Redesign of a cross-reactive antibody to dengue virus with broad-spectrum activity and increased in vivo potency

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 110; no. 17; p. 6622
• Main Authors: Tharakaraman, Kannan, Robinson, Luke N., Hatas, Andrew, Chen, Yi-Ling, Siyue, Liu, Raguram, S., Sasisekharan, V., Wogan, Gerald N., Sasisekharan, Ram
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 23.04.2013; National Acad Sciences
• Series: PNAS Plus
• Subjects: Animals; Antibodies, Neutralizing - biosynthesis; Antibodies, Viral - biosynthesis; Antibody Affinity - genetics; Antigens; Binding Sites, Antibody - genetics; Biological Sciences; Chemistry; Cross Reactions - immunology; Dengue fever; Dengue Virus - immunology; Enzyme-Linked Immunosorbent Assay; Epitopes - genetics; Immunoglobulins; Mice; Models, Immunological; PNAS Plus; PNAS PLUS: SIGNIFICANCE STATEMENTS; Protein Binding; Protein Engineering - methods; Proteins; Real-Time Polymerase Chain Reaction; Surface Plasmon Resonance; Viruses
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1303645110

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.