Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen
Open accessPublished version of a preprint
Abstract
Abstract Over the last two decades, therapeutic antibodies have emerged as a rapidly expanding domain within the field biologics. In silico tools that can streamline the process of antibody discovery and optimization are critical to support a pipeline that is growing more numerous and complex every year. In this study, DeepAb, a deep learning model for predicting antibody Fv structure directly from sequence, was used to design 200 potentially stabilized variants of an anti-hen egg lysozyme (HEL) antibody. We sought to determine whether DeepAb can enhance the stability of these antibody variants without relying on or predicting the antibody-antigen interface, and whether this stabilization could increase antibody affinity without impacting their developability profile. The 200 variants were produced through a robust highthroughput method and tested for thermal and colloidal stability (T onset , T m , T agg ), affinity (K D ) relative to the parental antibody, and for developability parameters (non-specific binding, aggregation propensity, self-association). In the designed clones, 91% and 94% exhibited increased thermal and colloidal stability and affinity, respectively. Of these, 10% showed a significantly increased affinity for HEL (5-to 21-fold increase), with most clones retaining the favorable developability profile of the parental antibody. These data open the possibility of in silico antibody stabilization and affinity maturation without the need to predict the antibody-antigen interface, which is notoriously difficult in the absence of crystal structures.
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- Authors
- Hutchinson, M., Ruffolo, J. A., Haskins, N., Iannotti, M., Vozza, G., Pham, T., Mehzabeen, N., Shandilya, H., Rickert, K., Croasdale-Wood, R., Damschroder, M., Fu, Y., Dippel, A., Gray, J. J., & Kaplan, G.
- Affiliations
- AstraZeneca (United States) (US)
- Johns Hopkins University (US)
- Amgen (United States) (US)
- AstraZeneca (United Kingdom) (GB)
- Corresponding author
- Gray, Jeffrey J.
- Kaplan, Gilad
- ORCID
- Venue
- mAbs
- Publisher
- Informa UK Limited
- Published
- 2024-06-20
- Volume
- 16
- Issue
- 1
- Pages
- 2362775-2362775
- ISSN
- 1942-0862 (ISSN-L)
- 1942-0870
- PMC
- PMC11195458
- OpenAlex
- W4399859005
- Cited by
- 22
- References
- 12
- Citations by year
- 2026: 9 · 2025: 6 · 2024: 7
- FWCI
- 5.60
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- mAbs (publishedVersion, cc-by-nc)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- AstraZeneca (R35-GM141881)
- Topics
- Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Monoclonal and Polyclonal Antibodies Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- deep mutational scanning, hen egg white lysozyme, antibody developability, thermal stability, colloidal stability, aggregation propensity, non-specific binding, self-association
- MeSH terms
- Animals, Antibody Affinity, Antigens, Computer Simulation, Humans, Muramidase, Protein Stability
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