Abstract
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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Change history
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.
References
Ferlay, J. et al. Cancer incidence and mortality worldwide: sources, methods and major patterns in GLOBOCAN 2012. Int. J. Cancer 136, E359–E386 (2015).
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).
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).
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).
Weinstein, J.N. et al. An information-intensive approach to the molecular pharmacology of cancer. Science 275, 343–349 (1997).
Bredel, M. & Jacoby, E. Chemogenomics: an emerging strategy for rapid target and drug discovery. Nat. Rev. Genet. 5, 262–275 (2004).
Weinstein, J.N. et al. Neural computing in cancer drug development: predicting mechanism of action. Science 258, 447–451 (1992).
Barretina, J. et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 483, 603–607 (2012).
Basu, A. et al. An interactive resource to identify cancer genetic and lineage dependencies targeted by small molecules. Cell 154, 1151–1161 (2013).
Garnett, M.J. et al. Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature 483, 570–575 (2012).
Staunton, J.E. et al. Chemosensitivity prediction by transcriptional profiling. Proc. Natl. Acad. Sci. USA 98, 10787–10792 (2001).
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).
Crews, C.M. Targeting the undruggable proteome: the small molecules of my dreams. Chem. Biol. 17, 551–555 (2010).
Collins, I. & Workman, P. New approaches to molecular cancer therapeutics. Nat. Chem. Biol. 2, 689–700 (2006).
Swinney, D.C. & Anthony, J. How were new medicines discovered? Nat. Rev. Drug Discov. 10, 507–519 (2011).
Krönke, J. et al. Lenalidomide causes selective degradation of IKZF1 and IKZF3 in multiple myeloma cells. Science 343, 301–305 (2014).
Lu, G. et al. The myeloma drug lenalidomide promotes the cereblon-dependent destruction of Ikaros proteins. Science 343, 305–309 (2014).
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).
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).
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).
Lawrence, M.S. et al. Discovery and saturation analysis of cancer genes across 21 tumour types. Nature 505, 495–501 (2014).
Francis, S.H., Blount, M.A. & Corbin, J.D. Mammalian cyclic nucleotide phosphodiesterases: molecular mechanisms and physiological functions. Physiol. Rev. 91, 651–690 (2011).
Maurice, D.H. et al. Advances in targeting cyclic nucleotide phosphodiesterases. Nat. Rev. Drug Discov. 13, 290–314 (2014).
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).
Burgin, A.B. et al. Design of phosphodiesterase 4D (PDE4D) allosteric modulators for enhancing cognition with improved safety. Nat. Biotechnol. 28, 63–70 (2010).
Gurney, M.E., D'Amato, E.C. & Burgin, A.B. Phosphodiesterase-4 (PDE4) molecular pharmacology and Alzheimer's disease. Neurotherapeutics 12, 49–56 (2015).
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).
Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819–823 (2013).
Millar, J.K. et al. DISC1 and PDE4B are interacting genetic factors in schizophrenia that regulate cAMP signaling. Science 310, 1187–1191 (2005).
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).
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).
Malovannaya, A. et al. Analysis of the human endogenous coregulator complexome. Cell 145, 787–799 (2011).
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).
Pierson, E. et al. GTEx Consortium. Sharing and specificity of co-expression networks across 35 human tissues. PLoS Comput. Biol. 11, e1004220 (2015).
Ahmad, F., Degerman, E. & Manganiello, V.C. Cyclic nucleotide phosphodiesterase 3 signaling complexes. Horm. Metab. Res. 44, 776–785 (2012).
Bedenis, R. et al. Cilostazol for intermittent claudication. Cochrane Database Syst. Rev. 10, CD003748 (2014).
Movsesian, M., Wever-Pinzon, O. & Vandeput, F. PDE3 inhibition in dilated cardiomyopathy. Curr. Opin. Pharmacol. 11, 707–713 (2011).
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).
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).
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).
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).
Card, G.L. et al. Structural basis for the activity of drugs that inhibit phosphodiesterases. Structure 12, 2233–2247 (2004).
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).
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).
Nagao, M. et al. Role of protein phosphatases in malignant transformation. Int. Symp. Princess Takamatsu Cancer Res. Fund 20, 177–184 (1989).
Imielinski, M. et al. Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing. Cell 150, 1107–1120 (2012).
Lawrence, M.S. et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 499, 214–218 (2013).
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).
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).
Altman, D.G. & Bland, J.M. Measurement in medicine: the analysis of method comparison studies. Statistician 32, 307–317 (1983).
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).
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).
Acknowledgements
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.
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Contributions
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.
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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). https://doi.org/10.1038/nchembio.1984
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DOI: https://doi.org/10.1038/nchembio.1984
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