Abstract
A major challenge in the development of antibody biotherapeutics is their tendency to aggregate. One root cause for aggregation is exposure of hydrophobic surface regions to the solvent. Many current techniques predict the relative aggregation propensity of antibodies via precalculated scales for the hydrophobicity or aggregation propensity of single amino acids. However, those scales cannot describe the nonadditive effects of a residue’s surrounding on its hydrophobicity. Therefore, they are inherently limited in their ability to describe the impact of subtle differences in molecular structure on the overall hydrophobicity. Here, we introduce a physics-based approach to describe hydrophobicity in terms of the hydration free energy using grid inhomogeneous solvation theory (GIST). We apply this method to assess the effects of starting structures, conformational sampling, and protonation states on the hydrophobicity of antibodies. Our results reveal that high-quality starting structures, i.e., crystal structures, are crucial for the prediction of hydrophobicity and that conformational sampling can compensate errors introduced by the starting structure. On the other hand, sampling of protonation states only leads to good results when combined with high-quality structures, whereas it can even be detrimental otherwise. We conclude by pointing out that a single static homology model may not be adequate for predicting hydrophobicity.
Highlights
In the past few decades, biopharmaceuticals have emerged as one of the largest areas of interest in the pharmaceutical industry
We investigate the ability of our method to distinguish antibodies that strongly bind hydrophobic interaction chromatography (HIC), Standup monolayer adsorption chromatography (SMAC), or crossinteraction chromatography (CIC) columns from those that bind weakly to the same column
Following the procedure described in the Methods, we calculated solvation free energies DGsolv, as well as DGunfavorable, for 49 Protein Data Bank (PDB) structures and 77 homology models and compared the results to the experimental HIC retention times, as shown in Fig. 1, A and D
Summary
In the past few decades, biopharmaceuticals have emerged as one of the largest areas of interest in the pharmaceutical industry. Though large improvements have been made in the discovery of mAbs binding to a certain target [5], problems may arise regarding the stability, solubility, or pharmacokinetics while developing an active mAb into a drug. Those properties are generally referred to by the term developability [6]. A major problem in the development process is the inherent tendency of some concentrated protein solutions to form aggregates This problem may be influenced by various factors such as temperature, mechanical stress, and pH [7,8,9]. Structural instability may lead to aggregation at both hot and cold temperatures [11,12], and hydrophobic surface patches have repeatedly been discussed to be involved [13,14] especially in the formation
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
