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
1A2Y 1998-04-29 1.5 HEN EGG WHITE LYSOZYME, D18A MUTANT, IN COMPLEX WITH MOUSE MONOCLONAL ANTIBODY D1.3
1G7J 2000-11-22 1.75 CRYSTAL STRUCTURE OF HEN EGG WHITE LYSOZYME (HEL) COMPLEXED WITH THE MUTANT ANTI-HEL MONOCLONAL ANTIBODY D1.3 (VLW92H)
1J1O 2003-01-14 1.8 Crystal Structure of HyHEL-10 Fv mutant LY50F complexed with hen egg white lysozyme
1VFA 1994-05-31 1.8 BOUND WATER MOLECULES AND CONFORMATIONAL STABILIZATION HELP MEDIATE AN ANTIGEN-ANTIBODY ASSOCIATION
1WEJ 1998-12-09 1.8 IGG1 FAB FRAGMENT (OF E8 ANTIBODY) COMPLEXED WITH HORSE CYTOCHROME C AT 1.8 A RESOLUTION
1J1X 2003-01-14 1.8 Crystal Structure of HyHEL-10 Fv mutant LS93A complexed with hen egg white lysozyme
1G7I 2000-11-22 1.8 CRYSTAL STRUCTURE OF HEN EGG WHITE LYSOZYME (HEL) COMPLEXED WITH THE MUTANT ANTI-HEL MONOCLONAL ANTIBODY D1.3 (VLW92F)
1VFB 1994-05-31 1.8 BOUND WATER MOLECULES AND CONFORMATIONAL STABILIZATION HELP MEDIATE AN ANTIGEN-ANTIBODY ASSOCIATION
1J1P 2003-01-14 1.8 Crystal structure of HyHEL-10 Fv mutant LS91A complexed with hen egg white lysozyme
1T2Q 2005-06-07 1.83 The Crystal Structure of an NNA7 Fab that recognizes an N-type blood group antigen
1KIQ 1996-12-23 1.85 FV MUTANT Y(B 101)F (VH DOMAIN) OF MOUSE MONOCLONAL ANTIBODY D1.3 COMPLEXED WITH HEN EGG WHITE LYSOZYME
1G7H 2000-11-22 1.85 CRYSTAL STRUCTURE OF HEN EGG WHITE LYSOZYME (HEL) COMPLEXED WITH THE MUTANT ANTI-HEL MONOCLONAL ANTIBODY D1.3(VLW92A)
1G7M 2000-11-22 1.9 CRYSTAL STRUCTURE OF HEN EGG WHITE LYSOZYME (HEL) COMPLEXED WITH THE MUTANT ANTI-HEL MONOCLONAL ANTIBODY D1.3 (VLW92V)
1DVF 1996-08-17 1.9 IDIOTOPIC ANTIBODY D1.3 FV FRAGMENT-ANTIIDIOTOPIC ANTIBODY E5.2 FV FRAGMENT COMPLEX
4CKD 2014-01-15 13.0 Model of complex between the E.coli enzyme beta-galactosidase and four single chain Fv antibody domains scFv13R4.
1A7O 1998-04-29 2.0 FV FRAGMENT OF MOUSE MONOCLONAL ANTIBODY D1.3 (BALB/C, IGG1, K) R96L DELETION MUTANT ON VARIANT FOR CHAIN L GLU81->ASP AND CHAIN H LEU312->VAL
1A7Q 1998-04-29 2.0 FV FRAGMENT OF MOUSE MONOCLONAL ANTIBODY D1.3 (BALB/C, IGG1, K) HIGH AFFINITY EXPRESSED VARIANT CONTAINING SER26L->GLY, ILE29L->THR, GLU81L->ASP, THR97L->SER, PRO240H->LEU, ASP258H->ALA, LYS281H->GLU, ASN283H->ASP AND LEU312H->VAL
1G7L 2000-11-22 2.0 CRYSTAL STRUCTURE OF HEN EGG WHITE LYSOZYME (HEL) COMPLEXED WITH THE MUTANT ANTI-HEL MONOCLONAL ANTIBODY D1.3 (VLW92S)
1KIR 1996-12-23 2.0 FV MUTANT Y(A 50)S (VL DOMAIN) OF MOUSE MONOCLONAL ANTIBODY D1.3 COMPLEXED WITH HEN EGG WHITE LYSOZYME
1A7P 1998-04-29 2.01 FV FRAGMENT OF MOUSE MONOCLONAL ANTIBODY D1.3 (BALB/C, IGG1, K) ENGINEERED MUTANT PRO95L->SER ON VARIANT CHAIN L GLU81->ASP AND CHAIN H LEU312->VAL
1A7N 1998-04-29 2.01 FV FRAGMENT OF MOUSE MONOCLONAL ANTIBODY D1.3 (BALB/C, IGG1, K) VARIANT FOR CHAIN L GLU81->ASP AND CHAIN H LEU312->VAL
1A7R 1998-04-29 2.01 FV FRAGMENT OF MOUSE MONOCLONAL ANTIBODY D1.3 (BALB/C, IGG1, K) VARIANT CHAIN L GLU81->ASP
1IC7 2001-07-18 2.1 CRYSTAL STRUCTURE OF HYHEL-10 FV MUTANT(HD32A99A)-HEN LYSOZYME COMPLEX
1KIP 1996-12-23 2.1 FV MUTANT Y(B 32)A (VH DOMAIN) OF MOUSE MONOCLONAL ANTIBODY D1.3 COMPLEXED WITH HEN EGG WHITE LYSOZYME
43C9 1999-08-18 2.2 CRYSTALLOGRAPHIC STRUCTURE OF THE ESTEROLYTIC AND AMIDOLYTIC 43C9 ANTIBODY
1QBL 1998-12-02 2.26 FAB E8 (FABE8A) X-RAY STRUCTURE AT 2.26 ANGSTROM RESOLUTION
43CA 1999-08-18 2.3 CRYSTALLOGRAPHIC STRUCTURE OF THE ESTEROLYTIC AND AMIDOLYTIC 43C9 ANTIBODY WITH BOUND P-NITROPHENOL
1IC5 2001-07-18 2.3 CRYSTAL STRUCTURE OF HYHEL-10 FV MUTANT(HD99A)-HEN LYSOZYME COMPLEX
1C08 2000-07-19 2.3 CRYSTAL STRUCTURE OF HYHEL-10 FV-HEN LYSOZYME COMPLEX
1DL7 2000-12-13 2.35 THE STRUCTURAL BASIS OF REPERTOIRE SHIFT IN AN IMMUNE RESPONSE TO PHOSPHOCHOLINE
1P4B 2004-05-04 2.35 Three-Dimensional Structure Of a Single Chain Fv Fragment Complexed With The peptide GCN4(7P-14P).
1QBM 1999-01-27 2.37 FAB E8B ANTIBODY, X-RAY STRUCTURE AT 2.37 ANGSTROMS RESOLUTION
1IC4 2001-07-18 2.5 CRYSTAL STRUCTURE OF HYHEL-10 FV MUTANT(HD32A)-HEN LYSOZYME COMPLEX
1P4I 2004-05-04 2.8 Crystal Structure of scFv against peptide GCN4

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
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
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