Computational Modeling and Biophysical Analysis of Novel Biologics
Sandra Ríos*, Jennifer M. Johnson**, Brad Sherborne**, Francis Insaidoo* and David Roush*
Bioprocess development modalities (e.g. affinity, ion exchange, hydrophobic interaction chromatography) have been optimized and used extensively in monoclonal antibody purification from where several template purification schemes have emerged. Because of the inherent and engineered variations in therapeutic antibody structures, there is no “one-size-fits-all” when it comes to techniques for purification of monoclonal antibodies (mAbs).
Conditions optimal for antibody purification like elution pH, ionic strength, and temperature may induce aggregation or susceptibility to protease degradation for other biologics. This may pose a challenge for hold times, formulation and overall protein stability. Understanding structure and biophysical properties for novel molecules (e.g. patch analysis for charge and hydrophobicity) may give us a preliminary assessment of purification and formulation challenges and may be exploited to enhance process development to fit novel biologics to current platform purification modalities. To address the aforementioned limitations, computational algorithms were used to build homology models of multiple novel molecules and correlate structural properties with experimental data to assess the impact of these biophysical properties on purification options, including platform fit.
In this study, we employed molecules, which possess antibody-like structural features and yet different in structure. While the MOE antibody modeler tool is useful for optimal CDR (Complement Determining Region) determination, functionality is limited by the single sequence of the novel biologic. Further, homology-modeling tools might not completely capture the complexity of identifying a representative CDR for these molecules. Thus, a hybrid approach may be required such as leveraging homology models from other proteins.
Once a final homology structure is achieved, in-silico docking and biophysical characterization could be explored to understand the impact of the molecular structure in purification, stability and formulation.