Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Perspective
  • Published:

Screening for peptide drugs from the natural repertoire of biodiverse protein folds

Nature Biotechnology volume 24, pages 177–183 (2006)Cite this article

Abstract

Although monoclonal antibody (mAb) drugs targeting protein interactions exist, these therapeutics cannot access intracellular proteins involved in disease complexes. Moreover, mAbs are more difficult to deliver and are frequently associated with a prohibitive 'royalty stack.' Outlined here is an alternative approach based on libraries of natural, highly structured peptides that offers new opportunities for identifying effective, specific inhibitors of protein-protein interactions. Libraries of such peptides (referred to hereafter as phylomers) comprise both random and structured peptides encoded by natural genes of diverse bacterial genomes. Because the number of protein subdomain structures found in nature is limited, diverse libraries containing millions of phylomers constitute virtually all of the available classes of protein fold structures, providing a rich source of peptides that interact specifically and with high affinity to human proteins. This approach may help not only in understanding the implications of each interaction identified within the interactome but also in the development of effective drugs targeted to particular protein functions. Although phylomers are active in animal models, the challenge remains to demonstrate efficacy and safety in a clinical setting.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Constructing libraries from subdomains encoded by biodiverse genomes.

Similar content being viewed by others

References

  1. Pritchard, J.F. et al. Making better drugs: decision gates in nonclinical drug development. Nat. Rev. Drug Discov. 2, 542–553 (2003).

    Article  CAS  Google Scholar 

  2. Bleicher, K.H., Bohm, H.J., Muller, K. & Alanine, A.I. Hit and lead generation: beyond high-throughput screening. Nat. Rev. Drug Discov. 2, 369–378 (2003).

    Article  CAS  Google Scholar 

  3. Strosberg, A.D. Protein interaction mapping for target validation: the need for an integrated combinatory process involving complementary approaches. Curr. Opin. Mol. Ther. 4, 594–600 (2002).

    Article  CAS  Google Scholar 

  4. Archakov, A. et al. Protein-protein interactions as a target for drugs in proteomics. Proteomics 3, 380–391 (2003).

    Article  CAS  Google Scholar 

  5. Vassilev, L.T. Small-molecule antagonists of p53–MDM2 binding: research tools and potential therapeutics. Cell Cycle 3, 419–421 (2004).

    Article  CAS  Google Scholar 

  6. Vassilev, L.T. et al. In vivo activation of the p53 pathway by small-molecule antagonists of MDM2. Science 303, 844–848 (2004).

    Article  CAS  Google Scholar 

  7. Fischer, P. & Lane, D.P. Small-molecule inhibitors of the p53 suppressor HDM2: have protein-protein interactions come of age as drug targets? Trends Pharmacol. Sci. 25, 343–346 (2004).

    Article  CAS  Google Scholar 

  8. Maroun, R.G. et al. Peptide inhibitors of HIV-1 integrase dissociate the enzyme oligomers. Biochemistry 40, 13840–13848 (2001).

    Article  CAS  Google Scholar 

  9. Zhao, L., O'Reilly, M.K., Shultz, M.D. & Chmielewski, J. Interfacial peptide inhibitors of HIV-1 integrase activity and dimerization. Bioorg. Med. Chem. Lett. 13, 1175–1177 (2003).

    Article  CAS  Google Scholar 

  10. Barr, R.K., Hopkins, R.M., Watt, P.M. & Bogoyevitch, M.A. Reverse two-hybrid screening identifies residues of JNK required for interaction with the kinase interaction motif of JNK-interacting protein-1. J. Biol. Chem. 279, 43178–43189 (2004).

    Article  CAS  Google Scholar 

  11. Barr, R.K., Boehm, I., Attwood, P.V., Watt, P.M. & Bogoyevitch, M.A. The critical features and the mechanism of inhibition of a kinase interaction motif-based peptide inhibitor of JNK. J. Biol. Chem. 279, 36327–36338 (2004).

    Article  CAS  Google Scholar 

  12. Kaneto, H. et al. Possible novel therapy for diabetes with cell-permeable JNK-inhibitory peptide. Nat. Med. 10, 1128–1132 (2004).

    Article  CAS  Google Scholar 

  13. Borsello, T. et al. A peptide inhibitor of c-Jun N-terminal kinase protects against excitotoxicity and cerebral ischemia. Nat. Med. 9, 1180–1186 (2003).

    Article  CAS  Google Scholar 

  14. Dasgupta, P. et al. Disruption of the Rb-Raf-1 interaction inhibits tumor growth and angiogenesis. Mol. Cell. Biol. 24, 9527–9541 (2004).

