Cited by 200Protein purification and stabilityProtein Structure and DynamicsMonoclonal and Polyclonal Antibodies Research

Prediction of aggregation prone regions of therapeutic proteins

Chennamsetty, Naresh, Voynov, Vladimir, Kayser, Veysel, Helk, Bernhard, Trout, Bernhardt L.·2010·The Journal of Physical Chemistry B

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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Crossref · 10.1021/jp911706q

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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
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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