Combining random mutagenesis, structure-guided design and next-generation sequencing to mitigate polyreactivity of an anti-IL-21R antibody

Binding Promiscuity of Therapeutic Factor VIII

The binding promiscuity of proteins defines their ability to indiscriminately bind multiple unrelated molecules. Binding promiscuity is implicated, at least in part, in the off-target reactivity, nonspecific biodistribution, immunogenicity, and/or short half-life of potentially efficacious protein drugs, thus affecting their clinical use. In this review, we discuss the current evidence for the binding promiscuity of factor VIII (FVIII), a protein used for the treatment of hemophilia A, which displays poor pharmacokinetics, and elevated immunogenicity. We summarize the different canonical and noncanonical interactions that FVIII may establish in the circulation and that could be responsible for its therapeutic liabilities. We also provide information suggesting that the FVIII light chain, and especially its C1 and C2 domains, could play an important role in the binding promiscuity. We believe that the knowledge accumulated over years of FVIII usage could be exploited for the development of strategies to predict protein binding promiscuity and therefore anticipate drug efficacy and toxicity. This would open a mutational space to reduce the binding promiscuity of emerging protein drugs while conserving their therapeutic potency.

Human-murine chimeric autoantibodies with high affinity and specificity for systemic sclerosis

Scleroderma 70 (Scl-70) is commonly used in the clinic for aiding systemic sclerosis (SSc) diagnosis due to its recognition as autoantibodies in the serum of SSc patients. However, obtaining sera positive for anti-Scl-70 antibody can be challenging; therefore, there is an urgent need to develop a specific, sensitive, and easily available reference for SSc diagnosis. In this study, murine-sourced scFv library were screened by phage display technology against human Scl-70, and the scFvs with high affinity were constructed into humanized antibodies for clinical application. Finally, ten high-affinity scFv fragments were obtained. Three fragments (2A, 2AB, and 2HD) were select for humanization. The physicochemical properties of the amino acid sequence, three-dimensional structural basis, and electrostatic potential distribution of the protein surface of different scFv fragments revealed differences in the electrostatic potential of their CDR regions determined their affinity for Scl-70 and expression. Notably, the specificity test showed the half-maximal effective concentration values of the three humanized antibodies were lower than that of positive patient serum. Moreover, these humanized antibodies showed high specificity for Scl-70 in diagnostic immunoassays for ANA. Among these three antibodies, 2A exhibited most positive electrostatic potential on the surface of the CDRs and highest affinity and specificity for Scl-70 but with least expression level; thus, it may provide new foundations for developing enhanced diagnostic strategies for SSc.

Non-specificity as the sticky problem in therapeutic antibody development

Antibodies are highly potent therapeutic scaffolds with more than a hundred different products approved on the market. Successful development of antibody-based drugs requires a trade-off between high target specificity and target binding affinity. In order to better understand this problem, we here review non-specific interactions and explore their fundamental physicochemical origins. We discuss the role of surface patches - clusters of surface-exposed amino acid residues with similar physicochemical properties - as inducers of non-specific interactions. These patches collectively drive interactions including dipole-dipole, π-stacking and hydrophobic interactions to complementary moieties. We elucidate links between these supramolecular assembly processes and macroscopic development issues, such as decreased physical stability and poor in vivo half-life. Finally, we highlight challenges and opportunities for optimizing protein binding specificity and minimizing non-specificity for future generations of therapeutics.

Reconstruction of full antibody sequences in NGS datasets and accurate VL:VH coupling by cluster coordinate matching of non-overlapping reads

Next-generation sequencing (NGS) is an indispensable tool in antibody discovery projects. However, the limits on NGS read length make it difficult to reconstruct full antibody sequences from the sequencing runs, especially if the six CDRs are randomized. To overcome that, we took advantage of Illumina’s cluster mapping capabilities to pair non-overlapping reads and reconstruct full Fab sequences with accurate V_L:V_H pairings. The method relies on in silico cluster coordinate information, and not on extensive in vitro manipulation, making the protocol easily deployable and less prone to PCR-derived errors. This work maintains the throughput necessary for antibody discovery campaigns, and a high degree of fidelity, which potentiates not only phage-display and synthetic library-based discovery methods, but also the NGS-driven analysis of naïve and immune libraries.

Polyreactivity and polyspecificity in therapeutic antibody development: risk factors for failure in preclinical and clinical development campaigns

Antibody-based drugs, which now represent the dominant biologic therapeutic modality, are used to modulate disparate signaling pathways across diverse disease indications. One fundamental premise that has driven this therapeutic antibody revolution is the belief that each monoclonal antibody exhibits exquisitely specific binding to a single-drug target. Herein, we review emerging evidence in antibody off-target binding and relate current key findings to the risk of failure in therapeutic development. We further summarize the current state of understanding of structural mechanisms underpining the different phenomena that may drive polyreactivity and polyspecificity, and highlight current thinking on how de-risking studies may be best implemented in the screening triage. We conclude with a summary of what we believe to be key observations in the field to date, and a call for the wider antibody research community to work together to build the tools needed to maximize our understanding in this nascent area.