • Protein Binding
  • Protein Structure, Secondary


  • Ligands
  • Oligopeptides
  • Protease Inhibitors
  • HIV Protease