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Published (Version of record)CC BY V4.0, Open Access
Published (Version of record)CC BY V4.0, Open Access
Journal article
Optimizing antibody affinity and stability by the automated design of the variable light-heavy chain interfaces
PLoS computational biology, Vol.15(8), e1007207
23/Aug/2019
PMCID: PMC6728052
PMID: 31442220
Abstract
Antibodies developed for research and clinical applications may exhibit suboptimal stability, expressibility, or affinity. Existing optimization strategies focus on surface mutations, whereas natural affinity maturation also introduces mutations in the antibody core, simultaneously improving stability and affinity. To systematically map the mutational tolerance of an antibody variable fragment (Fv), we performed yeast display and applied deep mutational scanning to an anti-lysozyme antibody and found that many of the affinity-enhancing mutations clustered at the variable light-heavy chain interface, within the antibody core. Rosetta design combined enhancing mutations, yielding a variant with tenfold higher affinity and substantially improved stability. To make this approach broadly accessible, we developed AbLIFT, an automated web server that designs multipoint core mutations to improve contacts between specific Fv light and heavy chains (http://AbLIFT.weizmann.ac.il). We applied AbLIFT to two unrelated antibodies targeting the human antigens VEGF and QSOX1. Strikingly, the designs improved stability, affinity, and expression yields. The results provide proof-of-principle for bypassing laborious cycles of antibody engineering through automated computational affinity and stability design.
Details
- Title
- Optimizing antibody affinity and stability by the automated design of the variable light-heavy chain interfaces
- Creators
- Shira Warszawski - 972WIS_INST___112Aliza Katz - 972WIS_INST___9Rosalie Lipsh - 972WIS_INST___112Lev Khmelnitsky - 972WIS_INST___9Gili Ben Nissan - 972WIS_INST___112Gabriel Javitt - 972WIS_INST___9Orly Dym - 972WIS_INST___113Tamar Unger - 972WIS_INST___113Orli Knop - 972WIS_INST___112Shira Albeck - 972WIS_INST___113Ron Diskin - 972WIS_INST___9Deborah Fass - 972WIS_INST___9Michal Sharon - 972WIS_INST___112Sarel-Jacob Fleishman (Corresponding Author) - 972WIS_INST___112
- Resource Type
- Journal article
- Publication Details
- PLoS computational biology, Vol.15(8), e1007207; 23/Aug/2019
- Number of pages
- 24
- Publisher
- United States
- Language
- English
- DOI
- https://doi.org/10.1371/journal.pcbi.1007207
- PMID
- 31442220
- PMCID
- PMC6728052
- Grants
- Grant note
- We thank Assaf Elazar for providing deep-sequencing analysis scripts, Gideon Lapidoth for providing PSSMs for antibody design, Adi Goldenzweig and Daniel Christ for critical reading, and Ori Cohavi, Aharon Rabinkov, Gideon Schreiber for help with the SPR experiments and analysis and Jaime Prilusky for establishing the AbLIFT web server. The research was supported by grants from the European Research Council (335439 to SJF, 636752 to MS, and 310649 and 825076 to DF), the Israel Science Foundation to MS (300/17) and through its Center of Excellence in Structural Cell Biology to SJF and DF (1775/12), a research grant from Sheri and David E. Stone and by a charitable donation from Sam Switzer and family. M.S. is an incumbent of the Aharon and Ephraim Katzir Memorial Professorial Chair. Conceptualization: Shira Warszawski, Gili Ben Nissan, Deborah Fass, Michal Sharon, Sarel J. Fleishman. Data curation: Shira Warszawski, Orly Dym, Ron Diskin, Deborah Fass, Michal Sharon, Sarel J. Fleishman. Formal analysis: Shira Warszawski, Aliza Borenstein Katz, Lev Khmelnitsky, Gili Ben Nissan, Gabriel Javitt, Orly Dym, Ron Diskin, Deborah Fass, Michal Sharon, Sarel J. Fleishman. Funding acquisition: Ron Diskin, Deborah Fass, Michal Sharon, Sarel J. Fleishman. Investigation: Shira Warszawski, Aliza Borenstein Katz, Gili Ben Nissan, Ron Diskin, Deborah Fass, Michal Sharon, Sarel J. Fleishman. Methodology: Shira Warszawski, Lev Khmelnitsky, Gili Ben Nissan, Gabriel Javitt, Orly Dym, Tamar Unger, Orli Knop, Shira Albeck, Ron Diskin, Deborah Fass, Michal Sharon, Sarel J. Fleishman. Project administration: Sarel J. Fleishman. Resources: Orly Dym, Tamar Unger, Shira Albeck, Sarel J. Fleishman. Software: Shira Warszawski, Rosalie Lipsh, Sarel J. Fleishman. Supervision: Ron Diskin, Deborah Fass, Michal Sharon, Sarel J. Fleishman. Validation: Shira Warszawski, Ron Diskin, Deborah Fass, Michal Sharon, Sarel J. Fleishman. Visualization: Shira Warszawski, Orly Dym, Michal Sharon, Sarel J. Fleishman. Writing – original draft: Shira Warszawski, Deborah Fass, Sarel J. Fleishman. Writing – review & editing: Shira Warszawski, Aliza Borenstein Katz, Gili Ben Nissan, Ron Diskin, Deborah Fass, Michal Sharon, Sarel J. Fleishman.
- Record Identifier
- 993181919503596
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