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Alternative Scaffolds as Bispecific Antibody Mimetics

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Bispecific Antibodies

Abstract

The use of non-immunoglobulin-based protein scaffolds for engineering of specific recognition was first described some 15 years ago and has matured as a discipline in parallel with the rapidly expanding monoclonal antibody field. As bispecific antibodies and antibody fragments have come into focus lately, the corresponding development of bispecific alternative scaffolds is also emerging. Here, the concept of alternative scaffold proteins is introduced along with comparisons to the antibody and antibody derivatives counterparts. Although the field of bispecifics is anticipated to grow rapidly in the near future, relatively few examples of bispecific binders based on alternative protein scaffolds are reported in the literature. This chapter will present an overview of work that have been published, including a brief introduction to the particular molecular scaffolds with the structural basis and some of the biophysical and biochemical properties before describing the bispecific application.

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References

  • Ahlgren S, Orlova A, Wållberg H, Hansson M, Sandström M, Lewsley R, Wennborg A, Abrahmsén L, Tolmachev V, Feldwisch J (2010) Targeting of HER2-expressing tumors using 111In-ABY-025, a second-generation affibody molecule with a fundamentally reengineered scaffold. J Nucl Med 51:1131–1138

    Article  PubMed  CAS  Google Scholar 

  • Alm T, Yderland L, Nilvebrant J, Halldin A, Hober S (2010) A small bispecific protein selected for orthogonal affinity purification. Biotechnol J 5:605–617

    Article  PubMed  CAS  Google Scholar 

  • Bertschinger J, Grabulovski D, Neri D (2007) Selection of single domain binding proteins by covalent DNA display. Protein Eng Des Sel 20:57–68

    Article  PubMed  CAS  Google Scholar 

  • Binz HK, Amstutz P, Kohl A, Stumpp MT, Briand C, Forrer P, Grutter MG, Plückthun A (2004) High-affinity binders selected from designed ankyrin repeat protein libraries. Nat Biotechnol 22:575–582

    Article  PubMed  CAS  Google Scholar 

  • Deisenhofer J (1981) Crystallographic refinement and atomic models of a human Fc fragment and its complex with fragment B of protein A from Staphylococcus aureus at 2.9- and 2.8-A resolution. Biochemistry 20:2361–2370

    Article  PubMed  CAS  Google Scholar 

  • Dincbas-Renqvist V, Lendel C, Dogan J, Wahlberg E, Härd T (2004) Thermodynamics of folding, stabilization, and binding in an engineered protein–protein complex. J Am Chem Soc 126:11220–11230

    Article  PubMed  CAS  Google Scholar 

  • Dogan J, Lendel C, Hard T (2006) Thermodynamics of folding and binding in an affibody:affibody complex. J Mol Biol 359:1305–1315

    Article  PubMed  CAS  Google Scholar 

  • Ebersbach H, Fiedler E, Scheuermann T, Fiedler M, Stubbs MT, Reimann C, Proetzel G, Rudolph R, Fiedler U (2007) Affilin-novel binding molecules based on human gamma-B-crystallin, an all beta-sheet protein. J Mol Biol 372:172–185

    Article  PubMed  CAS  Google Scholar 

  • Eggel A, Baumann MJ, Amstutz P, Stadler BM, Vogel M (2009) DARPins as bispecific receptor antagonists analyzed for immunoglobulin E receptor blockage. J Mol Biol 393:598–607

    Article  PubMed  CAS  Google Scholar 

  • Eigenbrot C, Ultsch M, Dubnovitsky A, Abrahmsén L, Härd T (2010) Structural basis for high-affinity HER2 receptor binding by an engineered protein. Proc Natl Acad Sci USA 107:15039–15044

    Article  PubMed  CAS  Google Scholar 

  • Emanuel SL et al. (2011) A fibronectin scaffold approach to bispecific inhibitors of epidermal growth factor receptor and insulin-like growth factor-I receptor. MAbs 3:38–48