    Article  CAS  Google Scholar 

  15. Chan, B., Greenan, G., McKeon, F. & Ellenberger, T. Identification of a peptide fragment of DSCR1 that competitively inhibits calcineurin activity in vitro and in vivo. Proc. Natl. Acad. Sci. USA 102, 13075–13080 (2005).

    Article  CAS  Google Scholar 

  16. Stockton, R.A., Schaefer, E. & Schwartz, M.A. p21-activated kinase regulates endothelial permeability through modulation of contractility. J. Biol. Chem. 279, 46621–46630 (2004).

    Article  CAS  Google Scholar 

  17. Kiosses, W.B. et al. A dominant-negative p65 PAK peptide inhibits angiogenesis. Circ. Res. 90, 697–702 (2002).

    Article  CAS  Google Scholar 

  18. Park, S. & Raines, R. Genetic selection for dissociative inhibitors of designated protein/protein interactions. Nat. Biotechnol. 18, 847–851 (2000).

    Article  CAS  Google Scholar 

  19. Colas, P. et al. Genetic selection of peptide aptamers that recognize and inhibit cyclin-dependent kinase 2. Nature 380, 548–550 (1996).

    Article  CAS  Google Scholar 

  20. Xu, C. & Luo, Z. Inactivation of Ras function by allele-specific peptide apatamers. Oncogene 21, 5753–5757 (2002).

    Article  CAS  Google Scholar 

  21. Vranken, W.F., James, S., Bennett, H.P. & Ni, F. Solution structures of a 30-residue amino-terminal domain of the carp granulin-1 protein and its amino-terminally truncated 3–30 subfragment: implications for the conformational stability of the stack of two beta-hairpins. Proteins 47, 14–24 (2002).

    Article  CAS  Google Scholar 

  22. Adler, M. et al. The structure of a 19-residue fragment from the C-loop of the fourth epidermal growth factor-like domain of thrombomodulin. J. Biol. Chem. 270, 23366–23372 (1995).

    Article  CAS  Google Scholar 

  23. Riechmann, L. & Winter, G. Novel folded protein domains generated by combinatorial shuffling of polypeptide segments. Proc. Natl. Acad. Sci. USA 97, 10068–10073 (2000).

    Article  CAS  Google Scholar 

  24. Matthews, L., Davis, R. & Smith, G. Immunogenetically fit subunit vaccine components via epitope discovery from natural peptide libraries. J. Immunol. 169, 837–846 (2002).

    Article  CAS  Google Scholar 

  25. Wolf, Y., Grishin, N. & Koonin, E. Estimating the number of protein folds and families from complete genome data. J. Mol. Biol. 299, 897–905 (2000).

    Article  CAS  Google Scholar 

  26. Orengo, C., Michie, A., Jones, S., Swindells, M. & Thornton, J. CATH—a hierarchic classification of protein domain structures. Structure 5, 1093–1108 (1997).

    Article  CAS  Google Scholar 

  27. Harrison, A. et al. Recognising the fold of a protein structure. Bioinformatics 19, 1748–1759 (2003).

    Article  CAS  Google Scholar 

  28. Coulson, A. & Moult, J. A unifold mesofold and superfold model of protein fold use. Proteins 46, 61–71 (2002).

    Article  CAS  Google Scholar 

  29. Chothia, C. Proteins. One thousand families for the molecular biologist. Nature 357, 543–544 (1992).

    Article  CAS  Google Scholar 

  30. Zhang, C.-T. Relations of the number of protein sequences families and folds. Protein Eng. 10, 757–761 (1997).

    Article  CAS  Google Scholar 

  31. Service, R. Structural genomics, round 2. Science 307, 1554–1557 (2005).

    Article  CAS  Google Scholar 

  32. Koch, M. & Waldmann, H. Protein structure similarity clustering and natural product structure as guiding principles in drug discovery. Drug Discov. Today 10, 471–483 (2005).

    Article  CAS  Google Scholar 

  33. Irback, A., Peterson, C. & Potthast, F. Evidence for nonrandom hydrophobicity structures in protein chains. Proc. Natl. Acad. Sci. USA 93, 9533–9538 (1996).

    Article  CAS  Google Scholar 

  34. Pande, V.S., Grosberg, A.Y. & Tanaka, T. Nonrandomness in protein sequences: evidence for a physically driven stage of evolution? Proc. Natl. Acad. Sci. USA 91, 12972–12975 (1994).

