Sequence plasticity in the antigen-binding site of a therapeutic anti-Her2 antibody

Journal of Molecular Biology

Volumn 321, Issue 5, 2002, Pages 851-862

  Gerstner, Resi B ^a   Carter, Paul ^a   Lowman, Henry B ^a  

^a GENENTECH INC   (United States)

Author keywords

Affinity maturation; erb B2; Phage display; Trastuzumab; Tumor antigen

Indexed keywords

ANTIBODY; ANTIGEN;

ANTIBODY COMBINING SITE; ANTIGEN ANTIBODY COMPLEX; ARTICLE; BINDING AFFINITY; BINDING SITE; CALCULATION; CONTROLLED STUDY; CORRELATION COEFFICIENT; GENE MUTATION; MUTAGENESIS; NONHUMAN; PLASTICITY; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; SCANNING ELECTRON MICROSCOPY; SEQUENCE HOMOLOGY;

TRIXIS;

EID: 0036382946     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(02)00677-0     Document Type: Article

References (40)

1. Fell, H. P. & Tucker, P. W. (1989). Immunoglobulin genes. Immunol. Ser. 43, 181-202.
2. Wu, T. T. & Kabat, E. A. (1970). An analysis of the sequences of the variable regions of Bence Jones proteins and myeloma light chains and their implications for antibody complementarity. J. Expt. Med. 132, 211-250.
3. Rader, C. & Barbas, C. F., III (1997). Phage display of combinatorial antibody libraries. Curr. Opin. Biotechnol. 8, 503-508.
4. Hoogenboom, H. R. & Chames, P. (2000). Natural and designer binding sites made by phage display technology. Immunol. Today, 21, 371-378.
5. Maynard, J. & Georgiou, G. (2000). Antibody engineering. Annu. Rev. Biomed. Eng. 2, 339-376.
6. Foote, J. & Milstein, C. (1991). Kinetic maturation of an immune response. Nature, 352, 530-532.
7. Boder, E. T., Midelfort, K. S. & Wittrup, K. D. (2000). Directed evolution of antibody fragments with monovalent femtomolar antigen-binding affinity. Proc. Natl Acad. Sci. USA, 97, 10701-10705.
8. Schier, R., McCall, A., Adams, G. P., Marshall, K. W., Merritt, H., Yim, M. et al. (1996). Isolation of pico-molar 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. 263, 551-567.
9. Chen, Y., Wiesmann, C., Fuh, G., Li, B., Christinger, H. W., McKay, P., de Vos, A. M. & Lowman, H. B. (1999). Selection and analysis of an optimized anti-VEGF antibody: crystal structure of an affinity-matured Fab in complex with antigen. J. Mol. Biol. 293, 865-881.
10. Barbas, C. F., III, Hu, D., Dunlop, N., Sawyer, L., Cababa, D., Hendry, R. M. et al. (1994). In vitro evolution of a neutralizing human antibody to human immunodeficiency virus type 1 to enhance affinity and broaden strain cross-reactivity. Proc. Natl Acad. Sci. USA, 91, 3809-3813.
11. Atwell, S., Ultsch, M., De Vos, A. M. & Wells, J. A. (1997). Structural plasticity in a remodeled protein-protein interface. Science, 278, 1125-1128.
12. Atwell, S., Ridgway, J. B., Wells, J. A. &, Carter, P. (1997). Stable heterodimers from remodeling the domain interface of a homodimer using a phage display library. J. Mol. Biol. 270, 26-35.
13. Swint-Kruse, L., Elam, C. R., Lin, J. W., Wycuff, D. R. & Shive Matthews, K. (2001). Plasticity of quaternary structure: twenty-two ways to form a LacI dimer. Protein Sci. 10, 262-276.
14. Kabat, E. A., Wu, T. T., Perry, H. M., Gottesman, K. S. & Foeller, C. (1991). Sequences of Proteins of Immunological Interest, 5th edit., National Institutes of Health, Bethesda, MD.
15. Carter, P., Presta, L., Gorman, C. M., Ridgway, J. B., Henner, D., Wong, W. L. et al. (1992). Humanization of an anti-p185HER2 antibody for human cancer therapy. Proc. Natl Acad. Sci. USA, 89, 4285-4289.
16. Fendly, B. M., Winget, M., Hudziak, R. M., Lipari, M. T., Napier, M. A. & Ullrich, A. (1990). Characterization of murine monoclonal antibodies reactive to either the human epidermal growth factor receptor or HER2/neu gene product. Cancer Res. 50, 1550-1558.
17. Slamon, D. J., Godolphin, W., Jones, L. A., Holt, J. A., Wong, S. G., Keith, D. E. et al. (1989). Studies of the HER-2/neu proto-oncogene in human breast and ovarian cancer. Science, 244, 707-712.
