Identification of cancer-cytotoxic modulators of PDE3A by predictive chemogenomics

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High cancer death rates indicate the need for new anticancer therapeutic agents. Approaches to discovering new cancer drugs include target-based drug discovery and phenotypic screening. Here, we identified phosphodiesterase 3A modulators as cell-selective cancer cytotoxic compounds through phenotypic compound library screening and target deconvolution by predictive chemogenomics. We found that sensitivity to 6-(4-(diethylamino)-3-nitrophenyl)-5-methyl-4,5-dihydropyridazin-3(2H)-one, or DNMDP, across 766 cancer cell lines correlates with expression of the gene PDE3A, encoding phosphodiesterase 3A. Like DNMDP, a subset of known PDE3A inhibitors kill selected cancer cells, whereas others do not. Furthermore, PDE3A depletion leads to DNMDP resistance. We demonstrated that DNMDP binding to PDE3A promotes an interaction between PDE3A and Schlafen 12 (SLFN12), suggestive of a neomorphic activity. Coexpression of SLFN12 with PDE3A correlates with DNMDP sensitivity, whereas depletion of SLFN12 results in decreased DNMDP sensitivity. Our results implicate PDE3A modulators as candidate cancer therapeutic agents and demonstrate the power of predictive chemogenomics in small-molecule discovery.

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Figure 1: Identification and characterization of DNMDP, a potent and selective cancer cell cytotoxic agent.
Figure 2: PDE3A expression correlates with sensitivity to DNMDP, but inhibition of PDE3A-mediated cAMP hydrolysis does not correlate with cytotoxicity.
Figure 3: Nonlethal PDE3 inhibitors rescue cell death induced by DNMDP by competing for the binding of PDE3A.
Figure 4: PDE3A is not essential in sensitive cell lines but is required for relaying the cytotoxic signal.
Figure 5: PDE3A immunoprecipitation in the presence of DNMDP reveals novel SIRT7 and SLFN12 interaction.
Figure 6: Cell lines with dual expression of SLFN12 and PDE3A are significantly enriched for DNMDP-sensitive cell lines.

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  • 22 December 2015

    In the version of this article initially published, there was a typographical error in the Additional Information section that switched H.G. to H.H. The error has been corrected in the print, HTML and PDF versions of the article.


  1. 1

    Ferlay, J. et al. Cancer incidence and mortality worldwide: sources, methods and major patterns in GLOBOCAN 2012. Int. J. Cancer 136, E359–E386 (2015).

    CAS  PubMed  Google Scholar 

  2. 2

    Moffat, J.G., Rudolph, J. & Bailey, D. Phenotypic screening in cancer drug discovery - past, present and future. Nat. Rev. Drug Discov. 13, 588–602 (2014).

    CAS  PubMed  Google Scholar 

  3. 3

    Simons, S.S. Jr., Edwards, D.P. & Kumar, R. Minireview: dynamic structures of nuclear hormone receptors: new promises and challenges. Mol. Endocrinol. 28, 173–182 (2014).

    PubMed  Google Scholar 

  4. 4

    Drake, C.G., Lipson, E.J. & Brahmer, J.R. Breathing new life into immunotherapy: review of melanoma, lung and kidney cancer. Nat. Rev. Clin. Oncol. 11, 24–37 (2014).

    CAS  PubMed  Google Scholar 

  5. 5

    Weinstein, J.N. et al. An information-intensive approach to the molecular pharmacology of cancer. Science 275, 343–349 (1997).

    CAS  Google Scholar 

  6. 6

    Bredel, M. & Jacoby, E. Chemogenomics: an emerging strategy for rapid target and drug discovery. Nat. Rev. Genet. 5, 262–275 (2004).

    CAS  PubMed  Google Scholar 

  7. 7

    Weinstein, J.N. et al. Neural computing in cancer drug development: predicting mechanism of action. Science 258, 447–451 (1992).

    CAS  PubMed  Google Scholar 

  8. 8

    Barretina, J. et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 483, 603–607 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  9. 9

    Basu, A. et al. An interactive resource to identify cancer genetic and lineage dependencies targeted by small molecules. Cell 154, 1151–1161 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  10. 10

    Garnett, M.J. et al. Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature 483, 570–575 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. 11

    Staunton, J.E. et al. Chemosensitivity prediction by transcriptional profiling. Proc. Natl. Acad. Sci. USA 98, 10787–10792 (2001).

