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.
ID: ajwk5676
Submitter: Shu-Ching Ou
Submission Date: March 12, 2019, 11:43 a.m.
Version: 1
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.
Number of data points | 194 |
Proteins | Fab heavy chain,Fab light chain |
Unique complexes | 97 |
Assays/Quantities/Protocols | Experimental Assay: Fold Changes in Mean Fluorescence Intensity (between overexpressing cells relative to their parental) ; Experimental Assay: Hydrophobic interaction chromatography retention time (HIC RT) |
Libraries | Variants for mAb |
Colors: | D | E | R | H | K | S | T | N | Q | A | V | I | L | M | F | Y | W | C | G | P |
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Structure ID | Release Date | Resolution | Structure Title |
---|---|---|---|
1F6L | 2000-06-22T00:00:00+0000 | 2.8 | VARIABLE LIGHT CHAIN DIMER OF ANTI-FERRITIN ANTIBODY |
3UPA | 2011-11-17T00:00:00+0000 | 1.8 | A general strategy for the generation of human antibody variable domains with increased aggregation resistance |
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 |
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 |
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 |
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 |
1BBJ | 1992-04-30T00:00:00+0000 | 3.1 | CRYSTAL STRUCTURE OF A CHIMERIC FAB' FRAGMENT OF AN ANTIBODY BINDING TUMOUR CELLS |
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 |
4B53 | 2012-08-02T00:00:00+0000 | 1.8 | Crystal structure of the isolated IgG4 CH3 domain |
Percent Identity | Matching Chains | Protein | Accession | Entry Name |
---|---|---|---|---|
100.0 | H | Fab heavy chain,Fab light chain | P01857 | IGHG1_HUMAN |
94.1 | H | Fab heavy chain,Fab light chain | P01860 | IGHG3_HUMAN |
91.1 | H | Fab heavy chain,Fab light chain | P01861 | IGHG4_HUMAN |
90.2 | L | Fab heavy chain,Fab light chain | P0DOX7 | IGK_HUMAN |
100.0 | L | Fab heavy chain,Fab light chain | P01834 | IGKC_HUMAN |
91.6 | L | Fab heavy chain,Fab light chain | P01597 | KV139_HUMAN |
91.6 | L | Fab heavy chain,Fab light chain | P04432 | KVD39_HUMAN |