Antibody VH and VL recombination using phage and ribosome display technologies reveals distinct structural routes to affinity improvements with VH-VL interface residues providing important structural diversity

mAbs

Volumn 6, Issue 1, 2014, Pages 236-245

  Groves, Maria A T ^a   Amanuel, Lily ^a   Campbell, Jamie I ^b   Rees, D Gareth ^a   Sridharan, Sudharsan ^a   Finch, Donna K ^a   Lowe, David C ^a   Vaughan, Tristan J ^a  

^a MEDIMMUNE   (United States)

^b Kymab Ltd   (United Kingdom)

Author keywords

Antibody; IL 1R1; Mutagenesis; Phage display; Recombination; Ribosome display

Indexed keywords

INTERLEUKIN 1 RECEPTOR; JEDI067 ANTIBODY; KENB061 ANTIBODY; RECEPTOR ANTIBODY; UNCLASSIFIED DRUG;

ANTIBODY AFFINITY; ANTIBODY ISOLATION; ANTIBODY LIBRARY; ANTIBODY STRUCTURE; ARTICLE; COMPLEMENTARITY DETERMINING REGION; CONTROLLED STUDY; GENE DELETION; GENE MUTATION; GENETIC RECOMBINATION; HEAVY CHAIN; HUMAN; HUMAN CELL; MUTAGENESIS; NUCLEOTIDE SEQUENCE; PHAGE DISPLAY; RIBOSOME; STRUCTURAL HOMOLOGY; STRUCTURE ANALYSIS; VH CDR3 SEQUENCE; VL CDR3 SEQUENCE;

ANTIBODY AFFINITY; COMPLEMENTARITY DETERMINING REGIONS; HEK293 CELLS; HUMANS; IMMUNOGLOBULIN HEAVY CHAINS; IMMUNOGLOBULIN LIGHT CHAINS; MODELS, MOLECULAR; PROTEIN STRUCTURE, SECONDARY; RECEPTORS, INTERLEUKIN-1 TYPE I; RECOMBINANT PROTEINS; SINGLE-CHAIN ANTIBODIES;

EID: 84892621931     PISSN: 19420862     EISSN: 19420870     Source Type: Journal    
DOI: 10.4161/mabs.27261     Document Type: Article

References (31)

