Biomedical Microdevices

, Volume 12, Issue 2, pp 283–286 | Cite as

Implications of available design space for identification of non-immunogenic protein therapeutics

  • Stephen Craig Lee
Invited Perspective


Immunogenicity/antibody responses are major issues for parenteral proteins and nanotherapeutics (nanovectors, diagnostics, theranostics, etc.), and robust antibody responses require T-helper epitopes. T-helper epitopes consist of specific amino acids at specific positions (anchor positions) in immunogens which contact the major histocompatibility complex (MHC), provide most of the energy for MHC binding and constitute the binding motif for the corresponding MHC alleles. We developed an algorithm that considers motifs to design vaccines lacking unwanted T-cell epitopes, and found numbers of such vaccines can be astronomical (Lee et al. 2009). The algorithm can be used to design reduced immunogenicity proteins, and numbers of predicted proteins are also immense. Reducing T-helper epitope content reduces protein immunogenicity, but the depth of mutagensis needed to eliminate immunogenicity is commonly assumed to be too great for retention of protein bioactivity. However, very deep, but successful substitution, insertion and deletion mutagenesis have been reported. These reports and design space the algorithm reveals suggest development of non-immunogenic therapeutics might be more feasible than commonly assumed.


MHC-motifs Supertypes-vaccines Aggretopes T-helper epitopes Immunogenicity Immune mitigation Nonimmunogenic Antibody responses Recombinant protein Theranostic Nanoparticulate 


