Skip to main navigation menu Skip to main content Skip to site footer
##common.pageHeaderLogo.altText##

Review article: Biomedical intelligence

Vol. 147 No. 4748 (2017)

Monobodies as possible next-generation protein therapeutics – a perspective

  • Oliver Hantschel
DOI
https://doi.org/10.4414/smw.2017.14545
Cite this as:
Swiss Med Wkly. 2017;147:w14545
Published
20.11.2017

Summary

Over the past two decades, hundreds of new somatic mutations have been identified in tumours, and a few dozen novel cancer therapeutics that selectively target these mutated oncoproteins have entered clinical practice. This development has resulted in clinical breakthroughs for a few tumour types, but more commonly patients' overall survival has not improved because of the development of drug resistance. Furthermore, only a very limited number of oncoproteins, largely protein kinases, are successfully targeted, whereas most non-kinase oncoproteins inside cancer cells remain untargeted. Engineered small protein inhibitors offer great promise in targeting a larger variety of oncoproteins with better efficacy and higher selectivity. In this article, I focus on a promising class of synthetic binding proteins, termed monobodies, that we have shown to inhibit previously untargetable protein-protein interactions in different oncoproteins. I will discuss the great promise alongside the technical challenges inherent in converting monobodies from potent pre-clinical target validation tools to next-generation protein-based therapeutics.

