title: Redesign of a cross-reactive antibody to dengue virus with broad-spectrum activity and increased in vivo potency.
abstract: Affinity improvement of proteins, including antibodies, by computational chemistry broadly relies on physics-based energy functions coupled with refinement. However, achieving significant enhancement of binding affinity (>10-fold) remains a challenging exercise, particularly for cross-reactive antibodies. We describe here an empirical approach that captures key physicochemical features common to antigen-antibody interfaces to predict protein-protein interaction and mutations that confer increased affinity. We apply this approach to the design of affinity-enhancing mutations in 4E11, a potent cross-reactive neutralizing antibody to dengue virus (DV), without a crystal structure. Combination of predicted mutations led to a 450-fold improvement in affinity to serotype 4 of DV while preserving, or modestly increasing, affinity to serotypes 1-3 of DV. We show that increased affinity resulted in strong in vitro neutralizing activity to all four serotypes, and that the redesigned antibody has potent antiviral activity in a mouse model of DV challenge. Our findings demonstrate an empirical computational chemistry approach for improving protein-protein docking and engineering antibody affinity, which will help accelerate the development of clinically relevant antibodies.
authors.affiliation: Department of Biological Engineering, Infectious Diseases Interdisciplinary Research Group, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Kannan
authors.initials: K
authors.lastname: Tharakaraman
authors.forename: Luke N
authors.initials: LN
authors.lastname: Robinson
authors.forename: Andrew
authors.initials: A
authors.lastname: Hatas
authors.forename: Yi-Ling
authors.initials: YL
authors.lastname: Chen
authors.forename: Liu
authors.initials: L
authors.lastname: Siyue
authors.forename: S
authors.initials: S
authors.lastname: Raguram
authors.forename: V
authors.initials: V
authors.lastname: Sasisekharan
authors.forename: Gerald N
authors.initials: GN
authors.lastname: Wogan
authors.forename: Ram
authors.initials: R
authors.lastname: Sasisekharan
mesh_terms: D000818:Animals; D057134:Antibodies, Neutralizing / Q000096:biosynthesis*; D000914:Antibodies, Viral / Q000096:biosynthesis*; D000915:Antibody Affinity / Q000235:genetics; D001666:Binding Sites, Antibody / Q000235:genetics; D003429:Cross Reactions / Q000276:immunology; D003716:Dengue Virus / Q000276:immunology*; D004797:Enzyme-Linked Immunosorbent Assay; D000939:Epitopes / Q000235:genetics; D051379:Mice; D018448:Models, Immunological; D011485:Protein Binding; D015202:Protein Engineering / Q000379:methods*; D060888:Real-Time Polymerase Chain Reaction; D020349:Surface Plasmon Resonance
chemical_list: D057134:Antibodies, Neutralizing; D000914:Antibodies, Viral; D000939:Epitopes