18. Hudziak, R. M., Lewis, G. D., Winget, M., Fendly, B. M., Shepard, H. M. & Ullrich, A. (1989). p185HER2 monoclonal antibody has antiproliferative effects in vitro and sensitizes human breast tumor cells to tumor necrosis factor. Mol. Cell. Biol. 9, 1165-1172.
19. McKeage, K. & Perry, C. M. (2002). Trastuzumab: a review of its use in the treatment of metastatic breast cancer overexpressing HER2. Drugs, 62, 209-243.
20. Eigenbrot, C., Randal, M., Presta, L., Carter, P. & Kossiakoff, A. A. (1993). X-ray structures of the antigen-binding domains from three variants of humanized anti-p185HER2 antibody 4D5 and comparison with molecular modeling. J. Mol. Biol. 229, 969-995.
21. Kelley, R. F. & O'Connell, M. P. (1993). Thermodynamic analysis of an antibody functional epitope. Biochemistry, 32, 6828-6835.
22. Chothia, C. & Lesk, A. M. (1987). Canonical structures for the hypervariable regions of immunoglobulins. J. Mol. Biol. 196, 901-917.
23. Chothia, C., Lesk, A. M., Tramontano, A., Levitt, M., Smith-Gill, S. J., Air, G. et al. (1989). Conformations of immunoglobulin hypervariable regions. Nature, 342, 877-883.
24. Johnson, G. & Wu, T. T. (2001). Kabat database and its applications: future directions. Nucl. Acids Res. 29, 205-206.
25. Dubaquie, Y. & Lowman, H. B. (1999). Total alanine-scanning mutagenesis of insulin-like growth factor I (IGF-I) identifies differential binding epitopes for IGFBP-1 and IGFBP-3. Biochemistry, 38, 6386-6396.
26. Kelley, R. F., O'Connell, M. P., Carter, P., Presta, L., Eigenbrot, C., Covarrubias, M. et al. (1992). Antigen binding thermodynamics and antipro-liferative effects of chimeric and humanized anti-p185HER2 antibody Fab fragments. Biochemistry, 31, 5434-5441.
27. Wilmot, C. M. & Thornton, J. M. (1988). Analysis and prediction of the different types of beta-turn in proteins. J. Mol. Biol. 203, 221-232.
28. Gallivan, J. P. & Dougherty, D. A. (1999). Cation-pi interactions in structural biology. Proc. Natl Acad. Sci. USA, 96, 9459-9464.
29. Burley, S. K. & Petsko, G. A. (1985). Aromatic-aromatic interaction: a mechanism of protein structure stabilization. Science, 229, 23-28.
30. Wells, J. A. (1990). Additivity of mutational effects in proteins. Biochemistry, 29, 8509-8517.
31. Vajdos, F. F., Adams, C., Breece, T. N., Presta, L. G., de Vos, A. A. & Sidhu, S. S. (2002). Comprehensive functional maps of the antigen binding site of an anti-ErbB2 antibody obtained with shotgun scanning mutagenesis. J. Mol. Biol., 320, 415-428.
32. Lu, S. M., Lu, W., Qasim, M. A., Anderson, S., Apostol, I., Ardelt, W. et al. (2001). Humanization of an anti-p185HER2 antibody for human cancer therapy. Proc. Natl Acad. Sci. USA, 98, 4285-4289.
33. Cacia, J., Keck, R., Presta, L. G. & Frenz, J. (1996). Isomerization of an aspartic acid residue in the complementarity-determining regions of a recombinant antibody to human IgE: identification and effect on binding affinity. Biochemistry, 35, 1897-1903.
34. Sidhu, S. S., Lowman, H. B., Cunningham, B. C. & Wells, J. A. (2000). Phage display for selection of novel binding peptides. Methods Enzymol. 328, 333-363.
35. Lowman, H. B. (1998). Phage display of peptide libraries on protein scaffolds. Methods Mol. Biol. 87, 249-264.
36. Kunkel, T. A., Bebenek, K. & McClary, J. (1991). Efficient site-directed mutagenesis using uracil-containing DNA. Methods Enzymol. 204, 125-139.
37. Hawkins, R. E., Russell, S. J. & Winter, G. (1992). Selection of phage antibodies by binding affinity. Mimicking affinity maturation. J. Mol. Biol. 226, 889-896.
38. Weiss, G. A., Watanabe, C. K., Zhong, A., Goddard, A. & Sidhu, S. S. (2000). Rapid mapping of protein functional epitopes by combinatorial alanine scanning. Proc. Natl Acad. Sci. USA, 97, 8950-8954.
39. Carter, P., Kelley, R. F., Rodrigues, M. L., Snedecor, B., Covarrubias, M., Velligan, M. D. et al. (1992). High level Escherichia coli expression and production of a bivalent humanized antibody fragment. Biotechnology (NY), 10, 163-167.
40. Karlsson, R., Michaelsson, A. & Mattsson, L. (1991). Kinetic analysis of monoclonal antibody-antigen interactions with a new biosensor based analytical system. J. Immunol. Methods, 145, 229-240.