Affinity enhancement of an in vivo matured therapeutic antibody using structure-based computational design.
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 approximately 7 nM) and the moderate resolution (2.8 A) 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 A. 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.
Clark
Louis A
LA
Biogen Idec, Inc., Cambridge, Massachusetts 02142, USA. louie@alumni.northwestern.edu
Boriack-Sjodin
P Ann
PA
Eldredge
John
J
Fitch
Christopher
C
Friedman
Bethany
B
Hanf
Karl J M
KJ
Jarpe
Matthew
M
Liparoto
Stefano F
SF
Li
You
Y
Lugovskoy
Alexey
A
Miller
Stephan
S
Rushe
Mia
M
Sherman
Woody
W
Simon
Kenneth
K
Van Vlijmen
Herman
H
D019943:Amino Acid Substitution; D000906:Antibodies / Q000627:therapeutic use*; D000915:Antibody Affinity; D000936:Antigen-Antibody Complex / Q000737:chemistry; D001666:Binding Sites, Antibody; D017076:Computer-Aided Design; D018360:Crystallography, X-Ray; D015195:Drug Design; D007136:Immunoglobulins; D039222:Integrin alpha1beta1 / Q000276:immunology; D008958:Models, Molecular; D013329:Structure-Activity Relationship
D000906:Antibodies; D000936:Antigen-Antibody Complex; D007136:Immunoglobulins; D039222:Integrin alpha1beta1