Computational design of antibody-affinity improvement beyond in vivo maturation.


Abstract

Antibodies are used extensively in diagnostics and as therapeutic agents. Achieving high-affinity binding is important for expanding detection limits, extending dissociation half-times, decreasing drug dosages and increasing drug efficacy. However, antibody-affinity maturation in vivo often fails to produce antibody drugs of the targeted potency, making further affinity maturation in vitro by directed evolution or computational design necessary. Here we present an iterative computational design procedure that focuses on electrostatic binding contributions and single mutants. By combining multiple designed mutations, a tenfold affinity improvement to 52 pM was engineered into the anti-epidermal growth factor receptor drug cetuximab (Erbitux), and a 140-fold improvement in affinity to 30 pM was obtained for the anti-lysozyme model antibody D44.1. The generality of the methods was further demonstrated through identification of known affinity-enhancing mutations in the therapeutic antibody bevacizumab (Avastin) and the model anti-fluorescein antibody 4-4-20. These results demonstrate computational capabilities for enhancing and accelerating the development of protein reagents and therapeutics.

Submission Details

ID: cZzUip9W4

Submitter: Marie Ary

Submission Date: Dec. 3, 2018, 5:39 p.m.

Version: 1

Publication Details
Lippow SM;Wittrup KD;Tidor B,Nat Biotechnol (2007) Computational design of antibody-affinity improvement beyond in vivo maturation. PMID:17891135
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
1T2Q 2004-04-22T00:00:00+0000 1.83 The Crystal Structure of an NNA7 Fab that recognizes an N-type blood group antigen
1J1P 2002-12-13T00:00:00+0000 1.8 Crystal structure of HyHEL-10 Fv mutant LS91A complexed with hen egg white lysozyme
1J1O 2002-12-13T00:00:00+0000 1.8 Crystal Structure of HyHEL-10 Fv mutant LY50F complexed with hen egg white lysozyme
1J1X 2002-12-20T00:00:00+0000 1.8 Crystal Structure of HyHEL-10 Fv mutant LS93A complexed with hen egg white lysozyme
1IC5 2001-03-30T00:00:00+0000 2.3 CRYSTAL STRUCTURE OF HYHEL-10 FV MUTANT(HD99A)-HEN LYSOZYME COMPLEX
1IC7 2001-03-30T00:00:00+0000 2.1 CRYSTAL STRUCTURE OF HYHEL-10 FV MUTANT(HD32A99A)-HEN LYSOZYME COMPLEX
1IC4 2001-03-30T00:00:00+0000 2.5 CRYSTAL STRUCTURE OF HYHEL-10 FV MUTANT(HD32A)-HEN LYSOZYME COMPLEX
1C08 1999-07-15T00:00:00+0000 2.3 CRYSTAL STRUCTURE OF HYHEL-10 FV-HEN LYSOZYME COMPLEX
4CKD 2014-01-03T00:00:00+0000 13.0 Model of complex between the E.coli enzyme beta-galactosidase and four single chain Fv antibody domains scFv13R4.
1KIQ 1996-10-23T00:00:00+0000 1.85 FV MUTANT Y(B 101)F (VH DOMAIN) OF MOUSE MONOCLONAL ANTIBODY D1.3 COMPLEXED WITH HEN EGG WHITE LYSOZYME

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
95.6 Anti-epidermal growth factor receptor (EGFR) (cetuximab) scFv P01642 KV5A9_MOUSE
93.8 Anti-epidermal growth factor receptor (EGFR) (cetuximab) scFv P01821 HVM45_MOUSE
96.7 Anti-hen egg white lysozyme D1.3 scFv P01635 KV5A3_MOUSE
96.9 Anti-hen egg white lysozyme D1.3 scFv P01820 HVM44_MOUSE