Three-dimensional model of the BR96 monoclonal antibody variable fragment

Molecular modeling was used to build a three-dimensional model of the variable regions of the tumor-reactive monoclonal antibody BR96. An immunoconjugate of this antibody with the anticancer drug doxorubicin is currently in a phase I clinical trial for the treatment of solid tumors. A model structure of the BR96 variable fragment was generated to guide site-specific mutagenesis experiments and further improve the affinity of the antibody. The model displayed a distinct groove-type binding site which contained a significant number of aromatic residues. The dimensions and nature of the proposed binding site were consistent with the binding of the Ley tetrasaccharide which was found to bind to BR96. On the basis of the model, some BR96 residues are proposed to be crucial for antigen binding. BR96 and its complex with the Ley determinant have recently been crystallized, and structure determination is currently underway. Therefore, the detailed prediction of the BR96 combining site will soon be assessed, as a "blind test", based on crystallographic data.