    CAS  PubMed  Google Scholar 

  12. 12

    Zheng, X.F.S. & Chan, T.-F. Chemical genomics: a systematic approach in biological research and drug discovery. Curr. Issues Mol. Biol. 4, 33–43 (2002).

    CAS  PubMed  Google Scholar 

  13. 13

    Crews, C.M. Targeting the undruggable proteome: the small molecules of my dreams. Chem. Biol. 17, 551–555 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  14. 14

    Collins, I. & Workman, P. New approaches to molecular cancer therapeutics. Nat. Chem. Biol. 2, 689–700 (2006).

    CAS  PubMed  Google Scholar 

  15. 15

    Swinney, D.C. & Anthony, J. How were new medicines discovered? Nat. Rev. Drug Discov. 10, 507–519 (2011).

    CAS  Google Scholar 

  16. 16

    Krönke, J. et al. Lenalidomide causes selective degradation of IKZF1 and IKZF3 in multiple myeloma cells. Science 343, 301–305 (2014).

    PubMed  PubMed Central  Google Scholar 

  17. 17

    Lu, G. et al. The myeloma drug lenalidomide promotes the cereblon-dependent destruction of Ikaros proteins. Science 343, 305–309 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  18. 18

    Nakajima, H., Kim, Y.B., Terano, H., Yoshida, M. & Horinouchi, S. FR901228, a potent antitumor antibiotic, is a novel histone deacetylase inhibitor. Exp. Cell Res. 241, 126–133 (1998).

    CAS  PubMed  Google Scholar 

  19. 19

    Marks, P.A. & Breslow, R. Dimethyl sulfoxide to vorinostat: development of this histone deacetylase inhibitor as an anticancer drug. Nat. Biotechnol. 25, 84–90 (2007).

    CAS  PubMed  Google Scholar 

  20. 20

    Ledermann, J. et al. Olaparib maintenance therapy in patients with platinum-sensitive relapsed serous ovarian cancer: a preplanned retrospective analysis of outcomes by BRCA status in a randomised phase 2 trial. Lancet Oncol. 15, 852–861 (2014).

    CAS  PubMed  Google Scholar 

  21. 21

    Lawrence, M.S. et al. Discovery and saturation analysis of cancer genes across 21 tumour types. Nature 505, 495–501 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. 22

    Francis, S.H., Blount, M.A. & Corbin, J.D. Mammalian cyclic nucleotide phosphodiesterases: molecular mechanisms and physiological functions. Physiol. Rev. 91, 651–690 (2011).

    CAS  PubMed  Google Scholar 

  23. 23

    Maurice, D.H. et al. Advances in targeting cyclic nucleotide phosphodiesterases. Nat. Rev. Drug Discov. 13, 290–314 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  24. 24

    Tefferi, A., Silverstein, M.N., Petitt, R.M., Mesa, R.A. & Solberg, L.A. Jr. Anagrelide as a new platelet-lowering agent in essential thrombocythemia: mechanism of actin, efficacy, toxicity, current indications. Semin. Thromb. Hemost. 23, 379–383 (1997).

    CAS  PubMed  Google Scholar 

  25. 25

    Burgin, A.B. et al. Design of phosphodiesterase 4D (PDE4D) allosteric modulators for enhancing cognition with improved safety. Nat. Biotechnol. 28, 63–70 (2010).

    CAS  PubMed  Google Scholar 

  26. 26

    Gurney, M.E., D'Amato, E.C. & Burgin, A.B. Phosphodiesterase-4 (PDE4) molecular pharmacology and Alzheimer's disease. Neurotherapeutics 12, 49–56 (2015).

    CAS  PubMed  Google Scholar 

  27. 27

    Ruppert, D. & Weithmann, K.U. HL 725, an extremely potent inhibitor of platelet phosphodiesterase and induced platelet aggregation in vitro. Life Sci. 31, 2037–2043 (1982).

    CAS  PubMed  Google Scholar 

  28. 28

    Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819–823 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  29. 29

    Millar, J.K. et al. DISC1 and PDE4B are interacting genetic factors in schizophrenia that regulate cAMP signaling. Science 310, 1187–1191 (2005).

    CAS  PubMed  Google Scholar 

  30. 30

    Beca, S. et al. Phosphodiesterase type 3A regulates basal myocardial contractility through interacting with sarcoplasmic reticulum calcium ATPase type 2a signaling complexes in mouse heart. Circ. Res. 112, 289–297 (2013).

    CAS  PubMed  Google Scholar 

  31. 31

    Pozuelo Rubio, M., Campbell, D.G., Morrice, N.A. & Mackintosh, C. Phosphodiesterase 3A binds to 14-3-3 proteins in response to PMA-induced phosphorylation of Ser428. Biochem. J. 392, 163–172 (2005).

    PubMed  PubMed Central  Google Scholar 

  32. 32

    Malovannaya, A. et al. Analysis of the human endogenous coregulator complexome. Cell 145, 787–799 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  33. 33

    Chavez, J.A., Gridley, S., Sano, H., Lane, W.S. & Lienhard, G.E. The 47kDa Akt substrate associates with phosphodiesterase 3B and regulates its level in adipocytes. Biochem. Biophys. Res. Commun. 342, 1218–1222 (2006).

    CAS  PubMed  Google Scholar 

  34. 34

    Pierson, E. et al. GTEx Consortium. Sharing and specificity of co-expression networks across 35 human tissues. PLoS Comput. Biol. 11, e1004220 (2015).

    PubMed  PubMed Central  Google Scholar 

  35. 35

    Ahmad, F., Degerman, E. & Manganiello, V.C. Cyclic nucleotide phosphodiesterase 3 signaling complexes. Horm. Metab. Res. 44, 776–785 (2012).

    CAS  PubMed  Google Scholar 

  36. 36

    Bedenis, R. et al. Cilostazol for intermittent claudication. Cochrane Database Syst. Rev. 10, CD003748 (2014).

    Google Scholar 

  37. 37

    Movsesian, M., Wever-Pinzon, O. & Vandeput, F. PDE3 inhibition in dilated cardiomyopathy. Curr. Opin. Pharmacol. 11, 707–713 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  38. 38

    Sun, L. et al. Phosphodiesterase 3/4 inhibitor zardaverine exhibits potent and selective antitumor activity against hepatocellular carcinoma both in vitro and in vivo independently of phosphodiesterase inhibition. PLoS One 9, e90627 (2014).

    PubMed  PubMed Central  Google Scholar 

  39. 39

    Fryknäs, M. et al. Phenotype-based screening of mechanistically annotated compounds in combination with gene expression and pathway analysis identifies candidate drug targets in a human squamous carcinoma cell model. J. Biomol. Screen. 11, 457–468 (2006).

    PubMed  Google Scholar 

  40. 40

    Wang, G., Franklin, R., Hong, Y. & Erusalimsky, J.D. Comparison of the biological activities of anagrelide and its major metabolites in haematopoietic cell cultures. Br. J. Pharmacol. 146, 324–332 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  41. 41

    Espasandin, Y.R. et al. Anagrelide platelet-lowering effect is due to inhibition of both megakaryocyte maturation and proplatelet formation: insight into potential mechanisms. J. Thromb. Haemost. 13, 631–42 (2015).

    CAS  PubMed  Google Scholar 

  42. 42

    Card, G.L. et al. Structural basis for the activity of drugs that inhibit phosphodiesterases. Structure 12, 2233–2247 (2004).

    CAS  PubMed  Google Scholar 

  43. 43

    Zhang, W., Ke, H. & Colman, R.W. Identification of interaction sites of cyclic nucleotide phosphodiesterase type 3A with milrinone and cilostazol using molecular modeling and site-directed mutagenesis. Mol. Pharmacol. 62, 514–520 (2002).

    CAS  PubMed  Google Scholar 

  44. 44

    Lee, M.E., Markowitz, J., Lee, J.O. & Lee, H. Crystal structure of phosphodiesterase 4D and inhibitor complex(1). FEBS Lett. 530, 53–58 (2002).

    CAS  PubMed  Google Scholar 

  45. 45

    Nagao, M. et al. Role of protein phosphatases in malignant transformation. Int. Symp. Princess Takamatsu Cancer Res. Fund 20, 177–184 (1989).

    CAS  PubMed  Google Scholar 

  46. 46

    Imielinski, M. et al. Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing. Cell 150, 1107–1120 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  47. 47

    Lawrence, M.S. et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 499, 214–218 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  48. 48

    Kaheinen, P. et al. Positive inotropic effect of levosimendan is correlated to its stereoselective Ca2+-sensitizing effect but not to stereoselective phosphodiesterase inhibition. Basic Clin. Pharmacol. Toxicol. 98, 74–78 (2006).