References

  1. Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell. 2011;144(5):646–74. doi:.https://doi.org/10.1016/j.cell.2011.02.013
  2. Sliwkowski MX, Mellman I. Antibody therapeutics in cancer. Science. 2013;341(6151):1192–8. doi:.https://doi.org/10.1126/science.1241145
  3. Hantschel O. Unexpected off-targets and paradoxical pathway activation by kinase inhibitors. ACS Chem Biol. 2015;10(1):234–45. doi:.https://doi.org/10.1021/cb500886n
  4. Gambacorti-Passerini C, Antolini L, Mahon F-X, Guilhot F, Deininger M, Fava C, et al. Multicenter independent assessment of outcomes in chronic myeloid leukemia patients treated with imatinib. J Natl Cancer Inst. 2011;103(7):553–61. doi:.https://doi.org/10.1093/jnci/djr060
  5. Holohan C, Van Schaeybroeck S, Longley DB, Johnston PG. Cancer drug resistance: an evolving paradigm. Nat Rev Cancer. 2013;13(10):714–26. doi:.https://doi.org/10.1038/nrc3599
  6. Garraway LA, Lander ES. Lessons from the cancer genome. Cell. 2013;153(1):17–37. doi:.https://doi.org/10.1016/j.cell.2013.03.002
  7. Davis MI, Hunt JP, Herrgard S, Ciceri P, Wodicka LM, Pallares G, et al. Comprehensive analysis of kinase inhibitor selectivity. Nat Biotechnol. 2011;29(11):1046–51. doi:.https://doi.org/10.1038/nbt.1990
  8. Hantschel O, Rix U, Superti-Furga G. Target spectrum of the BCR-ABL inhibitors imatinib, nilotinib and dasatinib. Leuk Lymphoma. 2008;49(4):615–9. doi:.https://doi.org/10.1080/10428190801896103
  9. Marin D, Bazeos A, Mahon F-X, Eliasson L, Milojkovic D, Bua M, et al. Adherence is the critical factor for achieving molecular responses in patients with chronic myeloid leukemia who achieve complete cytogenetic responses on imatinib. J Clin Oncol. 2010;28(14):2381–8. doi:.https://doi.org/10.1200/JCO.2009.26.3087
  10. Fedorov O, Müller S, Knapp S. The (un)targeted cancer kinome. Nat Chem Biol. 2010;6(3):166–9. doi:.https://doi.org/10.1038/nchembio.297
  11. Binz HK, Amstutz P, Plückthun A. Engineering novel binding proteins from nonimmunoglobulin domains. Nat Biotechnol. 2005;23(10):1257–68. doi:.https://doi.org/10.1038/nbt1127
  12. Gilbreth RN, Koide S. Structural insights for engineering binding proteins based on non-antibody scaffolds. Curr Opin Struct Biol. 2012;22(4):413–20. doi:.https://doi.org/10.1016/j.sbi.2012.06.001
  13. Lee SC, Park K, Han J, Lee JJ, Kim HJ, Hong S, et al. Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering. Proc Natl Acad Sci USA. 2012;109(9):3299–304. doi:.https://doi.org/10.1073/pnas.1113193109
  14. Koide A, Bailey CW, Huang X, Koide S. The fibronectin type III domain as a scaffold for novel binding proteins. J Mol Biol. 1998;284(4):1141–51. doi:.https://doi.org/10.1006/jmbi.1998.2238
  15. Koide A, Wojcik J, Gilbreth RN, Hoey RJ, Koide S. Teaching an old scaffold new tricks: monobodies constructed using alternative surfaces of the FN3 scaffold. J Mol Biol. 2012;415(2):393–405. doi:.https://doi.org/10.1016/j.jmb.2011.12.019
  16. Sha F, Salzman G, Gupta A, Koide S. Monobodies and other synthetic binding proteins for expanding protein science. Protein Sci. 2017;26(5):910–24. doi:.https://doi.org/10.1002/pro.3148
  17. Koide A, Koide S. Monobodies: antibody mimics based on the scaffold of the fibronectin type III domain. Methods Mol Biol. 2007;352:95–109.
  18. Sadowski I, Stone JC, Pawson T. A noncatalytic domain conserved among cytoplasmic protein-tyrosine kinases modifies the kinase function and transforming activity of Fujinami sarcoma virus P130gag-fps. Mol Cell Biol. 1986;6(12):4396–408. doi:.https://doi.org/10.1128/MCB.6.12.4396
  19. Pawson T. Specificity in signal transduction: from phosphotyrosine-SH2 domain interactions to complex cellular systems. Cell. 2004;116(2):191–203. doi:.https://doi.org/10.1016/S0092-8674(03)01077-8
  20. Liu BA, Jablonowski K, Raina M, Arcé M, Pawson T, Nash PD. The human and mouse complement of SH2 domain proteins-establishing the boundaries of phosphotyrosine signaling. Mol Cell. 2006;22(6):851–68. doi:.https://doi.org/10.1016/j.molcel.2006.06.001
  21. Waksman G, Shoelson SE, Pant N, Cowburn D, Kuriyan J. Binding of a high affinity phosphotyrosyl peptide to the Src SH2 domain: crystal structures of the complexed and peptide-free forms. Cell. 1993;72(5):779–90. doi:.https://doi.org/10.1016/0092-8674(93)90405-F
