Prediction of aggregation prone regions of therapeutic proteins
Abstract
Therapeutic proteins such as antibodies are playing an increasingly prominent role in the treatment of numerous diseases including cancer and rheumatoid arthritis. However, these proteins tend to degrade due to aggregation during manufacture and storage. Aggregation decreases protein activity and raises concerns about an immunological response. We have recently developed a method based on full antibody atomistic simulations to predict antibody aggregation prone regions [Proc. Natl. Acac. Sci. 2009, 106, 11937]. This method is based on "spatial-aggregation-propensity (SAP)", a measure of the dynamic exposure of hydrophobic patches. In the present paper, we expand on this method to analyze the aggregation prone regions over a wide parameter range. We also explore the effect of different hydrophilic mutations on these predicted aggregation prone regions to engineer antibodies with enhanced stability. The mutation to lysine is more effective than serine but less effective than glutamic acid in enhancing antibody stability. Furthermore, we show that multiple simultaneous mutations on different SAP peaks can have a cumulative effect on enhancing protein stability. We also investigate the accuracy of various cheaper alternatives for SAP evaluation because the full antibody atomistic simulations are highly computationally expensive. These cheaper alternatives include antibody fragment (Fab, Fc) simulations, implicit solvent models, or direct computations from a static structure (i.e., a structure from X-ray or homology modeling). The SAP evaluation from the static structure is 200,000 times faster but less accurate compared to the SAP from explicit atom simulations. Nevertheless, the SAP from a static structure still predicts most of the major aggregation prone regions, making it a potential approach for use in high-throughput applications. Thus, the SAP technology described here could be employed either in high-throughput developability screening of therapeutic protein candidates or to improve their stability at later stages of manufacturing.
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The DI combines computed hydrophobicity, SAP score and net charge into a statistical score indicating APRs.
“The DI combines the computed hydrophobicity, SAP score [211] and net charge of the molecule into a statistical score indicating APRs.”
From Computational approaches to therapeutic antibody design: established methods and emerging trends (2020) · cites this paper as [211]
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“The DI combines the computed hydrophobicity, SAP score [211] and net charge of the molecule into a statistical score indicating APRs.”
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- Authors
- Chennamsetty, N., Voynov, V., Kayser, V., Helk, B., & Trout, B. L.
- Affiliations
- Novartis (Switzerland) (CH)
- Corresponding author
- Trout, Bernhardt L.
- Venue
- The Journal of Physical Chemistry B
- Publisher
- American Chemical Society (ACS)
- Published
- 2010-04-22
- Volume
- 114
- Issue
- 19
- Pages
- 6614-6624
- ISSN
- 1520-5207 (ISSN-L)
- 1520-6106
- OpenAlex
- W2026720253
- Cited by
- 200
- References
- 50
- Citations by year
- 2026: 6 · 2025: 8 · 2024: 14 · 2023: 13 · 2022: 13 · 2021: 9 · 2020: 13 · 2019: 15 · 2018: 28 · 2017: 13 · 2016: 5 · 2015: 18 · 2014: 10 · 2013: 10 · 2012: 11
- FWCI
- 4.29
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- The Journal of Physical Chemistry B (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein purification and stability
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Monoclonal and Polyclonal Antibodies Research
- Keywords
- antibody aggregation, aggregation-prone regions, therapeutic proteins, lysine substitution, implicit solvent, protein stability
- MeSH terms
- Antibodies, Immunoglobulin Fab Fragments, Immunoglobulin Fc Fragments, Protein Engineering, Mutagenesis, Site-Directed, Protein Structure, Tertiary, Protein Stability, Molecular Dynamics Simulation, Hydrophobic and Hydrophilic Interactions
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