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Affinity enhancement of an in vivo matured therapeutic antibody using structure‐based computational design
Author(s) -
Clark Louis A.,
BoriackSjodin P. Ann,
Eldredge John,
Fitch Christopher,
Friedman Bethany,
Hanf Karl J.M.,
Jarpe Matthew,
Liparoto Stefano F.,
Li You,
Lugovskoy Alexey,
Miller Stephan,
Rushe Mia,
Sherman Woody,
Simon Kenneth,
Van Vlijmen Herman
Publication year - 2006
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.052030506
Subject(s) - affinity maturation , mutant , mutagenesis , chemistry , protein engineering , hydrogen bond , biomolecule , protein design , computational biology , biophysics , protein structure , molecule , biochemistry , biology , enzyme , gene , organic chemistry
Improving the affinity of a high‐affinity protein–protein interaction is a challenging problem that has practical applications in the development of therapeutic biomolecules. We used a combination of structure‐based computational methods to optimize the binding affinity of an antibody fragment to the I‐domain of the integrin VLA1. Despite the already high affinity of the antibody (Kd ∼7 nM) and the moderate resolution (2.8 Å) of the starting crystal structure, the affinity was increased by an order of magnitude primarily through a decrease in the dissociation rate. We determined the crystal structure of a high‐affinity quadruple mutant complex at 2.2 Å. The structure shows that the design makes the predicted contacts. Structural evidence and mutagenesis experiments that probe a hydrogen bond network illustrate the importance of satisfying hydrogen bonding requirements while seeking higher‐affinity mutations. The large and diverse set of interface mutations allowed refinement of the mutant binding affinity prediction protocol and improvement of the single‐mutant success rate. Our results indicate that structure‐based computational design can be successfully applied to further improve the binding of high‐affinity antibodies.