  22. Kraskouskaya D, Duodu E, Arpin CC, Gunning PT. Progress towards the development of SH2 domain inhibitors. Chem Soc Rev. 2013;42(8):3337–70. doi:.https://doi.org/10.1039/c3cs35449k
  23. Quartararo JS, Wu P, Kritzer JA. Peptide bicycles that inhibit the Grb2 SH2 domain. ChemBioChem. 2012;13(10):1490–6. doi:.https://doi.org/10.1002/cbic.201200175
  24. Wojcik J, Hantschel O, Grebien F, Kaupe I, Bennett KL, Barkinge J, et al. A potent and highly specific FN3 monobody inhibitor of the Abl SH2 domain. Nat Struct Mol Biol. 2010;17(4):519–27. doi:.https://doi.org/10.1038/nsmb.1793
  25. Grebien F, Hantschel O, Wojcik J, Kaupe I, Kovacic B, Wyrzucki AM, et al. Targeting the SH2-kinase interface in Bcr-Abl inhibits leukemogenesis. Cell. 2011;147(2):306–19. doi:.https://doi.org/10.1016/j.cell.2011.08.046
  26. Wojcik J, Lamontanara AJ, Grabe G, Koide A, Akin L, Gerig B, et al. Allosteric Inhibition of Bcr-Abl Kinase by High Affinity Monobody Inhibitors Directed to the Src Homology 2 (SH2)-Kinase Interface. J Biol Chem. 2016;291(16):8836–47. doi:.https://doi.org/10.1074/jbc.M115.707901
  27. Sha F, Gencer EB, Georgeon S, Koide A, Yasui N, Koide S, et al. Dissection of the BCR-ABL signaling network using highly specific monobody inhibitors to the SHP2 SH2 domains. Proc Natl Acad Sci USA. 2013;110(37):14924–9. doi:.https://doi.org/10.1073/pnas.1303640110
  28. Kükenshöner T, Schmit NE, Bouda E, Sha F, Pojer F, Koide A, et al. Selective Targeting of SH2 Domain-Phosphotyrosine Interactions of Src Family Tyrosine Kinases with Monobodies. J Mol Biol. 2017;429(9):1364–80. doi:.https://doi.org/10.1016/j.jmb.2017.03.023
  29. Spencer-Smith R, Koide A, Zhou Y, Eguchi RR, Sha F, Gajwani P, et al. Inhibition of RAS function through targeting an allosteric regulatory site. Nat Chem Biol. 2017;13(1):62–8. doi:.https://doi.org/10.1038/nchembio.2231
  30. Tanaka S, Takahashi T, Koide A, Ishihara S, Koikeda S, Koide S. Monobody-mediated alteration of enzyme specificity. Nat Chem Biol. 2015;11(10):762–4. doi:.https://doi.org/10.1038/nchembio.1896
  31. Huang J, Makabe K, Biancalana M, Koide A, Koide S. Structural basis for exquisite specificity of affinity clamps, synthetic binding proteins generated through directed domain-interface evolution. J Mol Biol. 2009;392(5):1221–31. doi:.https://doi.org/10.1016/j.jmb.2009.07.067
  32. Yasui N, Findlay GM, Gish GD, Hsiung MS, Huang J, Tucholska M, et al. Directed network wiring identifies a key protein interaction in embryonic stem cell differentiation. Mol Cell. 2014;54(6):1034–41. doi:.https://doi.org/10.1016/j.molcel.2014.05.002
  33. Stockbridge RB, Kolmakova-Partensky L, Shane T, Koide A, Koide S, Miller C, et al. Crystal structures of a double-barrelled fluoride ion channel. Nature. 2015;525(7570):548–51. doi:.https://doi.org/10.1038/nature14981
  34. Weiss WA, Taylor SS, Shokat KM. Recognizing and exploiting differences between RNAi and small-molecule inhibitors. Nat Chem Biol. 2007;3(12):739–44. doi:.https://doi.org/10.1038/nchembio1207-739
  35. Verdurmen WPR, Luginbühl M, Honegger A, Plückthun A. Efficient cell-specific uptake of binding proteins into the cytoplasm through engineered modular transport systems. J Control Release. 2015;200:13–22. doi:.https://doi.org/10.1016/j.jconrel.2014.12.019
  36. Mitragotri S, Burke PA, Langer R. Overcoming the challenges in administering biopharmaceuticals: formulation and delivery strategies. Nat Rev Drug Discov. 2014;13(9):655–72. doi:.https://doi.org/10.1038/nrd4363
  37. Koren E, Torchilin VP. Cell-penetrating peptides: breaking through to the other side. Trends Mol Med. 2012;18(7):385–93. doi:.https://doi.org/10.1016/j.molmed.2012.04.012
  38. Raucher D, Ryu JS. Cell-penetrating peptides: strategies for anticancer treatment. Trends Mol Med. 2015;21(9):560–70. doi:.https://doi.org/10.1016/j.molmed.2015.06.005
  39. Blanco E, Shen H, Ferrari M. Principles of nanoparticle design for overcoming biological barriers to drug delivery. Nat Biotechnol. 2015;33(9):941–51. doi:.https://doi.org/10.1038/nbt.3330
  40. Du J, Jin J, Yan M, Lu Y. Synthetic nanocarriers for intracellular protein delivery. Curr Drug Metab. 2012;13(1):82–92. doi:.https://doi.org/10.2174/138920012798356862