1. Wilkinson T, Lowe D, Vaughan TJ. Affinity maturation approaches for antibody lead optimization. In Antibody drug discovery 2013; (Wood, C. R., ed.): pp. 85, IMPERIAL COLLEGE PRESS.
2. Carter PJ. Potent antibody therapeutics by design. Nat Rev Immunol 2006; 6:343-57; PMID:16622479; http://dx.doi.org/10.1038/nri1837
3. Gai SA, Wittrup KD. Yeast surface display for protein engineering and characterization. Curr Opin Struct Biol 2007; 17:467-73; PMID:17870469; http:// dx.doi.org/10.1016/j.sbi.2007.08.012
4. Löfblom J. Bacterial display in combinatorial protein engineering. Biotechnol J 2011; 6:1115-29; PMID:21786423; http://dx.doi.org/10.1002/ biot.201100129
5. Boder ET, Midelfort KS, Wittrup KD. Directed evolution of antibody fragments with monovalent femtomolar antigen-binding affinity. Proc Natl Acad Sci U S A 2000; 97:10701-5; PMID:10984501; http:// dx.doi.org/10.1073/pnas. 170297297
6. Steidl S, Ratsch O, Brocks B, Dürr M, Thomassen-Wolf E. In vitro affinity maturation of human GM-CSF antibodies by targeted CDR-diversification. Mol Immunol 2008; 46:135-44; PMID:18722015; http://dx.doi.org/10.1016/j.molimm. 2008.07.013
7. Finch DK, Sleeman MA, Moisan J, Ferraro F, Botterell S, Campbell J, Cochrane D, Cruwys S, England E, Lane S, et al. Whole-molecule antibody engineering: generation of a high-affinity anti-IL-6 antibody with extended pharmacokinetics. J Mol Biol 2011; 411:791-807; PMID:21723291; http://dx.doi. org/10.1016/j.jmb.2011.06.031
8. Plückthun A. Ribosome display: a perspective. Methods Mol Biol 2012; 805:3-28; PMID:22094797; http://dx.doi.org/10.1007/978-1-61779-379-0-1
9. Zahnd C, Amstutz P, Plückthun A. Ribosome display: selecting and evolving proteins in vitro that specifically bind to a target. Nat Methods 2007; 4:269-79; PMID:17327848; http://dx.doi.org/10.1038/ nmeth1003 (Pubitemid 46358879)
10. Groves M, Lane S, Douthwaite J, Lowne D, Rees DG, Edwards B, Jackson RH. Affinity maturation of phage display antibody populations using ribosome display. J Immunol Methods 2006; 313:129-39; PMID:16730741; http://dx.doi.org/ 10.1016/j. jim.2006.04.002
11. Sims JE, March CJ, Cosman D, Widmer MB, MacDonald HR, McMahan CJ, Grubin CE, Wignall JM, Jackson JL, Call SM, et al. cDNA expression cloning of the IL-1 receptor, a member of the immunoglobulin superfamily. Science 1988; 241:585-9; PMID:2969618; http://dx.doi.org/10.1126/ science.2969618
12. Dinarello CA, Simon A, van der Meer JW. Treating inflammation by blocking interleukin-1 in a broad spectrum of diseases. Nat Rev Drug Discov 2012; 11:633-52; PMID:22850787; http://dx.doi. org/10.1038/nrd3800
13. Dripps DJ, Brandhuber BJ, Thompson RC, Eisenberg SP. Interleukin-1 (IL-1) receptor antagonist binds to the 80-kDa IL-1 receptor but does not initiate IL-1 signal transduction. J Biol Chem 1991; 266:10331-6; PMID:1828071 (Pubitemid 21906808)
14. Darling RJ, Brault PA. Kinetic exclusion assay technology: characterization of molecular interactions. Assay Drug Dev Technol 2004; 2:647-57; PMID:15674023; http://dx.doi.org/10.1089/ adt.2004.2.647 (Pubitemid 40309424)
15. Rathanaswami P, Roalstad S, Roskos L, Su QJ, Lackie S, Babcook J. Demonstration of an in vivo generated sub-picomolar affinity fully human monoclonal antibody to interleukin-8. Biochem Biophys Res Commun 2005; 334:1004-13; PMID:16038881; http://dx.doi.org/10.1016/j.bbrc.2005.07.002 (Pubitemid 41074676)
16. Fredericks ZL, Forte C, Capuano IV, Zhou H, Vanden Bos T, Carter P. Identification of potent human anti-IL-1RI antagonist antibodies. Protein Eng Des Sel 2004; 17:95-106; PMID:14985542; http://dx.doi.org/10.1093/protein/gzh012 (Pubitemid 38173173)
17. Shirai H, Kidera A, Nakamura H. H3-rules: identification of CDR-H3 structures in antibodies. FEBS Lett 1999; 455:188-97; PMID:10428499; http:// dx.doi.org/10.1016/S0014-5793(99)00821-2 (Pubitemid 29322808)
18. Shirai H., Kidera A. & Nakamura H. (1999) H3-rules: identification of CDR-H3 structures in antibodies. FEBS Lett. 455, 188-197
19. Nakanishi T, Tsumoto K, Yokota A, Kondo H, Kumagai I. Critical contribution of VH-VL interaction to reshaping of an antibody: the case of humanization of anti-lysozyme antibody, HyHEL 10 Protein Sci 2008; 17:261-70; PMID:18227432; http://dx.doi.org/10.1110/ps.073156708 (Pubitemid 351171838)
20. Abhinandan KR, Martin ACR. Analysis and prediction of VH/VL packing in antibodies. Protein Eng Des Sel 2010; 23:689-97; PMID:20591902; http:// dx.doi.org/10.1093/protein/gzq043
21. Vaughan TJ, Williams AJ, Pritchard K, Osbourn JK, Pope AR, Earnshaw JC, McCafferty J, Hodits RA, Wilton J, Johnson KS. Human antibodies with sub-nanomolar affinities isolated from a large nonimmunized phage display library. Nat Biotechnol 1996; 14:309-14; PMID:9630891; http://dx.doi. org/10.1038/nbt0396-309
22. Lloyd C, Lowe D, Edwards B, Welsh F, Dilks T, Hardman C, Vaughan T. Modelling the human immune response: performance of a 1011 human antibody repertoire against a broad panel of therapeutically relevant antigens. Protein Eng Des Sel 2009; 22:159-68; PMID:18974080; http://dx.doi. org/10.1093/protein/ gzn058
23. Hawkins RE, Russell SJ, Winter G. Selection of phage antibodies by binding affinity. Mimicking affinity maturation. J Mol Biol 1992; 226:889-96; PMID:1507232; http://dx.doi. org/10.1016/0022-2836(92)90639-2
24. Persic L, Roberts A, Wilton J, Cattaneo A, Bradbury A, Hoogenboom HR. An integrated vector system for the eukaryotic expression of antibodies or their fragments after selection from phage display libraries. Gene 1997; 187:9-18; PMID:9073061; http://dx.doi. org/10.1016/S0378-1119(96)00628-2 (Pubitemid 27110429)
25. Mach H, Middaugh CR, Lewis RV. Statistical determination of the average values of the extinction coefficients of tryptophan and tyrosine in native proteins. Anal Biochem 1992; 200:74-80; PMID:1595904; http://dx.doi.org/10.1016/ 0003-2697(92)90279-G
26. Kunkel TA, Roberts JD, Zakour RA. Rapid and efficient site-specific mutagenesis without phenotypic selection. Methods Enzymol 1987; 154:367-82; PMID:3323813; http://dx.doi. org/10.1016/0076-6879(87)54085-X
27. Lewis L, Lloyd C. Optimisation of antibody affinity by ribosome display using error-prone or sitedirected mutagenesis. Methods Mol Biol 2012; 805:139-61; PMID:22094805; http://dx.doi. org/10.1007/978-1-61779-379-0-9
28. Groves MA, Nickson AA. Affinity maturation of phage display antibody populations using ribosome display. Methods Mol Biol 2012; 805:163-90; PMID:22094806; http://dx.doi. org/10.1007/978-1-61779-379-0-10
29. Plückthun A, Schaffitzel C, Hanes J, Jermutus L. In vitro selection and evolution of proteins. Adv Protein Chem 2000; 55:367-403; PMID:11050939; http:// dx.doi.org/10.1016/S0065-3233(01)55009-3 (Pubitemid 33717340)
30. Schaffitzel C, Hanes J, Jermutus L, Plückthun A. Ribosome display: an in vitro method for selection and evolution of antibodies from libraries. J Immunol Methods 1999; 231:119-35; PMID:10648932; http://dx.doi.org/10.1016/ S0022-1759(99)00149-0 (Pubitemid 30394728)
31. Myszka DG. Improving biosensor analysis. J Mol Recognit 1999; 12:279-84; PMID:10556875; http://dx.doi.org/10.1002/ (SICI)1099-1352(199909/10)12:5<279: :AIDJMR473> 3.0.CO;2-3 (Pubitemid 129708590)