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High Content Screening of Small Molecule Modulators Targeting Heat Shock Response Pathway

  • Daniel Zhang
  • Bin Zhang
Chapter
Part of the Heat Shock Proteins book series (HESP, volume 15)

Abstract

Phenotypic high content screening (HCS) has resurged in recent years as an important platform in the drug discovery paradigm, particularly to address the serious challenges in the current target based approaches. Using the highly conserved heat shock response (HSR) pathway as a therapeutic intervention point, we established a cell based, high throughput, multiplexing, and disease relevant phenotypic screening platform for small molecule HSF1 modulators in cancer and neurodegenerative diseases. In this chapter, the authors reviewed their systematic design of methodology and workflow in detail, including the characterization of cellular phenotypic changes, image analysis and quantification, assay development and automation, screening operation and quality control, counter-screen and lead optimization, target identification and mechanism of action study. Selected compounds from the phenotypic screening, including novel HSF1 activators and HSF1 inhibitors, were discussed in regard to their chemical structures, therapeutic effects, and cytotoxicity for potential drug development. The authors also addressed the uncertainties and risks in target deconvolution, which still remains to be the most difficult hurdle in phenotypic screening. Recent HCS advances in tissues, organs and whole organisms, such as 3D tissue imaging, organ-on-a chip, IPS derived cell models, relevant animal models, etc., may bring an effective solution for delivering target-specific, first-in-class drugs in the future.

Keywords

Drug discovery HCS HSF1 HSP HSR HTS Small molecule Target ID 

Notes

Acknowledgements

The authors would like to thank all the supports received from everyone at Alpine Therapeutics, Inc. Special acknowledgements are given to Dr. Dorothy Wang for her critical review of the manuscript.

References

  1. Alastalo TP, Hellesuo M, Sandqvist A, Hietakangas V, Kallio M, Sistonen L (2003) Formation of nuclear stress granules involves HSF2 and coincides with the nucleolar localization of Hsp70. J Cell Sci 116(Pt 17):3557–3570CrossRefGoogle Scholar
  2. Anckar J, Sistonen L (2011) Regulation of HSF1 function in the heat stress response: implications in aging and disease. Annu Rev Biochem 80:1089–1115CrossRefGoogle Scholar
  3. Au Q, Kanchanastit P, Barber JR, Ng SC, Zhang B (2008) High-content image-based screening for small-molecule chaperone amplifiers in heat shock. J Biomol Screen 13(10):953–959CrossRefGoogle Scholar
  4. Au Q, Zhang Y, Barber JR, Ng SC, Zhang B (2009) Identification of inhibitors of HSF1 functional activity by high-content target-based screening. J Biomol Screen 14(10):1165–1175CrossRefGoogle Scholar
  5. Avior Y, Sagi I, Benvenisty N (2016) Pluripotent stem cells in disease modelling and drug discovery. Nat Rev Mol Cell Biol 17(3):170–182CrossRefGoogle Scholar
  6. Bhatia SN, Ingber DE (2014) Microfluidic organs-on-chips. Nat Biotechnol 32(8):760–772CrossRefGoogle Scholar
  7. Bilgin CC, Fontenay G, Cheng Q, Chang H, Han J, Parvin B (2016) BioSig3D: high content screening of three-dimensional cell culture models. PLoS One 11(3):e0148379CrossRefGoogle Scholar
  8. Boutros M, Heigwer F, Laufer C (2015) Microscopy-based high-content screening. Cell 163(6):1314–1325CrossRefGoogle Scholar
  9. Calderwood SK, Murshid A (2017) Molecular chaperone accumulation in cancer and decrease in Alzheimer's disease: the potential roles of HSF1. Front Neurosci 11:192CrossRefGoogle Scholar
  10. Cheeseman MD, Chessum NE, Rye CS, Pasqua AE, Tucker MJ, Wilding B, Evans LE, Lepri S, Richards M, Sharp SY, Ali S, Rowlands M, O'Fee L, Miah A, Hayes A, Henley AT, Powers M, Te Poele R, De Billy E, Pellegrino L, Raynaud F, Burke R, van Montfort RL, Eccles SA, Workman P, Jones K (2017) Discovery of a chemical probe Bisamide (CCT251236): an orally bioavailable efficacious Pirin ligand from a heat shock transcription factor 1 (HSF1) phenotypic screen. J Med Chem 60(1):180–201CrossRefGoogle Scholar
  11. Cher C, Tremblay MH, Barber JR, Ng SC, Zhang B (2010) Identification of chaulmoogric acid as a small molecule activator of protein phosphatase 5. Appl Biochem Biotechnol 160(5):1450–1459CrossRefGoogle Scholar
  12. Chessel A (2017) An overview of data science uses in bioimage informatics. Methods 115:110–118CrossRefGoogle Scholar
  13. Cotto J, Fox S, Morimoto R (1997) HSF1 granules: a novel stress-induced nuclear compartment of human cells. J Cell Sci 110(Pt 23):2925–2934PubMedGoogle Scholar
  14. Dai C, Whitesell L, Rogers AB, Lindquist S (2007) Heat shock factor 1 is a powerful multifaceted modifier of carcinogenesis. Cell 130(6):1005–1018CrossRefGoogle Scholar
  15. Daugaard M, Rohde M, Jäättelä M (2007) The heat shock protein 70 family: highly homologous proteins with overlapping and distinct functions. FEBS Lett 581(19):3702–3710CrossRefGoogle Scholar
  16. Dayalan NS, Dinkova-Kostova AT (2017) Regulation of the mammalian heat shock factor 1. FEBS J 284(11):1606–1627CrossRefGoogle Scholar
  17. De Thonel A, Mezger V, Garrido C (2011) Implication of heat shock factors in tumorigenesis: therapeutical potential. Cancers (Basel) 3(1):1158–1181CrossRefGoogle Scholar
  18. Denegri M, Moralli D, Rocchi M, Biggiogera M, Raimondi E, Cobianchi F, De Carli L, Riva S, Biamonti G (2002) Human chromosomes 9, 12, and 15 contain the nucleation sites of stress- induced nuclear bodies. Mol Biol Cell 13(6):2069–2079CrossRefGoogle Scholar
  19. Donato MT, Gómez-Lechón MJ, Tolosa L (2017) Using high-content screening technology for studying drug-induced hepatotoxicity in preclinical studies. Expert Opin Drug Discovery 12(2):201–211CrossRefGoogle Scholar
  20. Eder J, Sedrani R, Wiesmann C (2014) The discovery of first-in-class drugs: origins and evolution. Nat Rev Drug Discov 13:577–587CrossRefGoogle Scholar
  21. Fellmann C, Gowen BG, Lin PC, Doudna JA, Corn JE (2017) Cornerstones of CRISPR-Cas in drug discovery and therapy. Nat Rev Drug Discov 16:89–100CrossRefGoogle Scholar
  22. Fetz V, Prochnow H, Bronstrup M, Sasse F (2016) Target identification by image analysis. Nat Prod Rep 33:655–667CrossRefGoogle Scholar
  23. Gao M, Nettles RE, Belema M, Snyder LB, Nguyen VN, Fridell RA, Serrano-Wu MH, Langley DR, Sun JH, O’Boyle DR 2nd, Lemm JA, Wang C, Knipe JO, Chien C, Colonno RJ, Grasela DM, Meanwell NA, Hamann LG (2010) Chemical genetics strategy identifies an HCV NS5A inhibitor with a potent clinical effect. Nature 465(7294):96–100CrossRefGoogle Scholar
  24. Gomez-Pastor R, Burchfiel ET, Thiele DJ (2017) Regulation of heat shock transcription factors and their roles in physiology and disease. Nat Rev Mol Cell Biol Aug 30.  https://doi.org/10.1038/nrm.2017.73 [Epub ahead of print]CrossRefGoogle Scholar
  25. Haigis MC, Sinclair DA (2010) Mammalian sirtuins: biological insights and disease relevance. Annu Rev Pathol 5:253–295CrossRefGoogle Scholar
  26. Harvey AL, Edrada-Ebel R, Quinn RJ (2015) The re-emergence of natural products for drug discovery in the genomics era. Nat Rev Drug Discov 14:111–129CrossRefGoogle Scholar
  27. Horvath P, Aulner N, Bickle M, Davies AM, Nery ED, Ebner D, Montoya MC, Östling P, Pietiäinen V, Price LS, Shorte SL, Turcatti G, von Schantz C, Carragher NO (2016) Screening out irrelevant cell-based models of disease. Nat Rev Drug Discov 15(11):751–769CrossRefGoogle Scholar
  28. Jolly C, Usson Y, Morimoto RI (1999) Rapid and reversible relocalization of heat shock factor 1 within seconds to nuclear stress granules. Proc Natl Acad Sci U S A 96(12):6769–6774CrossRefGoogle Scholar
  29. Jolly C, Konecny L, Grady DL, Kutskova YA, Cotto JJ, Morimoto RI, Vourc'h C (2002) In vivo binding of active heat shock transcription factor 1 to human chromosome 9 heterochromatin during stress. J Cell Biol 156(5):775–781CrossRefGoogle Scholar
  30. Jolly C, Metz A, Govin J, Vigneron M, Turner BM, Khochbin S, Vourc'h C (2004) Stress-induced transcription of satellite III repeats. J Cell Biol 164(1):25–33CrossRefGoogle Scholar
  31. Jones LH, Bunnage ME (2017) Applications of chemogenomic library screening in drug discovery. Nat Rev Drug Discov 16:285–296CrossRefGoogle Scholar
  32. Khurana V, Tardiff DF, Chung CY, Lindquist S (2015) Toward stem cell-based phenotypic screens for neurodegenerative diseases. Nat Rev Neurol 11(6):339–350CrossRefGoogle Scholar
  33. Li L, Zhou Q, Voss TC, Quick KL, LaBarbera DV (2016) High-throughput imaging: Focusing in on drug discovery in 3D. Methods 96:97–102CrossRefGoogle Scholar
  34. Lindquist SL, Kelly JW (2011) Chemical and biological approaches for adapting proteostasis to ameliorate protein misfolding and aggregation diseases: progress and prognosis. Cold Spring Harb Perspect Biol 3(12):a004507CrossRefGoogle Scholar
  35. Liu C, Su J, Yang F, Wei K, Ma J, Zhou X (2015) Compound signature detection on LINCS L1000 big data. Mol BioSyst 11(3):714–722CrossRefGoogle Scholar
  36. Mattiazzi UM, Styles EB, Verster AJ, Friesen H, Boone C, Andrews BJ (2016) High-content screening for quantitative cell biology. Trends Cell Biol 26(8):598–611CrossRefGoogle Scholar
  37. Moffat JG, Rudolph J, Bailey D (2014) Phenotypic screening in cancer drug discovery - past, present and future. Nat Rev Drug Discov 13:588–602CrossRefGoogle Scholar
  38. Moffat JG, Vincent F, Lee JA, Eder J, Prunotto M (2017) Opportunities and challenges in phenotypic drug discovery: an industry perspective. Nat Rev Drug Discov 16(8):531–543CrossRefGoogle Scholar
  39. Moore JD (2015) The impact of CRISPR–Cas9 on target identification and validation. (2015). Drug Discov Today 20:450–457CrossRefGoogle Scholar
  40. Moutsatsos IK, Parker CN (2016) Recent advances in quantitative high throughput and high content data analysis. Expert Opin Drug Discovery 11(4):415–423CrossRefGoogle Scholar
  41. Neef DW, Jaeger AM, Thiele DJ (2011) Heat shock transcription factor 1 as a therapeutic target in neurodegenerative diseases. Nat Rev Drug Discov 10(12):930–944CrossRefGoogle Scholar
  42. Neudegger T, Verghese J, Hayer-Hartl M, Hartl FU, Bracher A (2016) Structure of human heat-.shock transcription factor 1 in complex with DNA. Nat Struct Mol Biol 23(2):140–146CrossRefGoogle Scholar
  43. Nijman SM (2015) Functional genomics to uncover drug mechanism of action. Nat Chem Biol 11:942–948CrossRefGoogle Scholar
  44. Nyström A, Thriene K, Mittapalli V, Kern JS, Kiritsi D, Dengjel J, Bruckner-Tuderman L (2015) Losartan ameliorates dystrophic epidermolysis bullosa and uncovers new disease mechanisms. EMBO Mol Med 7(9):1211–1228CrossRefGoogle Scholar
  45. Pegoraro G, Misteli T (2017) High-throughput imaging for the discovery of cellular mechanisms of disease. Trends Genet 33(9):604–615CrossRefGoogle Scholar
  46. Persson M, Hornberg JJ (2016) Advances in predictive toxicology for discovery safety through high content screening. Chem Res Toxicol 29(12):1998–2007CrossRefGoogle Scholar
  47. Petersen DN, Hawkins J, Ruangsiriluk W, Stevens KA, Maguire BA, O’Connell TN, Rocke BN, Boehm M, Ruggeri RB, Rolph T, Hepworth D, Loria PM, Carpino PA (2016) A small-molecule anti-secretagogue of PCSK9 targets the 80S ribosome to inhibit PCSK9 protein translation. Cell Chem Biol 23(11):1362–1371CrossRefGoogle Scholar
  48. Phukan J (2010) Arimoclomol, a coinducer of heat shock proteins for the potential treatment of amyotrophic lateral sclerosis. IDrugs 13(7):482–496Google Scholar
  49. Rye CS, Chessum NE, Lamont S, Pike KG, Faulder P, Demeritt J, Kemmitt P, Tucker J, Zani L, Cheeseman MD, Isaac R, Goodwin L, Boros J, Raynaud F, Hayes A, Henley AT, de Billy E, Lynch CJ, Sharp SY, Te Poele R, Fee LO, Foote KM, Green S, Workman P, Jones K (2016) Discovery of 4,6-disubstituted pyrimidines as potent inhibitors of the heat shock factor 1 (HSF1) stress pathway and CDK9. Medchemcomm 7(8):1580–1586CrossRefGoogle Scholar
  50. Saibil H (2013) Chaperone machines for protein folding, unfolding and disaggregation. Nat Rev Mol Cell Biol 14(10):630–642CrossRefGoogle Scholar
  51. Sandqvist A, Sistonen L (2004) Nuclear stress granules: the awakening of a sleeping beauty? J Cell Biol 164(1):15–17CrossRefGoogle Scholar
  52. Santagata S, Xu YM, Wijeratne EM, Kontnik R, Rooney C, Perley CC, Kwon H, Clardy J, Kesari S, Whitesell L, Lindquist S, Gunatilaka AA (2012) Using the heat-shock response to discover anticancer compounds that target protein homeostasis. ACS Chem Biol 7(2):340–349CrossRefGoogle Scholar
  53. Santagata S, Mendillo ML, Tang YC, Subramanian A, Perley CC, Roche SP, Wong B, Narayan R, Kwon H, Koeva M, Amon A, Golub TR, Porco JA Jr, Whitesell L, Lindquist S (2013) Tight coordination of protein translation and HSF1 activation supports the anabolic malignant state. Science 341(6143):1238303CrossRefGoogle Scholar
  54. Santos R, Ursu O, Gaulton A, Bento AP, Donadi RS, Bologa CG, Karlsson A, Al-Lazikani B, Hersey A, Oprea TI, Overington JP (2017) A comprehensive map of molecular drug targets. Nat Rev Drug Discov 6(1):19–34CrossRefGoogle Scholar
  55. Sawyers CL (2005) Making progress through molecular attacks on cancer. Cold Spring Harb Symp Quant Biol 70:479–482CrossRefGoogle Scholar
  56. Scannell JW, Bosley J (2016) When quality beats quantity: decision theory, drug discovery, and the reproducibility crisis. PLoS One 11(2):e0147215CrossRefGoogle Scholar
  57. Schenone M, Dančík V, Wagner BK, Clemons PA (2013) Target identification and mechanism of action in chemical biology and drug discovery. Nat Chem Biol 9(4):232–240CrossRefGoogle Scholar
  58. Schirle M, Jenkins JL (2016) Identifying compound efficacy targets in phenotypic drug discovery. Drug Discov Today 21:82–89CrossRefGoogle Scholar
  59. Shi Y, Inoue H, Wu JC, Yamanaka S (2017) Induced pluripotent stem cell technology: a decade of progress. Nat Rev Drug Discov 16:115–130CrossRefGoogle Scholar
  60. Swinney DC, Anthony J (2011) How were new medicines discovered? Nat Rev Drug Discov 10:507–519CrossRefGoogle Scholar
  61. Thomas N (2010) High-content screening: a decade of evolution. J Biomol Screen 15(1):1–9CrossRefGoogle Scholar
  62. Vilaboa N, Boré A, Martin-Saavedra F, Bayford M, Winfield N, Firth-Clark S, Kirton SB, Voellmy R (2017) New inhibitor targeting human transcription factor HSF1: effects on the heat shock response and tumor cell survival. Nucleic Acids Res 45(10):5797–5817CrossRefGoogle Scholar
  63. Vydra N, Toma A, Widlak W (2014) Pleiotropic role of HSF1 in neoplastic transformation. Curr Cancer Drug Targets 14(2):144–155CrossRefGoogle Scholar
  64. Wagner BK (2016) The resurgence of phenotypic screening in drug discovery and development. Expert Opin Drug Discovery 11(2):121–125CrossRefGoogle Scholar
  65. Wagner BK, Schreiber SL (2016) The power of sophisticated phenotypic screening and modern mechanism-of-action methods. Cell Chem Biol 23:3–9CrossRefGoogle Scholar
  66. Wassermann AM, Lounkine E, Hoepfner D, Le Goff G, King FJ, Studer C, Peltier JM, Grippo ML, Prindle V, Tao J, Schuffenhauer A, Wallace IM, Chen S, Krastel P, Cobos-Correa A, Parker CN, Davies JW, Glick M (2015) Dark chemical matter as a promising starting point for drug lead discovery. Nat Chem Biol 11(12):958–966CrossRefGoogle Scholar
  67. Westerheide SD, Bosman JD, Mbadugha BN, Kawahara TL, Matsumoto G, Kim S, Gu W, Devlin JP, Silverman RB, Morimoto RI (2004) Celastrols as inducers of the heat shock response and cytoprotection. J Biol Chem 279(53):56,053–56,060CrossRefGoogle Scholar
  68. Westerheide SD, Kawahara TL, Orton K, Morimoto RI (2006) Triptolide, an inhibitor of the human heat shock response that enhances stress-induced cell death. J Biol Chem 281(14):9616–9622CrossRefGoogle Scholar
  69. Westerheide SD, Anckar J, Stevens SM Jr, Sistonen L, Morimoto RI (2009) Stress-inducible regulation of heat shock factor 1 by the deacetylase SIRT1. Science 323(5917):1063–1066CrossRefGoogle Scholar
  70. Workman P (2005) Drugging the cancer kinome: progress and challenges in developing personalized molecular cancer therapeutics. Cold Spring Harb Symp Quant Biol 70:499–515CrossRefGoogle Scholar
  71. Xu K, Sun X, Erokwu BO, Cernak I, Lamanna JC (2011) A heat-shock protein co-inducer treatment improves behavioral performance in rats exposed to hypoxia. Adv Exp Med Biol 701:313–318CrossRefGoogle Scholar
  72. Yoon IS, Au Q, Barber JR, Ng SC, Zhang B (2010) Development of a high-throughput screening assay for cytoprotective agents in rotenone-induced cell death. Anal Biochem 407(2):205–210CrossRefGoogle Scholar
  73. Yoon YJ, Kim JA, Shin KD, Shin DS, Han YM, Lee YJ, Lee JS, Kwon BM, Han DC (2011) KRIBB11 inhibits HSP70 synthesis through inhibition of heat shock factor 1 function by impairing the recruitment of positive transcription elongation factor b to the hsp70 promoter. J Biol Chem 286(3):1737–1747CrossRefGoogle Scholar
  74. Zeng XC, Bhasin S, Wu X, Lee JG, Maffi S, Nichols CJ, Lee KJ, Taylor JP, Greene LE, Eisenberg E (2004) Hsp70 dynamics in vivo: effect of heat shock and protein aggregation. J Cell Sci 117(Pt 21):4991–5000CrossRefGoogle Scholar
  75. Zhang D, Zhang B (2016) Selective killing of cancer cells by small molecules targeting heat shock stress response. Biochem Biophys Res Commun 478(4):1509–1514CrossRefGoogle Scholar
  76. Zhang JH, Chung TD, Oldenburg KR (1999) A simple statistical parameter for use in evaluation and validation of high throughput screening assays. J Biomol Screen 4(2):67–73CrossRefGoogle Scholar
  77. Zhang B, Gu X, Uppalapati U, Ashwell MA, Leggett DS, Li CJ (2008) High-content fluorescent-based assay for screening activators of DNA damage checkpoint pathways. J Biomol Screen 13(6):538–543CrossRefGoogle Scholar
  78. Zhang B, Au Q, Yoon IS, Tremblay MH, Yip G, Zhou Y, Barber JR, Ng SC (2009a) Identification of small-molecule HSF1 amplifiers by high content screening in protection of cells from stress induced injury. Biochem Biophys Res Commun 390(3):925–930CrossRefGoogle Scholar
  79. Zhang Y, Au Q, Zhang M, Barber JR, Ng SC, Zhang B (2009b) Identification of a small molecule SIRT2 inhibitor with selective tumor cytotoxicity. Biochem Biophys Res Commun 386(4):729–733CrossRefGoogle Scholar
  80. Zhang W, Bai Y, Wang Y, Xiao W (2016) Polypharmacology in drug discovery: a review from systems pharmacology perspective. Curr Pharm Des 22:3171–3181CrossRefGoogle Scholar
  81. Zhou Y, Liu G, Chen J, Reddy PS, Yoon IS, Zhang M, Zhang B (2009) Barber, J.R, Ng, S.C. (2009a) Pyrimido[5,4-e][1,2,4]triazine-5,7(1H,6H)-dione derivatives: their cytoprotection effect from rotenone toxicity and preliminary DMPK properties. Bioorg Med Chem Lett 19(21):6114–6118CrossRefGoogle Scholar
  82. Zhou Y, Vu K, Chen Y, Pham J, Brady T, Liu G, Chen J, Nam J, Murali Mohan Reddy PS, Au Q, Yoon IS, Tremblay MH, Yip G, Cher C, Zhang B, Barber JR, Ng SC (2009b) Chloro-oxime derivatives as novel small molecule chaperone amplifiers. Bioorg Med Chem Lett 19(11):3128–3135CrossRefGoogle Scholar
  83. Zhou Y, Wei L, Brady TP, Murali Mohan Redddy PS, Nguyen T, Chen J, Au Q, Yoon IS, Yip G, Zhang B, Barber JR, Ng SC (2009c) Pyrimido [5,4-e][1,2,4]triazine-5,7(1H,6H)-dione derivatives as novel small molecule chaperone amplifiers. Bioorg Med Chem Lett 19(15):4303–4307CrossRefGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Daniel Zhang
    • 1
    • 2
  • Bin Zhang
    • 1
  1. 1.Department of BiologyAlpine Therapeutics, Inc.San DiegoUSA
  2. 2.Massachusetts Institute of TechnologyCambridgeUSA

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