    Article  PubMed  Google Scholar 

  • Engfeldt T, Renberg B, Brumer H, Nygren PÅ, Karlström AE (2005) Chemical synthesis of triple-labelled three-helix bundle binding proteins for specific fluorescent detection of unlabelled protein. Chembiochem 6:1043–1050

    Article  PubMed  CAS  Google Scholar 

  • Engfeldt T, Orlova A, Tran T, Bruskin A, Widstrom C, Karlström AE, Tolmachev V (2007) Imaging of HER2-expressing tumours using a synthetic affibody molecule containing the 99mTc-chelating mercaptoacetyl-glycyl-glycyl-glycyl (MAG3) sequence. Eur J Nucl Med Mol Imaging 34:722–733

    Article  PubMed  CAS  Google Scholar 

  • Feldwisch J, Tolmachev V, Lendel C, Herne N, Sjöberg A, Larsson B, Rosik D, Lindqvist E, Fant G, Höidén-Guthenberg I et al (2010) Design of an optimized scaffold for affibody molecules. J Mol Biol 398:232–247

    Article  PubMed  CAS  Google Scholar 

  • Friedman M, Nordberg E, Höidén-Guthenberg I, Brismar H, Adams GP, Nilsson FY, Carlsson J, Ståhl S (2007) Phage display selection of affibody molecules with specific binding to the extracellular domain of the epidermal growth factor receptor. Protein Eng Des Sel 20:189–199

    Article  PubMed  CAS  Google Scholar 

  • Friedman M, Orlova A, Johansson E, Eriksson TL, Höidén-Guthenberg I, Tolmachev V, Nilsson FY, Ståhl S (2008) Directed evolution to low nanomolar affinity of a tumor-targeting epidermal growth factor receptor-binding affibody molecule. J Mol Biol 376:1388–1402

    Article  PubMed  CAS  Google Scholar 

  • Friedman M, Lindström S, Ekerljung L, Andersson-Svahn H, Carlsson J, Brismar H, Gedda L, Frejd FY, Ståhl S (2009) Engineering and characterization of a bispecific HER2 x EGFR-binding affibody molecule. Biotechnol Appl Biochem 54:121–131

    Article  PubMed  CAS  Google Scholar 

  • Gebauer M, Skerra A (2009) Engineered protein scaffolds as next-generation antibody therapeutics. Curr Opin Chem Biol 13:245–255

    Article  PubMed  CAS  Google Scholar 

  • Grönwall C, Jonsson A, Lindström S, Gunneriusson E, Ståhl S, Herne N (2007) Selection and characterization of affibody ligands binding to Alzheimer amyloid beta peptides. J Biotechnol 128:162–183

    Article  PubMed  Google Scholar 

  • Hogbom M, Eklund M, Nygren PÅ, Nordlund P (2003) Structural basis for recognition by an in vitro evolved affibody. Proc Natl Acad Sci USA 100:3191–3196

    Article  PubMed  CAS  Google Scholar 

  • Hopp J, Hornig N, Zettlitz KA, Schwarz A, Fuss N, Muller D, Kontermann RE (2010) The effects of affinity and valency of an albumin-binding domain (ABD) on the half-life of a single-chain diabody-ABD fusion protein. Protein Eng Des Sel. 23:827–834

    PubMed  Google Scholar 

  • Hufton SE, van Neer N, van den Beuken T, Desmet J, Sablon E, Hoogenboom HR (2000) Development and application of cytotoxic T lymphocyte-associated antigen 4 as a protein scaffold for the generation of novel binding ligands. FEBS Lett 475:225–231

    Article  PubMed  CAS  Google Scholar 

  • James LC, Roversi P, Tawfik DS (2003) Antibody multispecificity mediated by conformational diversity. Science 299:1362–1367

    Article  PubMed  CAS  Google Scholar 

  • Jonsson A, Dogan J, Herne N, Abrahmsén L, Nygren PÅ (2008) Engineering of a femtomolar affinity binding protein to human serum albumin. Protein Eng Des Sel 21:515–527

