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A universal combinatorial design of antibody framework to graft distinct CDR sequences: A bioinformatics approach
Author(s) -
Haidar Jaafar N.,
Yuan QingAn,
Zeng Lin,
Snavely Mark,
Luna Xenia,
Zhang Haifan,
Zhu Wei,
Ludwig Dale L.,
Zhu Zhenping
Publication year - 2012
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.23246
Subject(s) - monoclonal antibody , antibody , epitope , phage display , computational biology , sequence (biology) , biology , peptide sequence , microbiology and biotechnology , consensus sequence , genetics , gene
Antibody (Ab) humanization is crucial to generate clinically relevant biologics from hybridoma‐derived monoclonal antibodies (mAbs). In this study, we integrated antibody structural information from the Protein Data Bank with known back‐to‐mouse mutational data to build a universal consensus of framework positions (10 heavy and 7 light) critical for the preservation of the functional conformation of the Complimentarity Determining Region of antibodies. On the basis of FR consensus, we describe here a universal combinatorial library suitable for humanizing exogenous antibodies by CDR‐grafting. The six CDRs of the murine anti‐human EGFR Fab M225 were grafted onto a distinct (low FR sequence similarity to M225) human FR sequence that incorporates at the 17 FR consensus positions the permutations of the naturally observed amino acid diversities. Ten clones were selected from the combinatorial library expressing phage‐displayed humanized M225 Fabs. Surprisingly, 2 of the 10 clones were found to bind EGFR with stronger affinity than M225. Cell‐based assays demonstrated that the 10 selected clones retained epitope specificity by blocking EGFR phosphorylation and thus hindering cellular proliferation. Our results suggest that there is a universal and structurally rigid near‐CDR set of FR positions that cooperatively support the binding conformation of CDRs. Proteins 2011. © 2012 Wiley Periodicals, Inc.