    Article  CAS  Google Scholar 

  35. Baud, F. & Karlin, S. Measures of residue density in protein structures. Proc. Natl. Acad. Sci. USA 96, 12494–12499 (1999).

    Article  CAS  Google Scholar 

  36. Yang, A.S. & Honig, B. An integrated approach to the analysis and modeling of protein sequences and structures. III. A comparative study of sequence conservation in protein structural families using multiple structural alignments. J. Mol. Biol. 301, 691–711 (2000).

    Article  CAS  Google Scholar 

  37. Nettles, K. & Greene, G. Ligand control of coregulator recruitment to nuclear receptors. Annu. Rev. Physiol. 67, 309–333 (2005).

    Article  CAS  Google Scholar 

  38. Caponigro, G. et al. Transdominant genetic analysis of a growth control pathway. Proc. Natl. Acad. Sci. USA 95, 7508–7513 (1998).

    Article  CAS  Google Scholar 

  39. Gudkov, A.V. et al. Cloning mammalian genes by expression selection of genetic suppressor elements: association of kinesin with drug resistance and cell immortalization. Proc. Natl. Acad. Sci. USA 91, 3744–3748 (1994).

    Article  CAS  Google Scholar 

  40. Schmelzl, B. & Geli, M. An efficient genetic screen in mammalian cultured cells. EMBO Rep. 3, 682–687 (2002).

    Article  CAS  Google Scholar 

  41. Parissi, V. et al. Functional interactions of human immunodeficiency virus type 1 integrase with human and yeast HSP60. J. Virol. 75, 11344–11353 (2001).

    Article  CAS  Google Scholar 

  42. de Soultrait, V. et al. A novel short peptide is a specific inhibitor of human immunodeficiency virus type 1 integrase. J. Mol. Biol. 318, 45–58 (2002).

    Article  CAS  Google Scholar 

  43. Parish, C.A. et al. Broad-spectrum antimicrobial activity of hemoglobin. Bioorg. Med. Chem. 9, 377–382 (2001).

    Article  CAS  Google Scholar 

  44. Nibbering, P.H. et al. Human lactoferrin and peptides derived from its N terminus are highly effective against infections with antibiotic-resistant bacteria. Infect. Immun. 69, 1469–1476 (2001).

    Article  CAS  Google Scholar 

  45. Kieffer, A. et al. The N- and C-terminal fragments of ubiquitin are important for the antimicrobial activities. FASEB J. 17, 776–778 (2003).

    Article  CAS  Google Scholar 

  46. Short, J. Recombinant approaches for accessing biodiversity. Nat. Biotechnol. 15, 1322–1323 (1997).

    Article  CAS  Google Scholar 

  47. Ladner, R.C. & Ley, A.C. Novel frameworks as a source of high-affinity ligands. Curr. Opin. Biotechnol. 12, 406–410 (2001).

    Article  CAS  Google Scholar 

  48. Binz, H., Amstutz, P. & Pluckthun, A. Engineering novel binding proteins from nonimmunoglobulin domains. Nat. Biotechnol. 23, 1257–1268 (2005).

    Article  CAS  Google Scholar 

  49. Szymkowski, D. Creating the next generation of protein therapeutics through rational drug design. Curr. Opin. Drug Discov. Devel. 8, 590–600 (2005).

    CAS  Google Scholar 

  50. Silverman, J. et al. Multivalent avimer proteins evolved by exon shuffling of a family of human receptor domains. Nat. Biotechnol. 23, 1556–1561 (2005).

    Article  CAS  Google Scholar 

  51. Chirino, Ary, M.L. & Marshall, S. Minimizing the immunogenicity of protein therapeutics. Drug Discov. Today 9, 82–90 (2004).

    Article  CAS  Google Scholar 

  52. Gonzales, N.R., De Pascalis, R., Schlom, J. & Kashmiri, S.V. Minimizing the immunogenicity of antibodies for clinical application. Tumour Biol. 26, 31–43 (2005).

    Article  CAS  Google Scholar 

  53. Ernst, J.T., Becerril, J., Park, H.S., Yin, H. & Hamilton, A. Design and application of an α-Helix-mimetic scaffold based on an oligoamide-foldamer strategy: antagonism of the Bak BH3/Bcl-xL complex. Angew. Chem. Int. Ed. Engl. 42, 535–539 (2003).

    Article  CAS  Google Scholar 

  54. Park, H.S., Lin, Q. & Hamilton, A. Modulation of protein-protein interactions by synthetic receptors: design of molecules that disrupt serine protease-proteinaceous inhibitor interaction. Proc. Natl. Acad. Sci. USA 99, 5105–5109 (2002).