    Article  PubMed  CAS  Google Scholar 

  • Kim HJ, Eichinger A, Skerra A (2009) High-affinity recognition of lanthanide(III) chelate complexes by a reprogrammed human lipocalin 2. J Am Chem Soc 131:3565–3576

    Article  PubMed  CAS  Google Scholar 

  • Koide A, Bailey CW, Huang X, Koide S (1998) The fibronectin type III domain as a scaffold for novel binding proteins. J Mol Biol 284:1141–1151

    Article  PubMed  CAS  Google Scholar 

  • Koide A, Gilbreth RN, Esaki K, Tereshko V, Koide S (2007) High-affinity single-domain binding proteins with a binary-code interface. Proc Natl Acad Sci USA 104:6632–6637

    Article  PubMed  CAS  Google Scholar 

  • Kolmar H (2009) Biological diversity and therapeutic potential of natural and engineered cystine knot miniproteins. Curr Opin Pharmacol 9:608–614

    Article  PubMed  CAS  Google Scholar 

  • Kong A, Calleja V, Leboucher P, Harris A, Parker PJ, Larijani B (2008) HER2 oncogenic function escapes EGFR tyrosine kinase inhibitors via activation of alternative HER receptors in breast cancer cells. PLoS One 3. doi:10.1371/journal.pone.0002881

    Google Scholar 

  • Lehmann A (2008) Ecallantide (DX-88), a plasma kallikrein inhibitor for the treatment of hereditary angioedema and the prevention of blood loss in on-pump cardiothoracic surgery. Expert Opin Biol Ther 8:1187–1199

    Article  PubMed  CAS  Google Scholar 

  • Lendel C, Dincbas-Renqvist V, Flores A, Wahlberg E, Dogan J, Nygren PA, Härd T (2004) Biophysical characterization of Z(SPA-1)–a phage-display selected binder to protein A. Protein Sci 13:2078–2088

    Article  PubMed  CAS  Google Scholar 

  • Lendel C, Dogan J, Härd T (2006) Structural basis for molecular recognition in an affibody:affibody complex. J Mol Biol 359:1293–1304

    Article  PubMed  CAS  Google Scholar 

  • Lipovsek D, Lippow SM, Hackel BJ, Gregson MW, Cheng P, Kapila A, Wittrup KD (2007) Evolution of an interloop disulfide bond in high-affinity antibody mimics based on fibronectin type III domain and selected by yeast surface display: molecular convergence with single-domain camelid and shark antibodies. J Mol Biol 368:1024–1041

    Article  PubMed  CAS  Google Scholar 

  • Löfblom J, Feldwisch J, Tolmachev V, Carlsson J, Ståhl S, Frejd FY (2010) Affibody molecules: engineered proteins for therapeutic, diagnostic and biotechnological applications. FEBS Lett 584:2670–2680

    Article  PubMed  Google Scholar 

  • Milstein C, Cuello AC (1983) Hybrid hybridomas and their use in immunohistochemistry. Nature 305:537–540

    Article  PubMed  CAS  Google Scholar 

  • Mouquet H, Scheid JF, Zoller MJ, Krogsgaard M, Ott RG, Shukair S, Artyomov MN, Pietzsch J, Connors M, Pereyra F et al (2010) Polyreactivity increases the apparent affinity of anti-HIV antibodies by heteroligation. Nature 467:591–595

    Article  PubMed  CAS  Google Scholar 

  • Nilsson FY, Tolmachev V (2007) Affibody molecules: new protein domains for molecular imaging and targeted tumor therapy. Curr Opin Drug Discov Devel 10:167–175

    PubMed  CAS  Google Scholar 

  • Nord K, Nilsson J, Nilsson B, Uhlén M, Nygren PÅ (1995) A combinatorial library of an alpha-helical bacterial receptor domain. Protein Eng 8:601–608

