Skip to main content

Targeting Protein-Protein Interactions for Drug Discovery

  • Protocol
Protein-Protein Interactions

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1278))

Abstract

Protein-protein interactions are associated with key activities and pathways in the cell, and in that regard are promising targets for drug discovery. However, in terms of small molecule drugs, this promise has not been realized. The physical nature of many protein-protein interaction surfaces renders them unable to support binding of small drug-like molecules. In addition, there are other unique hurdles presented by this class that make the drug development process difficult and risky. Nevertheless, success stories have begun to steadily appear in this field. These experiences are starting to provide general strategies and tools to help overcome the problems inherent in pursuing proteinā€protein interaction targets. These lessons should improve the rate of success as these systems are pursued in the future.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 139.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 179.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Stumpf MPH, Thorne T, de Silva E, Stewart R, An HJ, Lappe M, Wiuf C (2008) Estimating the size of the human interactome. Proc Nat Acad Sci 105:6959ā€“6964

    ArticleĀ  PubMed CentralĀ  CASĀ  PubMedĀ  Google ScholarĀ 

  2. Overington JP, Al-Lazikani B, Hoopkins AL (2006) How many drug targets are there? Nat Rev Drug Disc 5:993ā€“996

    ArticleĀ  CASĀ  Google ScholarĀ 

  3. Fry DC (2006) Proteinā€protein interactions as targets for small molecule drug discovery. Biopolymers 84:535ā€“552

    ArticleĀ  CASĀ  PubMedĀ  Google ScholarĀ 

  4. Wells JA, McClendon CL (2007) Reaching for high-hanging fruit in drug discovery at proteinā€protein interfaces. Nature 450:1001ā€“1009

    ArticleĀ  CASĀ  PubMedĀ  Google ScholarĀ 

  5. Doemling A (2008) Small molecular weight proteinā€protein interaction antagonists ā€“ an insurmountable challenge? Curr Opin Chem Biol 12:281ā€“291

    ArticleĀ  Google ScholarĀ 

  6. Clackson T, Wells JA (1995) A hot spot of binding energy in a hormone-receptor interface. Science 267:383ā€“386

    ArticleĀ  CASĀ  PubMedĀ  Google ScholarĀ 

  7. Vassilev LT, Vu BT, Graves B, Carvajal D, Podlaski F, Filipovic Z, Kong N, Kammlott U, Lukacs C, Klein C, Fotouhi N, Liu E (2004) In vivo activation of the p53 pathway by small-molecule antagonists of MDM2. Science 303:844ā€“848

    ArticleĀ  CASĀ  PubMedĀ  Google ScholarĀ 

  8. Kussie PH, Gorina S, Marechal V, Elenbaas B, Moreau J, Levine AJ, Pavletich NP (1996) Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain. Science 274:948ā€“953

    ArticleĀ  CASĀ  PubMedĀ  Google ScholarĀ 

  9. Fry DC, Graves BJ, Vassilev LT (2005) Exploiting proteinā€protein interactions to design an activator of p53. In: Golemis EA, Adams PD (eds) Proteinā€protein interactions: a molecular cloning manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, pp 893ā€“906

    Google ScholarĀ 

  10. Fry DC, Graves BJ, Vassilev LT (2005) Development of E3-substrate (MDM2-p53) binding inhibitors: structural aspects. Methods Enzymol 399C:622ā€“633

    ArticleĀ  Google ScholarĀ 

  11. Vu BT, Vassilev L (2011) Small-molecule inhibitors of the p53-MDM2 interaction. In: Vassilev L, Fry D (eds) Small-molecule inhibitors of proteinā€protein interactions. Springer, Berlin, pp 151ā€“172

    Google ScholarĀ 

  12. Fry DC, Emerson SD, Palme S, Vu BT, Liu CM, Podlaski F (2004) NMR structure of a complex between MDM2 and a small molecule inhibitor. J Biomol NMR 30:163ā€“173

    ArticleĀ  CASĀ  PubMedĀ  Google ScholarĀ 

  13. Wang S, Zhao Y, Bernard D, Aguilar A, Kumar S (2012) Targeting the MDM2-p53 proteinā€protein interaction for new cancer therapies. Top Med Chem 8:57ā€“80

