Homology modeling and structure-based design improve hydrophobic interaction chromatography behavior of integrin binding antibodies.


Abstract

Monoclonal antibody (mAb) candidates from high-throughput screening or binding affinity optimization often contain mutations leading to liabilities for further development of the antibody, such as aggregation-prone regions and lack of solubility. In this work, we optimized a candidate integrin α11-binding mAb for developability using molecular modeling, rational design, and hydrophobic interaction chromatography (HIC). A homology model of the parental mAb Fv region was built, and this revealed hydrophobic patches on the surface of the complementarity-determining region loops. A series of 97 variants of the residues primarily responsible for the hydrophobic patches were expressed and their HIC retention times (RT) were measured. As intended, many of the computationally designed variants reduced the HIC RT compared to the parental mAb, and mutating residues that contributed most to hydrophobic patches had the greatest effect on HIC RT. A retrospective analysis was then performed where 3-dimentional protein property descriptors were evaluated for their ability to predict HIC RT using the current series of mAbs. The same descriptors were used to train a simple multi-parameter protein quantitative structure-property relationship model on this data, producing an improved correlation. We also extended this analysis to recently published HIC data for 137 clinical mAb candidates as well as 31 adnectin variants, and found that the surface area of hydrophobic patches averaged over a molecular dynamics sample consistently correlated to the experimental data across a diverse set of biotherapeutics.

Submission Details

ID: ajwk5676

Submitter: Shu-Ching Ou

Submission Date: March 12, 2019, 11:43 a.m.

Version: 1

Publication Details
Jetha A;Thorsteinson N;Jmeian Y;Jeganathan A;Giblin P;Fransson J,MAbs (2018) Homology modeling and structure-based design improve hydrophobic interaction chromatography behavior of integrin binding antibodies. PMID:30110240
Additional Information

PDB:2R8S was used as the framework template for the antibody. The actual parental sequence is in the complex description. HIC retention time (HIC RT) is marked as 30 even if the actual RT is longer than 30 min.

Structure view and single mutant data analysis

Study data

No weblogo for data of varying length.
Colors: D E R H K S T N Q A V I L M F Y W C G P
 

Data Distribution

Studies with similar sequences (approximate matches)

Correlation with other assays (exact sequence matches)


Relevant PDB Entries

Structure ID Release Date Resolution Structure Title
3UPA 2011-11-17T00:00:00+0000 1.8 A general strategy for the generation of human antibody variable domains with increased aggregation resistance
1F6L 2000-06-22T00:00:00+0000 2.8 VARIABLE LIGHT CHAIN DIMER OF ANTI-FERRITIN ANTIBODY
5W38 2017-06-07T00:00:00+0000 1.8 1.80A resolution structure of human IgG3 Fc (N392K)
6D58 2018-04-19T00:00:00+0000 2.39 Crystal structure of a Fc fragment of Human IgG3
4ZNC 2015-05-04T00:00:00+0000 2.28 Fc fragment of human IgG in complex with the C domain of staphylococcal protein A mutant - Q9W
4WWI 2014-11-11T00:00:00+0000 2.31 Crystal structure of the C domain of staphylococcal protein A in complex with the Fc fragment of human IgG at 2.3 Angstrom resolution
3EO1 2008-09-26T00:00:00+0000 3.1 Structure of the Fab Fragment of GC-1008 in Complex with Transforming Growth Factor-Beta 3
5LG1 2016-07-05T00:00:00+0000 2.7 Room temperature structure of human IgG4-Fc from crystals analysed in situ
4D2N 2014-05-12T00:00:00+0000 2.7 Crystal structure of deglycosylated serum-derived human IgG4 Fc
1ADQ 1997-02-18T00:00:00+0000 3.15 CRYSTAL STRUCTURE OF A HUMAN IGM RHEUMATOID FACTOR FAB IN COMPLEX WITH ITS AUTOANTIGEN IGG FC

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
91.6 L Fab heavy chain,Fab light chain P04432 KVD39_HUMAN
91.6 L Fab heavy chain,Fab light chain P01597 KV139_HUMAN
100.0 L Fab heavy chain,Fab light chain P01834 IGKC_HUMAN
90.2 L Fab heavy chain,Fab light chain P0DOX7 IGK_HUMAN
91.1 H Fab heavy chain,Fab light chain P01861 IGHG4_HUMAN
94.1 H Fab heavy chain,Fab light chain P01860 IGHG3_HUMAN
100.0 H Fab heavy chain,Fab light chain P01857 IGHG1_HUMAN