    CAS  PubMed  Google Scholar 

  49. 49

    Tang, K.M., Jang, E.K. & Haslam, R.J. Photoaffinity labelling of cyclic GMP-inhibited phosphodiesterase (PDE III) in human and rat platelets and rat tissues: effects of phosphodiesterase inhibitors. Eur. J. Pharmacol. 268, 105–114 (1994).

    CAS  PubMed  Google Scholar 

  50. 50

    Altman, D.G. & Bland, J.M. Measurement in medicine: the analysis of method comparison studies. Statistician 32, 307–317 (1983).

    Google Scholar 

  51. 51

    Rappsilber, J., Mann, M. & Ishihama, Y. Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat. Protoc. 2, 1896–1906 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  52. 52

    Udeshi, N.D. et al. Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. Mol. Cell. Proteomics 11, 148–159 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

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This work was supported in part by the US National Cancer Institute (NCI) Grant (grant number 1R35CA197568, awarded to M.M.), the American Cancer Society Research Professorship (awarded to M.M.), the Doctors Cancer Foundation (awarded to H.G.), the Friends of Dana-Farber Cancer Institute (awarded to H.G.), and the US National Institutes of Health's Molecular Libraries Program Center Network (MLPCN) (grant number 3U54HG005032-05S1, awarded to H.G., M.M. and S.L.S.). The cancer cell-line profiling studies were supported in part by the NCI's Cancer Target Discovery and Development (CTD2) Network (grant number U01CA176152, awarded to S.L.S.). We thank A. Bhatt, H. Gannon, J. Jung, T. Sharifnia and all members of the Meyerson laboratory for their advice and helpful discussions. S.L.S. is an Investigator of the Howard Hughes Medical Institute.

Author information




L.d.W., P.W.F., M.J.H., N.T., A.N.K., H.G. and M.M. designed and performed the phenotypic small-molecule screen. M.G.R., A.T., P.A.C., A.F.S. and S.L.S. designed and performed experiments identifying PDE3A expression correlation with DNMDP sensitivity. L.d.W., T.A.L., L.G., B.K.W., B.M. and H.G. designed and performed experiments demonstrating physical interaction of DNMDP with PDE3A and rescue phenotype by non-cytotoxic PDE3 inhibitors. L.d.W., P.S.C., H.G. and M.M. designed and performed PDE3A protein level reduction leading to DNMDP resistance. L.d.W., X.W., C.H., S.A.C., M.S., A.B.B., H.G. and M.M. designed and performed PDE3A immunoprecipitation experiment revealing novel protein-protein interaction partners facilitated by DNMDP binding. L.d.W., X.W., M.G.R., A.T., H.G. and M.M. designed and performed experiments showing requirement of SLFN12 for DNMDP phenotype and genomic correlation with DNMDP sensitivity. L.d.W. made the figures, and L.d.W., T.A.L., H.G. and M.M. wrote the manuscript.

Corresponding authors

Correspondence to Heidi Greulich or Matthew Meyerson.

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Competing interests

L.d.W., T.A.L., X.W., P.A.C., S.L.S., H.G. and M.M. receive research support from Bayer. M.M. is a founder, consultant and equity holder in Foundation Medicine. L.d.W., T.A.L., L.G., B.M., H.G. and M.M. are inventors on patent WO 2014/164704 A2, covering the chemical space around DNMDP and some of the analogs described in the supplementary information.

Supplementary information

Supplementary Text and Figures

Supplementary Results, Supplementary Figures 1–11, Supplementary Tables 1–6 and Supplementary Note. (PDF 2030 kb)

Supplementary Dataset 1

Screening data of 1924 compounds in A549 and NCI-H1734 (XLSX 293 kb)

Supplementary Dataset 2

Sensitivity data of 766 cancer cell lines treated with DNMDP (XLSX 70 kb)

Supplementary Dataset 3

Results from competition screen using 1600 bioactive compounds to rescue DNMDP cytotoxicity in the HeLa cell line. (XLSX 135 kb)

Supplementary Dataset 4

Results from PDE3A immunoprecipitation followed by iTRAQ/MS in the presence of blocking peptide, DMSO, DNMDP and trequinsin. (XLSX 1345 kb)

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de Waal, L., Lewis, T., Rees, M. et al. Identification of cancer-cytotoxic modulators of PDE3A by predictive chemogenomics. Nat Chem Biol 12, 102–108 (2016).

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