    ArticleĀ  Google ScholarĀ 

  14. Graves B, Thompson T, Xia M, Janson C, Lukacs C, Deo D, DiLello P, Fry D, Garvie C, Huang K, Gao L, Tovar C, Lovey A, Wanner J, Vassilev L (2012) Activation of the p53 pathway by small-molecule induced MDM2 and MDMX dimerization. Proc Nat Acad Sci 109:11788ā€“11793

    ArticleĀ  PubMed CentralĀ  CASĀ  PubMedĀ  Google ScholarĀ 

  15. Arkin MR, Wells JA (2004) Small-molecule inhibitors of proteinā€protein interactions: progressing towards the dream. Nat Rev Drug Disc 3:301ā€“317

    ArticleĀ  CASĀ  Google ScholarĀ 

  16. Fry DC (2008) Drug-like inhibitors of proteinā€protein interactions: a structural examination of effective protein mimicry. Curr Prot Pep Sci 9:240ā€“247

    ArticleĀ  CASĀ  Google ScholarĀ 

  17. Sperandio O, Reynes CH, Camproux AC, Villoutreix BO (2010) Rationalizing the chemical space of proteinā€protein interaction inhibitors. Drug Disc Today 15:220ā€“229

    ArticleĀ  CASĀ  Google ScholarĀ 

  18. Higueruelo AP, Schreyer A, Bickerton GRJ, Pitt WR, Groom CR, Blundell TL (2009) Atomic interactions and profile of small molecules disrupting proteinā€protein interfaces: the TIMBAL database. Chem Biol Drug Des 74:457ā€“467

    ArticleĀ  CASĀ  PubMedĀ  Google ScholarĀ 

  19. Morelli X, Bourgeas R, Roche P (2011) Chemical and structural lessons from recent successes in proteinā€protein interaction inhibition (2P2I). Curr Opin Chem Biol 15:1ā€“7

    ArticleĀ  Google ScholarĀ 

  20. Fry DC (2012) Small-molecule inhibitors of proteinā€protein interactions: how to mimic a protein partner. Curr Pharm Des 18:4679ā€“4684

    ArticleĀ  CASĀ  PubMedĀ  Google ScholarĀ 

  21. Cerchietti LC, Ghetu AF, Zhu X, DaSilva GF, Zhong S, Matthews M, Bunting KL, Plol JM, Fares C, Arrowsmith CH, Yang SN, Garcia M, Coop A, MacKerell AD, Prive GG, Melnick A (2010) A small-molecule inhibitor of BCL6 kills DLBCL cells in vitro and in vivo. Cancer Cell 17:400ā€“411

    ArticleĀ  PubMed CentralĀ  CASĀ  PubMedĀ  Google ScholarĀ 

  22. Buckley DL, Van Molle I, Gareiss PC, Tae HS, Michel J, Noblin DJ, Jorgensen WL, Ciulli A, Crews CM (2012) Targeting the von Hippel-Lindau E3 ubiquitin ligase using small molecules to disrupt the VHL/HIF-1alpha interaction. J Am Chem Soc 134:4465ā€“4468

    ArticleĀ  PubMed CentralĀ  CASĀ  PubMedĀ  Google ScholarĀ 

  23. Fry DC, So S-S (2012) Modulators of proteinā€protein interactions: the importance of three-dimensionality. In: Doemling A (ed) Proteinā€protein interactions in drug discovery. Wiley-VCH, Weinhelm, pp 55ā€“62

    Google ScholarĀ 

  24. Wanner J, Fry DC, Peng Z, Roberts J (2011) Druggability assessment of proteinā€protein interfaces. Future Med Chem 3:2021ā€“2038

    ArticleĀ  CASĀ  PubMedĀ  Google ScholarĀ 

  25. Fuller JC, Burgoyne NJ, Jackson RM (2008) Predicting druggable binding sites at the proteinā€protein interface. Drug Disc Today 14:155ā€“161

    ArticleĀ  Google ScholarĀ 

  26. Bourgeas R, Basse MJ, Morelli X, Roche P (2010) Atomic analysis of proteinā€protein interfaces with known inhibitors: the 2P2I database. PLoS One 5:e9598

