Computer-aided antibody design

• Published in: Protein engineering, design and selection Vol. 25; no. 10; pp. 507 - 522
• Main Authors: Kuroda, Daisuke, Shirai, Hiroki, Jacobson, Matthew P., Nakamura, Haruki
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.10.2012
• Subjects: Animals; Antibodies; Antibodies - chemistry; Antibodies - genetics; Antibodies - immunology; Antibody Affinity; Binding Sites, Antibody; Clinical trials; Computer applications; Computer-Aided Design; Crystal structure; Drug development; Energy; Homology; Humans; Immunoglobulin Subunits - chemistry; Immunoglobulin Subunits - genetics; Immunoglobulin Subunits - immunology; Immunoglobulin Variable Region - chemistry; Immunoglobulin Variable Region - genetics; Immunoglobulin Variable Region - immunology; Models, Molecular; Physicochemical properties; Protein Conformation; Review; Reviews; Toxicity; Vaccines; antibody design; antibody engineering; vaccine design; protein therapeutics
• ISSN: 1741-0126; 1741-0134; 1741-0134
• DOI: 10.1093/protein/gzs024

Recent clinical trials using antibodies with low toxicity and high efficiency have raised expectations for the development of next-generation protein therapeutics. However, the process of obtaining therapeutic antibodies remains time consuming and empirical. This review summarizes recent progresses in the field of computer-aided antibody development mainly focusing on antibody modeling, which is divided essentially into two parts: (i) modeling the antigen-binding site, also called the complementarity determining regions (CDRs), and (ii) predicting the relative orientations of the variable heavy (VH) and light (VL) chains. Among the six CDR loops, the greatest challenge is predicting the conformation of CDR-H3, which is the most important in antigen recognition. Further computational methods could be used in drug development based on crystal structures or homology models, including antibody–antigen dockings and energy calculations with approximate potential functions. These methods should guide experimental studies to improve the affinities and physicochemical properties of antibodies. Finally, several successful examples of in silico structure-based antibody designs are reviewed. We also briefly review structure-based antigen or immunogen design, with application to rational vaccine development.