Redesign of a cross-reactive antibody to dengue virus with broad-spectrum activity and increased in vivo potency

Proc Natl Acad Sci U S A. 2013 Apr 23;110(17):E1555-64. doi: 10.1073/pnas.1303645110. Epub 2013 Apr 8.


Affinity improvement of proteins, including antibodies, by computational chemistry broadly relies on physics-based energy functions coupled with refinement. However, achieving significant enhancement of binding affinity (>10-fold) remains a challenging exercise, particularly for cross-reactive antibodies. We describe here an empirical approach that captures key physicochemical features common to antigen-antibody interfaces to predict protein-protein interaction and mutations that confer increased affinity. We apply this approach to the design of affinity-enhancing mutations in 4E11, a potent cross-reactive neutralizing antibody to dengue virus (DV), without a crystal structure. Combination of predicted mutations led to a 450-fold improvement in affinity to serotype 4 of DV while preserving, or modestly increasing, affinity to serotypes 1-3 of DV. We show that increased affinity resulted in strong in vitro neutralizing activity to all four serotypes, and that the redesigned antibody has potent antiviral activity in a mouse model of DV challenge. Our findings demonstrate an empirical computational chemistry approach for improving protein-protein docking and engineering antibody affinity, which will help accelerate the development of clinically relevant antibodies.

Publication types

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

MeSH terms

  • Animals
  • Antibodies, Neutralizing / biosynthesis*
  • Antibodies, Viral / biosynthesis*
  • Antibody Affinity / genetics
  • Binding Sites, Antibody / genetics
  • Cross Reactions / immunology
  • Dengue Virus / immunology*
  • Enzyme-Linked Immunosorbent Assay
  • Epitopes / genetics
  • Mice
  • Models, Immunological
  • Protein Binding
  • Protein Engineering / methods*
  • Real-Time Polymerase Chain Reaction
  • Surface Plasmon Resonance


  • Antibodies, Neutralizing
  • Antibodies, Viral
  • Epitopes