  41. Gasparini G, Bang EK, Montenegro J, Matile S. Cellular uptake: lessons from supramolecular organic chemistry. Chem Commun (Camb). 2015;51(52):10389–402. doi:.https://doi.org/10.1039/C5CC03472H
  42. Rothbard JB, Garlington S, Lin Q, Kirschberg T, Kreider E, McGrane PL, et al. Conjugation of arginine oligomers to cyclosporin A facilitates topical delivery and inhibition of inflammation. Nat Med. 2000;6(11):1253–7. doi:.https://doi.org/10.1038/81359
  43. Gasparini G, Bang EK, Molinard G, Tulumello DV, Ward S, Kelley SO, et al. Cellular uptake of substrate-initiated cell-penetrating poly(disulfide)s. J Am Chem Soc. 2014;136(16):6069–74. doi:.https://doi.org/10.1021/ja501581b
  44. Gasparini G, Matile S. Protein delivery with cell-penetrating poly(disulfide)s. Chem Commun (Camb). 2015;51(96):17160–2. doi:.https://doi.org/10.1039/C5CC07460F
  45. Derivery E, Bartolami E, Matile S, Gonzalez-Gaitan M. Efficient Delivery of Quantum Dots into the Cytosol of Cells Using Cell-Penetrating Poly(disulfide)s. J Am Chem Soc. 2017;139(30):10172–5. doi:.https://doi.org/10.1021/jacs.7b02952
  46. Abegg D, Gasparini G, Hoch DG, Shuster A, Bartolami E, Matile S, et al. Strained Cyclic Disulfides Enable Cellular Uptake by Reacting with the Transferrin Receptor. J Am Chem Soc. 2017;139(1):231–8. doi:.https://doi.org/10.1021/jacs.6b09643
  47. Cronican JJ, Beier KT, Davis TN, Tseng J-C, Li W, Thompson DB, et al. A class of human proteins that deliver functional proteins into mammalian cells in vitro and in vivo. Chem Biol. 2011;18(7):833–8. doi:.https://doi.org/10.1016/j.chembiol.2011.07.003
  48. Cronican JJ, Thompson DB, Beier KT, McNaughton BR, Cepko CL, Liu DR. Potent delivery of functional proteins into Mammalian cells in vitro and in vivo using a supercharged protein. ACS Chem Biol. 2010;5(8):747–52. doi:.https://doi.org/10.1021/cb1001153
  49. Liao X, Rabideau AE, Pentelute BL. Delivery of antibody mimics into mammalian cells via anthrax toxin protective antigen. ChemBioChem. 2014;15(16):2458–66. doi:.https://doi.org/10.1002/cbic.201402290
  50. Ryou JH, Sohn YK, Hwang DE, Park WY, Kim N, Heo WD, et al. Engineering of bacterial exotoxins for highly efficient and receptor-specific intracellular delivery of diverse cargos. Biotechnol Bioeng. 2016;113(8):1639–46. doi:.https://doi.org/10.1002/bit.25935
  51. Kube S, Hersch N, Naumovska E, Gensch T, Hendriks J, Franzen A, et al. Fusogenic Liposomes as Nanocarriers for the Delivery of Intracellular Proteins. Langmuir. 2017;33(4):1051–9. doi:.https://doi.org/10.1021/acs.langmuir.6b04304
  52. Yim N, Ryu SW, Choi K, Lee KR, Lee S, Choi H, et al. Exosome engineering for efficient intracellular delivery of soluble proteins using optically reversible protein-protein interaction module. Nat Commun. 2016;7:12277. doi:.https://doi.org/10.1038/ncomms12277
  53. Ryou SM, Yeom JH, Kang HJ, Won M, Kim JS, Lee B, et al. Gold nanoparticle-DNA aptamer composites as a universal carrier for in vivo delivery of biologically functional proteins. J Control Release. 2014;196:287–94. doi:.https://doi.org/10.1016/j.jconrel.2014.10.021
  54. Uppalapati M, Lee DJ, Mandal K, Li H, Miranda LP, Lowitz J, et al. A Potent d-Protein Antagonist of VEGF-A is Nonimmunogenic, Metabolically Stable, and Longer-Circulating in Vivo. ACS Chem Biol. 2016;11(4):1058–65. doi:.https://doi.org/10.1021/acschembio.5b01006
  55. Mandal K, Uppalapati M, Ault-Riché D, Kenney J, Lowitz J, Sidhu SS, et al. Chemical synthesis and X-ray structure of a heterochiral D-protein antagonist plus vascular endothelial growth factor protein complex by racemic crystallography. Proc Natl Acad Sci USA. 2012;109(37):14779–84. doi:.https://doi.org/10.1073/pnas.1210483109
  56. Jevsevar S, Kunstelj M, Porekar VG. PEGylation of therapeutic proteins. Biotechnol J. 2010;5(1):113–28. doi:.https://doi.org/10.1002/biot.200900218
  57. Zorzi A, Middendorp SJ, Wilbs J, Deyle K, Heinis C. Acylated heptapeptide binds albumin with high affinity and application as tag furnishes long-acting peptides. Nat Commun. 2017;8:16092. doi:.https://doi.org/10.1038/ncomms16092
  58. Teesalu T, Sugahara KN, Ruoslahti E. Tumor-penetrating peptides. Front Oncol. 2013;3:216. doi:.https://doi.org/10.3389/fonc.2013.00216