    Article  CAS  Google Scholar 

  55. Pazos, F. & Sternberg, M.J. Automated prediction of protein function and detection of functional sites from structure. Proc. Natl. Acad. Sci. USA 101, 14754–14759 (2004).

    Article  CAS  Google Scholar 

  56. Bray, B. Large-scale manufacture of peptide therapeutics by chemical synthesis. Nat. Rev. Drug Discov. 2, 587–593 (2003).

    Article  CAS  Google Scholar 

  57. Liu, S. et al. Different from the HIV fusion inhibitor C34, the anti-HIV drug Fuzeon (T-20) inhibits HIV1 entry by targeting multiple sites in gp41 and gp120. J. Biol. Chem. 280, 11259–11273 (2005).

    Article  CAS  Google Scholar 

  58. Matthews, T. et al. Enfuvirtide: the first therapy to inhibit the entry of HIV-1 into host CD4 lymphocytes. Nat. Rev. Drug Discov. 3, 215–255 (2004).

    Article  CAS  Google Scholar 

  59. Wheeler, D. et al. Safety, tolerability, and plasma pharmacokinetics of high-strength formulations of enfuvirtide (T-20) in treatment-experienced HIV-1-infected patients. J. Clin. Virol. 30, 183–190 (2004).

    Article  CAS  Google Scholar 

  60. Rappocciolo, E. Antimicrobial peptides as carriers of drugs. Drug Discov. Today 9, 470 (2004).

    Article  Google Scholar 

  61. Cudic, P. et al. Complexation of peptidoglycan intermediates by the lipoglycodepsipeptide antibiotic ramoplanin: minimal structural requirements for intermolecular complexation and fibril formation. Proc. Natl. Acad. Sci. USA 99, 7384–7389 (2002).

    Article  CAS  Google Scholar 

  62. Cudic, M. et al. Development of novel antibacterial peptides that kill resistant isolates. Peptides 23, 2071–2083 (2002).

    Article  CAS  Google Scholar 

  63. Cudic, M., Ertl, H.C. & Otvos, L., Jr. Synthesis, conformation and T-helper cell stimulation of an O-linked glycopeptide epitope containing extended carbohydrate side-chains. Bioorg. Med. Chem. 10, 3859–3870 (2002).

    Article  CAS  Google Scholar 

  64. Cudic, M., Lockatell, C.V., Johnson, D.E. & Otvos, L., Jr. In vitro and in vivo activity of an antibacterial peptide analog against uropathogens. Peptides 24, 807–820 (2003).

    Article  CAS  Google Scholar 

  65. Cudic, M. & Otvos, L., Jr. Intracellular targets of antibacterial peptides. Curr. Drug Targets 3, 101–106 (2002).

    Article  CAS  Google Scholar 

  66. Cudic, P. et al. Functional analysis of the lipoglycodepsipeptide antibiotic ramoplanin. Chem. Biol. 9, 897–906 (2002).

    Article  CAS  Google Scholar 

  67. Lewis, R. & Garcia, M. Therapeutic potential of venom peptides. Nat. Rev. Drug Discov. 2, 790–802 (2003).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

I am grateful to Wayne Thomas, Prue Hart, John Finlay-Jones, Patrick Holt, Rob Aalberse, Vanessa Cull, Mark Fear, Richard Hopkins, Nadia Milech Graham Robertson, Frank Sotzik and laboratory colleagues for assisting with review of the manuscript. The assistance of Graham Carter (Accuro Biologics Ltd) in conducting the bioinformatics analysis of potential for immunogenicity of phylomer peptides is also gratefully acknowledged.

Author information

Authors and Affiliations

  1. Phylogica Ltd., 105 Roberts Road, Subiaco, Perth, 6008, Western Australia

    Paul M Watt

Authors
  1. Paul M Watt
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Paul M Watt.

Ethics declarations

Competing interests

P.W. is the scientific director of Phylogica, Ltd., the company that is commercializing the Phylomer technology. P.W. holds both shares and stock options in this company, which is publicly listed on the Australian Stock Exchange (ASX:PYC). This holding amounts to less than 5% of issued capital.

Supplementary information

Rights and permissions

Reprints and permissions

About this article

Cite this article

Watt, P. Screening for peptide drugs from the natural repertoire of biodiverse protein folds. Nat Biotechnol 24, 177–183 (2006). https://doi.org/10.1038/nbt1190

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nbt1190

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing