De novo design of an IL-4 antagonist and its structure at 1.9 A

Proc Natl Acad Sci U S A. 2005 Feb 8;102(6):1889-94. doi: 10.1073/pnas.0408890102. Epub 2005 Jan 31.

Abstract

An IL-4 antagonist was designed based on structural and biochemical analysis of unbound IL-4 and IL-4 in complex with its high-affinity receptor (IL-4Ralpha). Our design strategy sought to capture a protein-protein interaction targeting the high affinity that IL-4 has for IL-4Ralpha. This strategy has impact due to the potential relevance of IL-4Ralpha as a drug target in the treatment of asthma. To mimic the IL-4 binding surface, critical side chains for receptor binding were identified, and these side chains were transplanted onto a previously characterized, de novo-designed four-helix protein called designed helical protein 1 (DHP-1). This first-generation design resolved the ambiguity previously described for the connectivity between helices in DHP-1 and resulted in a protein capable of binding to IL-4Ralpha. The second-generation antagonist was based upon further molecular modeling, and it succeeded in binding IL-4Ralpha better than the first-generation. This protein, termed DHP-14-AB, yielded a protein with a cooperative unfolding transition (DeltaGu0=8.1 kcal/mol) and an IC50 of 27 microM when in competition with IL-4 whereas DHP-1 had no affinity for IL-4Ralpha. The crystal structure of DHP-14-AB was determined to 1.9-A resolution and was compared with IL-4. This comparison revealed how design strategies targeting protein-protein interactions require high-resolution 3D data and the incorporation of orientation-specific information at the level of side-chains and secondary structure element interactions.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Crystallography, X-Ray
  • Drug Design
  • Interleukin-4 / antagonists & inhibitors*
  • Interleukin-4 / chemistry*
  • Interleukin-4 / genetics
  • Interleukin-4 / metabolism
  • Models, Molecular
  • Protein Engineering*
  • Protein Structure, Secondary
  • Protein Structure, Tertiary*
  • Proteins / chemistry*
  • Receptors, Interleukin-4 / chemistry*
  • Receptors, Interleukin-4 / genetics
  • Receptors, Interleukin-4 / metabolism

Substances

  • DHP-14-AB protein
  • Proteins
  • Receptors, Interleukin-4
  • Interleukin-4

Associated data

  • PDB/1Y4C