Regulatory Approved Monoclonal Antibodies Contain Framework Mutations Predicted From Human Antibody Repertoires

Abstract

Monoclonal antibodies (mAbs) are an important class of therapeutics used to treat cancer, inflammation, and infectious diseases. Identifying highly developable mAb sequences in silico could greatly reduce the time and cost required for therapeutic mAb development. Here, we present position-specific scoring matrices (PSSMs) for antibody framework mutations developed using baseline human antibody repertoire sequences. Our analysis shows that human antibody repertoire-based PSSMs are consistent across individuals and demonstrate high correlations between related germlines. We show that mutations in existing therapeutic antibodies can be accurately predicted solely from baseline human antibody sequence data. We find that mAbs developed using humanized mice had more human-like FR mutations than mAbs originally developed by hybridoma technology. A quantitative assessment of entire framework regions of therapeutic antibodies revealed that there may be potential for improving the properties of existing therapeutic antibodies by incorporating additional mutations of high frequency in baseline human antibody repertoires. In addition, high frequency mutations in baseline human antibody repertoires were predicted in silico to reduce immunogenicity in therapeutic mAbs due to the removal of T cell epitopes. Several therapeutic mAbs were identified to have common, universally high-scoring framework mutations, and molecular dynamics simulations revealed the mechanistic basis for the evolutionary selection of these mutations. Our results suggest that baseline human antibody repertoires may be useful as predictive tools to guide mAb development in the future.

Hallucinating structure-conditioned antibody libraries for target-specific binders

“…To evaluate the human-likeness of the hallucinated designs, we turned to the work of Petersen et al . [35], which investigated the amino acid preference for framework mutations in human repertoires and FDA approved therapeutic antibodies. Petersen et al .…”

“…Petersen et al . [35] calculated the frequency of amino acids in human repertoires at framework positions for 25 VH genes that represent the precursors of several FDA approved antibodies and many of the most common VH genes. They converted these frequencies into “FR scores”, a measure of amino acid enrichment over the germline residue at each framework position.…”

Improved Characteristics of RANKL Immuno-PET Imaging Using Radiolabeled Antibody Fab Fragments

“…However, purification of denosumab Fab fragments proved more challenging, as protein A purification, generally the standard method, was ineffective ( Figure S1 ). It has been reported that Fab fragments containing a V H 3 variable domain (which is the case for denosumab) show protein A specific binding and are therefore unable to be purified from the Fc and intact antibody using this method [ 38 , 39 ]. Minor differences could be observed during the Kd evaluation of the antibody and Fab fragment that may be attributed to the antibody’s multivalent binding sites, leading to higher avidity—a phenomenon that has been described before [ 37 ].…”

AbDiver – A tool to explore the natural antibody landscape to aid therapeutic design

“…We created an online portal that facilitates the navigation of natural antibody diversity. We envisage particular application of the service to enable drawing parallels between natural and therapeutic antibodies (Krawczyk et al, 2019;Petersen et al, 2021) for the purpose of engineering to remove Post Translational Modification risks while maintaining favorable biophysical properties. For instance, removing a deamidation motif would require one to introduce one of few standard mutations (e.g., NA, QG) and re-assess the function of the antibody.…”

“…The richness of NGS data has implications for rational selection and design; models trained on these data have already shown promise for humanization (Marks et al, 2021) and binding prediction (Mason et al, 2021). It has also been shown that close sequence matches to clinically approved antibodies can be found in NGS datasets (Krawczyk et al, 2019), and clinically approved antibodies contain engineered mutations that can be recapitulated using the natural diversity from these datasets (Petersen et al, 2021). Exploration of natural antibody diversity from NGS datasets relative to a candidate therapeutic would therefore facilitate rapid and effective antibody engineering.…”