    ArticleĀ  PubMed CentralĀ  PubMedĀ  Google ScholarĀ 

  27. Meireles LMC, Doemling AS, Camacho CJ (2010) ANCHOR: a web server and database for analysis of proteinā€protein interaction binding pockets for drug discovery. Nucleic Acids Res 38:W407ā€“W411

    ArticleĀ  PubMed CentralĀ  CASĀ  PubMedĀ  Google ScholarĀ 

  28. Sugaya N, Kanai S, Furuya T (2012) Dr. PIAS 2.0: an update of a database of predicted druggable proteinā€protein interactions. Database 2012:bas034

    ArticleĀ  PubMed CentralĀ  PubMedĀ  Google ScholarĀ 

  29. Vlieghe P, Lisowski V, Martinez J, Khrestchatisky M (2009) Synthetic therapeutic peptides: science and market. Drug Disc Today 15:40ā€“56

    ArticleĀ  Google ScholarĀ 

  30. Fry D, Huang K-S, Di Lello P, Mohr P, Mueller K, So S-S, Harada T, Stahl M, Vu B, Mauser H (2013) Design of libraries targeting proteinā€protein interfaces. Chem Med Chem 8:726ā€“732

    ArticleĀ  CASĀ  PubMedĀ  Google ScholarĀ 

  31. Murray CW, Rees DC (2009) The rise of fragment-based drug discovery. Nat Chem 1:187ā€“192

    ArticleĀ  CASĀ  PubMedĀ  Google ScholarĀ 

  32. Hajduk PJ (2006) Fragment-based drug design: how big is too big? J Med Chem 49:6972ā€“6976

    ArticleĀ  CASĀ  PubMedĀ  Google ScholarĀ 

  33. Fry DC, Wartchow C, Graves B, Janson C, Lukacs C, Kammlott U, Beluins C, Palme S, Klein C, Vu B (2013) Deconstruction of a nutlin: dissecting the binding determinants of a potent proteinā€protein interaction inhibitor. ACS Med Chem Lett 4(7):660ā€“665

    ArticleĀ  PubMed CentralĀ  CASĀ  PubMedĀ  Google ScholarĀ 

  34. Grasberger BL, Lu T, Schubert C, Parks DJ, Carver TE, Koblish HK, Cummings MD, LaFrance LV, Milkiewicz KL, Calvo RR, Maguire D, Lattanze J, Franks CF, Zhao S, Ramachandren K, Bylebyi GR, Zhang M, Manthey CL, Petrella EC, Pantoliano MW, Deckman IC, Spurlino JC, Maroney AC, Tomczuk BE, Molloy CJ, Bone RF (2005) Discovery and cocrystal structure of benzodiazepinedione HDM2 antagonists that activate p53 in cells. J Med Chem 48:909ā€“912

    ArticleĀ  CASĀ  PubMedĀ  Google ScholarĀ 

  35. Allen JG, Bourbeau MP, Wohlhieter GE, Bartberger MD, Michelsen K, Hungate R, Gadwood RC, Gaston RD, Evans B, Mann LW, Matison ME, Schneider S, Huang X, Yu D, Andrews PS, Reichelt A, Long AM, Yakowec P, Yang E, Lee TA, Oliner JD (2009) Discovery and optimization of chromenotriazolopyrimidines as potent inhibitors of the mouse double minute 2 ā€“ tumor protein 53 protein interaction. J Med Chem 52:7044ā€“7053

    ArticleĀ  CASĀ  PubMedĀ  Google ScholarĀ 

  36. Popowicz GM, Czarna A, Wolf S, Wang K, Wang W, Doemling A, Holak T (2010) Structures of low molecular weight inhibitors bound to MDMX and MDM2 reveal new approaches for p53-MDMX/MDM2 antagonist drug discovery. Cell Cycle 9:1ā€“8

    ArticleĀ  Google ScholarĀ 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to David C. Fry .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

Ā© 2015 Springer Science+Business Media New York

About this protocol

Cite this protocol

Fry, D.C. (2015). Targeting Protein-Protein Interactions for Drug Discovery. In: Meyerkord, C., Fu, H. (eds) Protein-Protein Interactions. Methods in Molecular Biology, vol 1278. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2425-7_6

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-2425-7_6

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-2424-0

  • Online ISBN: 978-1-4939-2425-7

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics