Skip to main content

Protein–Protein Interaction Inhibitors of BRCA1 Discovered Using Small Molecule Microarrays

  • Protocol
  • First Online:
Small Molecule Microarrays

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1518))

Abstract

Microarray screening technology has transformed the life sciences arena over the last decade. The platform is widely used in the area of mapping interaction networks, to molecular fingerprinting and small molecular inhibitor discovery. The technique has significantly impacted both basic and applied research. The microarray platform can likewise enable high-throughput screening and discovery of protein–protein interaction (PPI) inhibitors. Herein we demonstrate the application of microarray-guided PPI inhibitor discovery, using human BRCA1 as an example. Mutations in BRCA1 have been implicated in ~50 % of hereditary breast cancers. By targeting the (BRCT)2 domain, we showed compound 15a and its prodrug 15b inhibited BRCA1 activities in tumor cells. Unlike previously reported peptide-based PPI inhibitors of BRCA1, the compounds identified could be directly administered to tumor cells, thus making them useful in targeting BRCA1/PARP-related pathways involved in DNA damage and repair response, for cancer therapy.

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 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
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. Fodor SP, Read JL, Pirrung MC, Stryer L, Lu AT, Solas D (1991) Light-directed, spatially addressable parallel chemical synthesis. Science 251:767–773

    Article  CAS  PubMed  Google Scholar 

  2. Schena M, Shalon D, Davis RW, Brown PB (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467–470

    Article  CAS  PubMed  Google Scholar 

  3. MacBeath G, Koehler AN, Schreiber SL (1999) Printing small molecule as microarrays and detecting protein-ligand interactions en Masse. J Am Chem Soc 121:7967–7968

    Article  CAS  Google Scholar 

  4. MacBeath G, Schreiber SL (2000) Printing proteins as microarrays for high-throughput function determination. Science 289:1760–1763

    CAS  PubMed  Google Scholar 

  5. Köhn M, Gutierrez-Rodriguez M, Jonkheijm P, Wetzel S, Wacker R, Schroeder H, Prinz H, Niemeyer CM, Breinbauer R, Szedlacsek SE, Waldmann H (2007) A microarray strategy for mapping the substrate specificity of protein tyrosine phosphates. Angew Chem Int Ed 46:7700–7703

    Article  Google Scholar 

  6. Sun H, Lu CHS, Uttamchandani M, Xia Y, Liou YC, Yao SQ (2008) Peptide microarray for high-throughput determination of phosphatase specificity and biology. Angew Chem Int Ed 47:1698–1702

    Article  CAS  Google Scholar 

  7. Popescu SG, Popescu GV, Bachan S, Zhang Z, Seay M, Gerstein M, Snyder M, Dinesh-Kumar SP (2007) Differential binding of calmodulin-related proteins to their targets revealed through high-density arabidopsis protein microarray. Proc Natl Acad Sci USA 104:4730–4735

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Vidal M, Brachmann RK, Fattaey A, Harlow E, Boeke JD (1996) Reverse two-hybrid and one-hybrid systems to detect dissociation of protein-protein and DNA-protein interactions. Proc Natl Acid Sci USA 93:10315–10320

    Article  CAS  Google Scholar 

  9. Krogan NJ, Cagney G, Yu H, Zhong G et al (2006) Global landscape of protein complexes in the yeast saccharomyces cerevisiae. Nature 440:637–643

    Article  CAS  PubMed  Google Scholar 

  10. Jones RB, Gordus A, Krall JA, MacBeath G (2006) A quantitative protein interaction network for the ErbB receptors using protein microarray. Nature 439:168–174

    Article  CAS  PubMed  Google Scholar 

  11. Hall DA, Zhu H, Zhu X, Royce T, Gerstein M (2004) Snyder M. Refulation of gene expression by a metabolic enzyme Science 306:482–484

    CAS  PubMed  Google Scholar 

  12. Huang J, Zhu H, Haggarty SJ, Spring DR, Hwang H, Jin F, Snyder M, Schreiber SL (2004) Finding new components of the target of rapamycin signing network through chemical genetics and proteome chips. Proc Natl Acad Sci U S A 101:16594–16599

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Zhu J, Gopinath K, Murali A, Yi G, Hayward SD, Zhu H, Kao C (2007) RNA-binding proteins that inhibit RNA virus infection. Proc Natl Acad Sci USA 104:3129–3134

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Kung LA, Tao SC, Qian J, Smith MG, Snyder M, Zhu H (2009) Global analysis of the glycoproteome in Saccharomyces cerevisiae reveals new role for protein glycosylation in eukaryotes. Mol Syst Biol 5:308–309

    Article  PubMed  PubMed Central  Google Scholar 

  15. Uttamchandani M, Walsh DP, Yao SQ, Chang Y-T (2005) Small molecule microarrays: recent advances and applications. Curr Opin Chem Biol 9:4–13

    Article  CAS  PubMed  Google Scholar 

  16. Duffner JL, Clemons PA, Koehler AN (2007) A pipeline for ligand discovery using small-molecule microarrays. Curr Opin Chem Biol 11:74–82

    Article  CAS  PubMed  Google Scholar 

  17. Kim YG, Shin DS, Kim EM, Park HY, Lee CS, Kim JH, Lee BS, Lee YS, Kim BG (2007) High-throughput identification of substrate specificity for protein kinase by using an improved one bead one compound library approach. Angew Chem Int Ed 46:5408–5411

    Article  CAS  Google Scholar 

  18. Wu H, Ge J, Yao SQ (2010) Microarray-assisted high-throughput identification of a cell-permeable small molecule binder of 14-3-3 proteins. Angew Chem Int Ed 49:6528–6532

    Article  CAS  Google Scholar 

  19. Hunter T (2000) Signaling-2000 and beyond. Cell 100:113–127

    Article  CAS  PubMed  Google Scholar 

  20. Hunter T (1995) Protein kinases and phosphatases: the yin and yang of protein phosphorylation and signaling. Cell 80:225–236

    Article  CAS  PubMed  Google Scholar 

  21. Seet BT, Dikic I, Zhou MM, Pawson T (2006) Reading protein modifications with interaction domains. Nat Rev Mol Cell Biol 7:473–483

    Article  CAS  PubMed  Google Scholar 

  22. Gerloff DL, Woods NT, Farago AA, Monteiro ANA (2012) BRCT domains: a little more than kin, and less than kind. FEBS Lett 586:2711–2716

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Thompson ME (2010) BRCA 16 years later: nuclear import and export processes. FEBS J 277:3072–3078

    Article  CAS  PubMed  Google Scholar 

  24. Cantor SB, Bell DW, Ganesan S, Kass EM, Drapkin R, Grossman S, Wahrer DC, Sgroi DC, Lane WS, Harber DA, Livingston DM (2001) BACH1, a novel helicase-like protein, interacts directly with BRCA1 and contributes to its DNA repair function. Cell 105:149–160

    Article  CAS  PubMed  Google Scholar 

  25. Miki Y, Swensen J, Shattuck-Eidens D, Futreal PA, Harshman K, Tavtigian S, Liu Q, Cochran C, Bennett LM, Ding W (1994) A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1. Science 266:66–71

    Article  CAS  PubMed  Google Scholar 

  26. Quinn JE, Kennedy RD, Mullan PB, Gilmore PM, Carty M, Johnston PG, Harkin DP (2003) BRCA1 functions as a differential modulator of chemotherapy-induced apoptosis. Cancer Res 63:6221–6228

    CAS  PubMed  Google Scholar 

  27. Watanabe N, Osada H (2012) Phosphorylation-dependent protein-protein interaction modules as potential molecular targets for cancer therapy. Curr Drug Targets 13:1654–1658

    Article  CAS  PubMed  Google Scholar 

  28. Yuan Z, Kumar EA, Campbell SJ, Palermo NY, Kizhake S, Glover JNM, Natarajan A (2011) Exploiting the P-1 pocket of BRCT domains toward a structure guided inhibitor design. ACS Med Chem Lett 2:764–767

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Shiozaki EN, Gu L, Yan N, Shi Y (2004) Structure of the BRCT repeats of BRCA1 bound to a BACH1 phosphopeptide: implications for signaling. Mol Cell 14:405–412

    Article  CAS  PubMed  Google Scholar 

  30. Arkin MR, Wells JA (2004) Small-molecule inhibitors of protein-protein interactions: progressing towards the dream. Nat Rev Drug Discov 3:301–317

    Article  CAS  PubMed  Google Scholar 

  31. Azzarito V, Long K, Murphy NS, Wilson AJ (2013) Inhibition of a-helix mediated protein-protein interactions using designed molecules. Nat Chem 5:161–173

    Article  CAS  PubMed  Google Scholar 

  32. Na Z, Pan S, Uttamchaandani M, Yao SQ (2014) Peptide library approach to uncover phosphomimetic inhibitors of the BRCA1 C-terminal domain. Angew Chem Int Ed 53:8421–8426

    Article  CAS  Google Scholar 

  33. Foong YM, Fu J, Yao SQ, Uttamchandani M (2012) Current advances in peptide and small molecule microarray technologies. Curr Opin Chem Biol 16:234–242

    Article  CAS  PubMed  Google Scholar 

  34. Chung C-W, Witherington J (2012) Progress in the discovery of small molecule inhibitors of bromodomain histone interactions. J Biomol Screen 16:1170–1185

    Article  Google Scholar 

  35. Lu CHS, Sun H, Abu Bakar FB, Uttamchandani M, Zhou W, Liou Y-C, Yao SQ (2008) Rapid affinity-based fingerprinting of 14-3-3 isoforms using a combinatorial peptide microarray. Angew Chem Int Ed 47:7438–7441

    Article  CAS  Google Scholar 

  36. Manke IA, Lowery DM, Nguyen A, Yaffe MB (2003) BRCT repeats as phosphopeptide-binding modules involved in protein targeting. Science 302:636–639

    Article  CAS  PubMed  Google Scholar 

  37. Campbell SJ, Edwards RA, Glover JNM (2010) Comparison of the structures and peptide binding specificities of the BRCT domains of MDC1 and BRCA1. Structure 18:167–176

    Article  CAS  PubMed  Google Scholar 

  38. Lokesh GL, Rachamallu A, Kumar G, Natarajan A (2006) High throughput fluorescence polarization assay to identify small molecule inhibitors of BRCT domains of breast cancer gene 1. Anal Biochem 352:135–141

    Article  CAS  PubMed  Google Scholar 

  39. Lokesh GL, Muralidhara BK, Surendra SN, Natarajan A (2007) Thermodynamics of phosphopeptide tethering to BRCT: the structural minima for inhibitor design. J Am Chem Soc 129:10658–10659

    Article  CAS  PubMed  Google Scholar 

  40. Zhao S, Etzkorn FA (2007) A phosphorylated prodrug for the inhibition of Pin1. Bioorg Med Chem Lett 17:6615–6618

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Hu Y, Scully R, Sobhian B, Xie A, Shestakova E, Livingston DM (2011) RAP80-directed tuning of BRCA1 homologous recombination function at ionizing radiation-induced nuclear foci. Genes Dev 25:685–700

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Hoeijmakers JH (2001) Genome maintenance for preventing cancer. Nature 411:366–374

    Article  CAS  PubMed  Google Scholar 

  43. Underhill C, Toulmonde M, Bonnefoi H (2011) A review of PARP inhibitors: from bench to bedside. Ann Oncol 22:268–279

    Article  CAS  PubMed  Google Scholar 

  44. Fong PC, Boss DS et al (2009) Inhibition of PARP in tumors from BRCA mutation carriers. N Engl J Med 361:123–134

    Article  CAS  PubMed  Google Scholar 

  45. Treszezamsky AD, Kachnic LA, Feng ZH (2007) Cancer Res 67:7078–7081 “BRCA1- and BRCA2-deficient cells are sensitive to etoposide-induced DNA double-strand breaks via topoisomerase II.

    Google Scholar 

Download references

Acknowledgment

Funding was provided by the Singapore National Medical Research Council (CBRG12nov100) and the Ministry of Education (MOE2012-T2-1-116, MOE2012-T2-2-051, and MOE2013-T2-1-048). We also acknowledge the financial support from the Singapore-Peking-Oxford Research Enterprise (COY-15-EWI-RCFSA/N197-1).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Shao Q. Yao .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer Science+Business Media New York

About this protocol

Cite this protocol

Na, Z., Pan, S., Uttamchandani, M., Yao, S.Q. (2017). Protein–Protein Interaction Inhibitors of BRCA1 Discovered Using Small Molecule Microarrays. In: Uttamchandani, M., Yao, S. (eds) Small Molecule Microarrays. Methods in Molecular Biology, vol 1518. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6584-7_10

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-6584-7_10

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6582-3

  • Online ISBN: 978-1-4939-6584-7

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics