Net charge of antibody complementarity-determining regions is a key predictor of specificity

• Published in: Protein engineering, design and selection Vol. 31; no. 11; pp. 409 - 418
• Main Authors: Rabia, Lilia A, Zhang, Yulei, Ludwig, Seth D, Julian, Mark C, Tessier, Peter M
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.11.2018
• Subjects: Amino Acid Sequence; Antibodies - chemistry; Antibodies - immunology; Antibody Specificity; Complementarity Determining Regions - chemistry; Humans; Original; CDR; aggregation; polyspecificity; non-specific binding; mAb
• ISSN: 1741-0126; 1741-0134; 1741-0134
• DOI: 10.1093/protein/gzz002

Specificity is one of the most important and complex properties that is central to both natural antibody function and therapeutic antibody efficacy. However, it has proven extremely challenging to define robust guidelines for predicting antibody specificity. Here we evaluated the physicochemical determinants of antibody specificity for multiple panels of antibodies, including >100 clinical-stage antibodies. Surprisingly, we find that the theoretical net charge of the complementarity-determining regions (CDRs) is a strong predictor of antibody specificity. Antibodies with positively charged CDRs have a much higher risk of low specificity than antibodies with negatively charged CDRs. Moreover, the charge of the entire set of six CDRs is a much better predictor of antibody specificity than the charge of individual CDRs, variable domains (VH or VL) or the entire variable fragment (Fv). The best indicators of antibody specificity in terms of CDR amino acid composition are reduced levels of arginine and lysine and increased levels of aspartic and glutamic acid. Interestingly, clinical-stage antibodies with negatively charged CDRs also have a lower risk for poor biophysical properties in general, including a reduced risk for high levels of self-association. These findings provide powerful guidelines for predicting antibody specificity and for identifying safe and potent antibody therapeutics.