title: Affinity enhancement of an in vivo matured therapeutic antibody using structure-based computational design.
abstract: 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.
authors.affiliation: Biogen Idec, Inc., Cambridge, Massachusetts 02142, USA. louie@alumni.northwestern.edu
authors.forename: Louis A
authors.initials: LA
authors.lastname: Clark
authors.forename: P Ann
authors.initials: PA
authors.lastname: Boriack-Sjodin
authors.forename: John
authors.initials: J
authors.lastname: Eldredge
authors.forename: Christopher
authors.initials: C
authors.lastname: Fitch
authors.forename: Bethany
authors.initials: B
authors.lastname: Friedman
authors.forename: Karl J M
authors.initials: KJ
authors.lastname: Hanf
authors.forename: Matthew
authors.initials: M
authors.lastname: Jarpe
authors.forename: Stefano F
authors.initials: SF
authors.lastname: Liparoto
authors.forename: You
authors.initials: Y
authors.lastname: Li
authors.forename: Alexey
authors.initials: A
authors.lastname: Lugovskoy
authors.forename: Stephan
authors.initials: S
authors.lastname: Miller
authors.forename: Mia
authors.initials: M
authors.lastname: Rushe
authors.forename: Woody
authors.initials: W
authors.lastname: Sherman
authors.forename: Kenneth
authors.initials: K
authors.lastname: Simon
authors.forename: Herman
authors.initials: H
authors.lastname: Van Vlijmen
mesh_terms: 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
chemical_list: D000906:Antibodies; D000936:Antigen-Antibody Complex; D007136:Immunoglobulins; D039222:Integrin alpha1beta1