  1. S. Akanuma, T. Kigawa, S. Yokoyama, Combinatorial mutagenesis to restrict amino acid usage in an enzyme to a reduced set. Proc. Natl Acad. Sci. USA 99(21), 13549–53 (2002)CrossRefGoogle Scholar
  2. K.D. Bhalerao et al., Nanodevice design through the functional abstraction of biological macromolecules. App. Phys. Lett. 87, 14587–14590 (2005)CrossRefGoogle Scholar
  3. B.C. Braden et al., X-ray crystal structure of an anti-Buckminsterfullerene antibody fab fragment: biomolecular recognition of C(60). Proc. Natl Acad. Sci. USA 97(22), 12193–7 (2000)CrossRefGoogle Scholar
  4. B.M. Brown, R.T. Sauer, Tolerance of Arc repressor to multiple-alanine substitutions. Proc. Natl Acad. Sci. USA 96(5), 1983–8 (1999)CrossRefGoogle Scholar
  5. B.-X. Chen et al., Antigenicity of fullerenes: antibodies specific for fullerenes and their characteristics. Proc. Natl Acad. Sci. USA 95, 10809–10813 (1998)CrossRefGoogle Scholar
  6. A. Chirino, M. Ary, S. Marshall, Minimizing the immunogenicity of protein therapeutics. Drug Discov. Today 9, 82–90 (2004)CrossRefGoogle Scholar
  7. B.C. Cunningham, J.A. Wells, Minimized proteins. Curr. Opin. Struct. Biol. 7(4), 457–62 (1997)CrossRefGoogle Scholar
  8. P. Debbage, Targeted drugs and nanomedicine: present and future. Curr. Pharm. Des. 15(2), 153–72 (2009)CrossRefGoogle Scholar
  9. P. Debbage, W. Jaschke, Molecular imaging with nanoparticles: giant roles for dwarf actors. Histochem. Cell Biol. 130(5), 845–75 (2008)CrossRefGoogle Scholar
  10. R.J. Fox, G.W. Huisman, Enzyme optimization: moving from blind evolution to statistical exploration of sequence-function space. Trends Biotechnol. 26(3), 132–8 (2008)CrossRefGoogle Scholar
  11. B.K. Klein et al., Use of combinatorial mutagenesis to select for multiply substituted human interleukin-3 variants with improved pharmacologic properties. Exp. Hematol. 27(12), 1746–56 (1999)CrossRefGoogle Scholar
  12. E. Koren, L.A. Zuckerman, A.R. Mire-Sluis, Immune responses to therapeutic proteins in humans–clinical significance, assessment and prediction. Curr. Pharm. Biotechnol. 3(4), 349–60 (2002)CrossRefGoogle Scholar
  13. Y. Kuroda, P.S. Kim, Folding of bovine pancreatic trypsin inhibitor (BPTI) variants in which almost half the residues are alanine. J. Mol. Biol. 298(3), 493–501 (2000)CrossRefGoogle Scholar
  14. S.C. Lee et al., Recognition properties of antibodies to PAMAM dendrimers and their use in immune detection of dendrimers. Biomed. Microdevices: Biomems and Biomedical Nanotechnology 3, 51–57 (2001a)Google Scholar
  15. S.C. Lee et al., Phage display mutagenesis of the chimeric dual cytokine receptor agonist myelopoietin. Leukemia 15, 1277–1285 (2001b)CrossRefGoogle Scholar
  16. S.C. Lee et al., Biochemical and immunological properties of cytokines conjugated to dendritic polymers. Biomed Microdevices 6(3), 191–202 (2004a)CrossRefGoogle Scholar
  17. S.C. Lee, K. Bhalerao, M. Ferrari, Object oriented design tools for supramolecular devices and biomedical nanotechnology. N.Y. Acad. Sci. 1013, 1–14 (2004b)CrossRefGoogle Scholar
  18. S. Lee, M. Reugsegger, P.D. Barnes, B.R. Smith, M. Ferrari, Therapeutic nanodevices. Springer Handbook of Nanotechnology, 2nd Edn (2007) p. 461–504Google Scholar
  19. Y. Lee, G. Ferrari, S.C. Lee, Estimating design space avaialable for polyepitopes through consideration of major histocompatibility compmplex binding motifs. Biomedical microdevices, (2009) doi: 10.1007/s10544-009-9376-7
  20. C. Mateo et al., Removal of amphipathic epitopes from genetically engineered antibodies: production of modified immunoglobulins with reduced immunogenicity. Hybridoma 19(6), 463–71 (2000)CrossRefGoogle Scholar
  21. A. Nijdam, T. Nicholson III, J.P. Shapiro, B.R. Smith, J.T. Heverhagen, P. Schmalbrock, M.V. Knopp, A. Kebbel, D. Wang, S.C. Lee, Nanoparticulate iron oxide contrast agents for untargeted and targeted Cardiovascular magnetic resonance imaging. Curr. Nanosci. 5, 88–102 (2009)CrossRefGoogle Scholar
  22. P.O. Olins et al., Saturation mutagenesis of human interleukin-3. J. Biol. Chem. 270(40), 23754–60 (1995)CrossRefGoogle Scholar
  23. M. Onda, Reducing the immunogenicity of protein therapeutics. Curr. Drug Targets 10(2), 131–9 (2009)CrossRefGoogle Scholar
  24. D.S. Riddle et al., Functional rapidly folding proteins from simplified amino acid sequences. Nat. Struct. Biol. 4(10), 805–9 (1997)CrossRefGoogle Scholar
  25. L. Roque-Navarro et al., Humanization of predicted T-cell epitopes reduces the immunogenicity of chimeric antibodies: new evidence supporting a simple method. Hybrid Hybridomics 22(4), 245–57 (2003)CrossRefGoogle Scholar
  26. S.A. Ross, P.R. Srinivas, A.J. Clifford, S.C. Lee, M.A. Philbert, R.L. Hetich, New technologies for nutrition research. J. Nutr. 134, 681–685 (2004)Google Scholar
  27. J.H. Sakamoto, B.R. Smith, B. Xie, S.I. Rokhlin, S.C. Lee, M. Ferrari, The molecular analysis of breast cancer utilizing targeted nanoparticle ultrasound contrast agents. Tech. Canc. Res. Treat. 4, 627–636 (2005)Google Scholar
  28. H. Schellekens, Immunogenicity of therapeutic proteins: clinical implications and future prospects. Clin. Ther. 24(11), 1720–1740 (2002). discussion 1719CrossRefGoogle Scholar
  29. D. Shortle, J. Sondek, The emerging role of insertions and deletions in protein engineering. Curr. Opin. Biotechnol. 6(4), 387–93 (1995)CrossRefGoogle Scholar
  30. B.R. Smith, J. Heverhagen, M. Knopp, P. Schmalbrock, J. Shapiro, M. Shiomi, N. Moldovan, M. Ferrari, S.C. Lee, Magnetic Resonance Imaging of atherosclerosis in vivo using biochemically targeted ultrasmall superparamagnetic iron oxide particles (SPIONs). Biomed. Microdevices 9, 719–728 (2007)CrossRefGoogle Scholar
  31. J. Sondek, D. Shortle, Accommodation of single amino acid insertions by the native state of staphylococcal nuclease. Proteins 7(4), 299–305 (1990)CrossRefGoogle Scholar
  32. J. Sondek, D. Shortle, A general strategy for random insertion and substitution mutagenesis: substoichiometric coupling of trinucleotide phosphoramidites. Proc. Natl Acad. Sci. USA 89(8), 3581–5 (1992a)CrossRefGoogle Scholar
  33. J. Sondek, D. Shortle, Structural and energetic differences between insertions and substitutions in staphylococcal nuclease. Proteins 13(2), 132–40 (1992b)CrossRefGoogle Scholar
  34. S. Tangri et al., Rationally engineered proteins or antibodies with absent or reduced immunogenicity. Curr. Med. Chem. 9(24), 2191–9 (2002)Google Scholar
  35. S. Tangri et al., Rationally engineered therapeutic proteins with reduced immunogenicity. J. Immunol. 174(6), 3187–96 (2005)Google Scholar
  36. N.J. Turner, Directed evolution drives the next generation of biocatalysts. Nat. Chem. Biol. 5(8), 567–73 (2009)CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2009

Authors and Affiliations

  1. 1.Department of Biomedical EngineeringThe Ohio State UniversityColumbusUSA
  2. 2.Departments of Cellular and Molecular BiochemistryThe Ohio State UniversityColumbusUSA
  3. 3.Chemical and Biomolecular EngineeringThe Ohio State UniversityColumbusUSA
  4. 4.Davis Heart & Lung Research InstituteThe Ohio State UniversityColumbusUSA
  5. 5.College of MedicineThe Ohio State UniversityColumbusUSA

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