Robust in vitro affinity maturation strategy based on interface-focused high-throughput mutational scanning

Biochemical and Biophysical Research Communications

Volumn 428, Issue 3, 2012, Pages 395-400

  Fujino, Yasuhiro ^a,b   Fujita, Risako ^a   Wada, Kouichi ^a   Fujishige, Kotomi ^a   Kanamori, Takashi ^b   Hunt, Lindsey ^c   Shimizu, Yoshihiro ^b,d   Ueda, Takuya ^b  

^a MITSUBISHI TANABE PHARMA CORPORATION   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

^c Sapidyne Instruments Incorporated   (United States)

^d RIKEN Center for Biosystems Dynamics Research   (Japan)

Author keywords

Affinity maturation; Antibody Fab fragment; High throughput sequencing; Mutation scanning; Protein engineering; Ribosome display

Indexed keywords

IMMUNOGLOBULIN F(AB) FRAGMENT; TUMOR NECROSIS FACTOR ALPHA RECEPTOR;

AMINO ACID SUBSTITUTION; ARTICLE; BINDING AFFINITY; COMBINATORIAL LIBRARY; COMPLEMENTARITY DETERMINING REGION; DISSOCIATION CONSTANT; HIGH THROUGHPUT SEQUENCING; IN VITRO STUDY; PARTICULATE MATTER; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION;

AMINO ACID SUBSTITUTION; COMBINATORIAL CHEMISTRY TECHNIQUES; COMPLEMENTARITY DETERMINING REGIONS; DNA MUTATIONAL ANALYSIS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; IMMUNOGLOBULIN FAB FRAGMENTS; PROTEIN BINDING; RECEPTORS, TUMOR NECROSIS FACTOR; SMALL MOLECULE LIBRARIES;

EID: 84869868746     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2012.10.066     Document Type: Article

References (18)

1. Bradbury A.R., Sidhu S., Dubel S., McCafferty J. Beyond natural antibodies: the power of in vitro display technologies. Nat. Biotechnol. 2011, 29:245-254.
2. Schier R., McCall A., Adams G.P., Marshall K.W., Merritt H., Yim M., Crawford R.S., Weiner L.M., Marks C., Marks J.D. Isolation of picomolar affinity anti-c-erbB-2 single-chain Fv by molecular evolution of the complementarity determining regions in the center of the antibody binding site. J. Mol. Biol. 1996, 263:551-567.
3. Lippow S.M., Wittrup K.D., Tidor B. Computational design of antibody-affinity improvement beyond in vivo maturation. Nat. Biotechnol. 2007, 25:1171-1176.
4. Rajpal A., Beyaz N., Haber L., Cappuccilli G., Yee H., Bhatt R.R., Takeuchi T., Lerner R.A., Crea R. A general method for greatly improving the affinity of antibodies by using combinatorial libraries. Proc. Natl. Acad. Sci. USA 2005, 102:8466-8471.
5. Votsmeier C., Plittersdorf H., Hesse O., Scheidig A., Strerath M., Gritzan U., Pellengahr K., Scholz P., Eicker A., Myszka D., Coco W.M., Haupts U. Femtomolar Fab binding affinities to a protein target by alternative CDR residue co-optimization strategies without phage or cell surface display. MAbs 2012, 4.
6. Vajdos F.F., Adams C.W., Breece T.N., Presta L.G., de Vos A.M., Sidhu S.S. Comprehensive functional maps of the antigen-binding site of an anti-ErbB2 antibody obtained with shotgun scanning mutagenesis. J. Mol. Biol. 2002, 320:415-428.
7. Pal G., Kouadio J.L., Artis D.R., Kossiakoff A.A., Sidhu S.S. Comprehensive and quantitative mapping of energy landscapes for protein-protein interactions by rapid combinatorial scanning. J. Biol. Chem. 2006, 281:22378-22385.
8. Fowler D.M., Araya C.L., Fleishman S.J., Kellogg E.H., Stephany J.J., Baker D., Fields S. High-resolution mapping of protein sequence-function relationships. Nat. Methods 2010, 7:741-746.
9. Ernst A., Gfeller D., Kan Z., Seshagiri S., Kim P.M., Bader G.D., Sidhu S.S. Coevolution of PDZ domain-ligand interactions analyzed by high-throughput phage display and deep sequencing. Mol. Biosyst. 2010, 6:1782-1790.
10. Whitehead T.A., Chevalier A., Song Y., Dreyfus C., Fleishman S.J., De Mattos C., Myers C.A., Kamisetty H., Blair P., Wilson I.A., Baker D. Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing. Nat. Biotechnol. 2012, 30:543-548.
11. Shibui T., Kobayashi T., Kanatani K. A completely in vitro system for obtaining scFv using mRNA display, PCR, direct sequencing, and wheat embryo cell-free translation. Biotechnol. Lett. 2009, 31:1103-1110.
12. Muto H., Nakatogawa H., Ito K. Genetically encoded but nonpolypeptide prolyl-tRNA functions in the A site for SecM-mediated ribosomal stall. Mol. Cell 2006, 22:545-552.
13. Shimizu Y., Inoue A., Tomari Y., Suzuki T., Yokogawa T., Nishikawa K., Ueda T. Cell-free translation reconstituted with purified components. Nat. Biotechnol. 2001, 19:751-755.
14. Ohashi H., Shimizu Y., Ying B.W., Ueda T. Efficient protein selection based on ribosome display system with purified components. Biochem. Biophys. Res. Commun. 2007, 352:270-276.
15. Bee C., Abdiche Y.N., Stone D.M., Collier S., Lindquist K.C., Pinkerton A.C., Pons J., Rajpal A. Exploring the dynamic range of the kinetic exclusion assay in characterizing antigen-antibody interactions. PLoS One 2012, 7:e36261.
16. Yang W.P., Green K., Pinz-Sweeney S., Briones A.T., Burton D.R., Barbas C.F. CDR walking mutagenesis for the affinity maturation of a potent human anti-HIV-1 antibody into the picomolar range. J. Mol. Biol. 1995, 254:392-403.
17. Boder E.T., Midelfort K.S., Wittrup K.D. Directed evolution of antibody fragments with monovalent femtomolar antigen-binding affinity. Proc. Natl. Acad. Sci. USA 2000, 97:10701-10705.
18. Zahnd C., Spinelli S., Luginbuhl B., Amstutz P., Cambillau C., Pluckthun A. Directed in vitro evolution and crystallographic analysis of a peptide-binding single chain antibody fragment (scFv) with low picomolar affinity. J. Biol. Chem. 2004, 279:18870-18877.