Assisted Design of Antibody and Protein Therapeutics (ADAPT).


Abstract

Effective biologic therapeutics require binding affinities that are fine-tuned to their disease-related molecular target. The ADAPT (Assisted Design of Antibody and Protein Therapeutics) platform aids in the selection of mutants that improve/modulate the affinity of antibodies and other biologics. It uses a consensus z-score from three scoring functions and interleaves computational predictions with experimental validation, significantly enhancing the robustness of the design and selection of mutants. The platform was tested on three antibody Fab-antigen systems that spanned a wide range of initial binding affinities: bH1-VEGF-A (44 nM), bH1-HER2 (3.6 nM) and Herceptin-HER2 (0.058 nM). Novel triple mutants were obtained that exhibited 104-, 46- and 32-fold improvements in binding affinity for each system, respectively. Moreover, for all three antibody-antigen systems over 90% of all the intermediate single and double mutants that were designed and tested showed higher affinities than the parent sequence. The contributions of the individual mutants to the change in binding affinity appear to be roughly additive when combined to form double and triple mutants. The new interactions introduced by the affinity-enhancing mutants included long-range electrostatics as well as short-range nonpolar interactions. This diversity in the types of new interactions formed by the mutants was reflected in SPR kinetics that showed that the enhancements in affinities arose from increasing on-rates, decreasing off-rates or a combination of the two effects, depending on the mutation. ADAPT is a very focused search of sequence space and required only 20-30 mutants for each system to be made and tested to achieve the affinity enhancements mentioned above.

Submission Details

ID: Rff7o3ap

Submitter: Shu-Ching Ou

Submission Date: Nov. 8, 2018, 4:53 p.m.

Version: 1

Publication Details
Vivcharuk V;Baardsnes J;Deprez C;Sulea T;Jaramillo M;Corbeil CR;Mullick A;Magoon J;Marcil A;Durocher Y;O'Connor-McCourt MD;Purisima EO,PLoS One (2017) Assisted Design of Antibody and Protein Therapeutics (ADAPT). PMID:28750054
Additional Information

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
4HAF 2012-09-26T00:00:00+0000 2.04 Crystal structure of fc-fragment of human IgG2 antibody (primitive crystal form)
4HAG 2012-09-26T00:00:00+0000 3.4 Crystal structure of fc-fragment of human IgG2 antibody (centered crystal form)
4L4J 2013-06-07T00:00:00+0000 1.92 Crystal structure of fc-fragment of human IgG2-Sigma antibody
7LUS 2021-02-23T00:00:00+0000 2.45 IgG2 Fc Charge Pair Mutation version 1 (CPMv1)
7LUS 2021-02-23T00:00:00+0000 2.45 IgG2 Fc Charge Pair Mutation version 1 (CPMv1)
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

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
90.9 B Herceptin-HER2 P01859 IGHG2_HUMAN
91.9 B Herceptin-HER2 P01861 IGHG4_HUMAN
96.0 B Herceptin-HER2 P01860 IGHG3_HUMAN
100.0 B Herceptin-HER2 P01857 IGHG1_HUMAN
90.6 C Herceptin-HER2 O18735 ERBB2_CANLF
100.0 C Herceptin-HER2 P04626 ERBB2_HUMAN
100.0 A Herceptin-HER2 P01834 IGKC_HUMAN
96.7 V bH1-VEGF-A Q9MYV3 VEGFA_CANLF
94.9 V bH1-VEGF-A Q9GKR0 VEGFA_HORSE
91.2 V bH1-VEGF-A P50412 VEGFA_SHEEP
92.2 V bH1-VEGF-A P15691 VEGFA_BOVIN
96.0 V bH1-VEGF-A P49151 VEGFA_PIG
100.0 V bH1-VEGF-A P15692 VEGFA_HUMAN