    Article  PubMed  CAS  Google Scholar 

  • Nord K, Gunneriusson E, Ringdahl J, Ståhl S, Uhlén M, Nygren PÅ (1997) Binding proteins selected from combinatorial libraries of an alpha-helical bacterial receptor domain. Nat Biotechnol 15:772–777

    Article  PubMed  CAS  Google Scholar 

  • Nord K, Nord O, Uhlén M, Kelley B, Ljungqvist C, Nygren PÅ (2001) Recombinant human factor VIII-specific affinity ligands selected from phage-displayed combinatorial libraries of protein A. Eur J Biochem 268:4269–4277

    Article  PubMed  CAS  Google Scholar 

  • Nygren PÅ, Skerra A (2004) Binding proteins from alternative scaffolds. J Immunol Methods 290:3–28

    Article  PubMed  CAS  Google Scholar 

  • Orlova A, Magnusson M, Eriksson TL, Nilsson M, Larsson B, Höidén-Guthenberg I, Widström C, Carlsson J, Tolmachev V, Ståhl S et al (2006) Tumor imaging using a picomolar affinity HER2 binding affibody molecule. Cancer Res 66:4339–4348

    Article  PubMed  CAS  Google Scholar 

  • Orlova A, Tran T, Widström C, Engfeldt T, Eriksson Karlström A, Tolmachev V (2007a) Pre-clinical evaluation of [111In]-benzyl-DOTA-Z(HER2:342), a potential agent for imaging of HER2 expression in malignant tumors. Int J Mol Med 20:397–404

    PubMed  CAS  Google Scholar 

  • Orlova A, Tolmachev V, Pehrson R, Lindborg M, Tran T, Sandstrom M, Nilsson FY, Wennborg A, Abrahmsen L, Feldwisch J (2007b) Synthetic affibody molecules: a novel class of affinity ligands for molecular imaging of HER2-expressing malignant tumors. Cancer Res 67:2178–2186

    Article  PubMed  CAS  Google Scholar 

  • Osaki A, Toi M, Yamada H, Kawami H, Kuroi K, Toge T (1992) Prognostic significance of co-expression of c-erbB-2 oncoprotein and epidermal growth factor receptor in breast cancer patients. Am J Surg 164:323–326

    Article  PubMed  CAS  Google Scholar 

  • Sandström K, Xu Z, Forsberg G, Nygren PÅ (2003) Inhibition of the CD28-CD80 co-stimulation signal by a CD28-binding affibody ligand developed by combinatorial protein engineering. Protein Eng 16:691–697

    Article  PubMed  Google Scholar 

  • Schlehuber S, Skerra A (2001) Duocalins: engineered ligand-binding proteins with dual specificity derived from the lipocalin fold. Biol Chem 382:1335–1342

    Article  PubMed  CAS  Google Scholar 

  • Schlehuber S, Skerra A (2005) Lipocalins in drug discovery: from natural ligand-binding proteins to “anticalins”. Drug Discov Today 10:23–33

    Article  PubMed  CAS  Google Scholar 

  • Silverman J, Liu Q, Bakker A, To W, Duguay A, Alba BM, Smith R, Rivas A, Li P, Le H et al (2005) Multivalent avimer proteins evolved by exon shuffling of a family of human receptor domains. Nat Biotechnol 23:1556–1561

    Article  PubMed  CAS  Google Scholar 

  • Skerra A (2008) Alternative binding proteins: anticalins – harnessing the structural plasticity of the lipocalin ligand pocket to engineer novel binding activities. FEBS J 275:2677–2683

    Article  PubMed  CAS  Google Scholar 

  • Steffen AC, Orlova A, Wikman M, Nilsson FY, Ståhl S, Adams GP, Tolmachev V, Carlsson J (2006) Affibody-mediated tumour targeting of HER-2 expressing xenografts in mice. Eur J Nucl Med Mol Imaging 33:631–638

