Abstract
Cyclin-dependent kinases (CDKs) regulate cell cycle progression, and some of them are also involved in the control of cellular transcription. Dysregulation of these critical cellular processes, due to the aberrant expression of some of these proteins, is common in many neoplastic malignancies. Consequently, the development of chemical compounds capable of inhibiting the biological activity of CDKs represents an attractive strategy in the anticancer area. CDK inhibition can trigger apoptosis and could be particularly useful in hematological malignancies, which are more sensitive to inhibition of cell cycle and apoptosis induction. Over the last few years, a number of pharmacological inhibitors of CDKs (CDKIs) belonging to different chemical families have been developed, and some of them have been tested in clinical trials. Given the complexity of the role of CDKs in cell functioning, it would be desirable to develop new tools that could facilitate a better understanding of the new insights into CDK functions and the mode-of-actions of CDKIs. In this context, this chapter describes an experimental approach to evaluate the metabolic consequences of CDKIs at the cellular level based on metabolomics by NMR. More specifically, a description of a strategy to characterize the biochemical effects of CDKIs acting on mammalian cells is provided, including protocols for the extraction of hydrophilic and lipophilic metabolites, the acquisition of 1D and 2D metabolomic Nuclear Magnetic Resonance (NMR) experiments, the identification and quantification of metabolites, and the annotation of the results in the context of biochemical pathways.
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References
Hirama T, Koeffler H (1995) Role of the cyclin-dependent kinase inhibitors in the development of cancer. Blood 86:841–854
Murray AW (2004) Recycling the cell cycle: cyclins revisited. Cell 116:221–234
Malumbres M, Barbacid M (2009) Cell cycle, CDKs and cancer: a changing paradigm. Nat Rev Cancer 9:153–166
Shapiro GI (2006) Cyclin-dependent kinase pathways as targets for cancer treatment. J Clin Oncol 24:1770–1783
Fischer PM, Gianella-Borradori A (2005) Recent progress in the discovery and development of cyclin-dependent kinase inhibitors. Expert Opin Investig Drugs 14:457–477
Bose P, Simmons GL, Grant S (2013) Cyclin-dependent kinase inhibitor therapy for hematologic malignancies. Expert Opin Investig Drugs 22:723–738
Blachly JS, Byrd JC (2013) Emerging drug profile: cyclin-dependent kinase inhibitors. Leuk Lymphoma 54:2133–2143
Nicholson JK, Lindon JC (2008) Systems biology: metabonomics. Nature 455:1054–1056
Spratlin JL, Serkova NJ, Eckhardt SG (2009) Clinical applications of metabolomics in oncology: a review. Clin Cancer Res 15:431–440
Wei R (2011) Metabolomics and its practical value in pharmaceutical industry. Curr Drug Metab 12:345–358
Powers R (2014) The current state of drug discovery and a potential role for NMR metabolomics. J Med Chem 57:5860–5870
Zhang A, Sun H, Xu H et al (2013) Cell metabolomics. OMICS 17:495–501
Aranibar N, Borys M, Mackin NA et al (2011) NMR-based metabolomics of mammalian cell and tissue cultures. J Biomol NMR 49:195–206
Barding GA Jr, Salditos R, Larive CK (2012) Quantitative NMR for bioanalysis and metabolomics. Anal Bioanal Chem 404:1165–1179
Wishart DS, Jewison T, Guo AC et al (2013) HMDB 3.0 – the human metabolome database in 2013. Nucleic Acids Res 41:D801–D807
Teng Q, Huang W, Collette TW et al (2009) A direct cell quenching method for cell-culture based metabolomics. Metabolomics 5:199–208
Beckonert O, Keun HC, Ebbels TM et al (2007) Metabolic profiling, metabolomic and metabonomic procedures for NMR spectroscopy of urine, plasma, serum and tissue extracts. Nat Protoc 2:2692–2703
Barupal DK, Haidiya PK, Wohlgemuth G et al (2012) MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity. BMC Bioinformatics 13:99
Gao J, Tarcea VG, Karnovsky A et al (2010) Metscape: a cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks. Bioinformatics 26:971–973
Duarte TM, Carinhas N, Silva AC et al (2014) 1H-NMR protocol for exametabolome analysis of cultured mammalian cells. Methods Mol Biol 1104:237–247
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Palomino-Schätzlein, M., Pineda-Lucena, A. (2016). Metabolomic Applications to the Characterization of the Mode-of-Action of CDK Inhibitors. In: Orzáez, M., Sancho Medina, M., Pérez-Payá, E. (eds) Cyclin-Dependent Kinase (CDK) Inhibitors. Methods in Molecular Biology, vol 1336. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2926-9_16
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DOI: https://doi.org/10.1007/978-1-4939-2926-9_16
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-2925-2
Online ISBN: 978-1-4939-2926-9
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