    Article  PubMed  CAS  Google Scholar 

  • Steiner D, Forrer P, Stumpp MT, Plückthun A (2006) Signal sequences directing cotranslational translocation expand the range of proteins amenable to phage display. Nat Biotechnol 24:823–831

    Article  PubMed  CAS  Google Scholar 

  • Stork R, Campigna E, Robert B, Muller D, Kontermann RE (2009) Biodistribution of a bispecific single-chain diabody and its half-life extended derivatives. J Biol Chem 284:25612–25619

    Article  PubMed  CAS  Google Scholar 

  • Stumpp MT, Binz HK, Amstutz P (2008) DARPins: a new generation of protein therapeutics. Drug Discov Today 13:695–701

    Article  PubMed  CAS  Google Scholar 

  • Tolmachev V, Nilsson FY, Widström C, Andersson K, Rosik D, Gedda L, Wennborg A, Orlova A (2006) 111In-benzyl-DTPA-ZHER2:342, an affibody-based conjugate for in vivo imaging of HER2 expression in malignant tumors. J Nucl Med 47:846–853

    PubMed  CAS  Google Scholar 

  • Tolmachev V, Orlova A, Nilsson FY, Feldwisch J, Wennborg A, Abrahmsén L (2007a) Affibody molecules: potential for in vivo imaging of molecular targets for cancer therapy. Expert Opin Biol Ther 7:555–568

    Article  PubMed  CAS  Google Scholar 

  • Tolmachev V, Orlova A, Pehrson R, Galli J, Baastrup B, Andersson K, Sandström M, Rosik D, Carlsson J, Lundqvist H et al (2007b) Radionuclide therapy of HER2-positive microxenografts using a 177Lu-labeled HER2-specific affibody molecule. Cancer Res 67:2773–2782

    Article  PubMed  CAS  Google Scholar 

  • Tsutsui S, Ohno S, Murakami S, Kataoka A, Kinoshita J, Hachitanda Y (2003) Prognostic value of the combination of epidermal growth factor receptor and c-erbB-2 in breast cancer. Surgery 133:219–221

    Article  PubMed  Google Scholar 

  • Wahlberg E, Lendel C, Helgstrand M, Allard P, Dincbas-Renqvist V, Hedqvist A, Berglund H, Nygren PÅ, Härd T (2003) An affibody in complex with a target protein: structure and coupled folding. Proc Natl Acad Sci USA 100:3185–3190

    Article  PubMed  CAS  Google Scholar 

  • Wållberg H et al. (2010) Bi-specific affibody molecules for targeting of EGFR and HER2. Sixth annual protein engineering summit PEGS, May 17–21, Boston. Poster Abstract 78

    Google Scholar 

  • Weissleder R (2006) Molecular imaging in cancer. Science 312:1168–1171

    Article  PubMed  CAS  Google Scholar 

  • Wikman M, Steffen AC, Gunneriusson E, Tolmachev V, Adams GP, Carlsson J, Ståhl S (2004) Selection and characterization of HER2/neu-binding affibody ligands. Protein Eng Des Sel 17:455–462

    Article  PubMed  CAS  Google Scholar 

  • Wikman M, Rowcliffe E, Friedman M, Henning P, Lindholm L, Olofsson S, Ståhl S (2006) Selection and characterization of an HIV-1 gp120-binding affibody ligand. Biotechnol Appl Biochem 45:93–105

    Article  PubMed  CAS  Google Scholar 

  • Xu L, Aha P, Gu K, Kuimelis RG, Kurz M, Lam T, Lim AC, Liu H, Lohse PA, Sun L et al (2002) Directed evolution of high-affinity antibody mimics using mRNA display. Chem Biol 9:933–942

    Article  PubMed  CAS  Google Scholar 

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Correspondence to Fredrik Y. Frejd .

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Löfblom, J., Frejd, F.Y. (2011). Alternative Scaffolds as Bispecific Antibody Mimetics. In: Kontermann, R. (eds) Bispecific Antibodies. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-20910-9_7

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