Single cell network profiling (SCNP): mapping drug and target interactions

Assay Drug Dev Technol. 2010 Jun;8(3):321-43. doi: 10.1089/adt.2009.0251.


Measuring target coverage of small molecule inhibitors is paramount-first, for selection of molecules to progress through the drug development process and second, once a candidate drug moves to clinical testing, for guiding dose/schedule selection. Single cell network profiling (SCNP) using multiparameter flow cytometry can measure compound effects on multiple signaling cascades in a cell-type-specific manner. We applied SCNP to a panel of compounds with reported inhibitory effects on Jak/Stat signaling using a novel system where modulation of multiple signaling cascades are simultaneously measured in discrete cell subsets in whole (ie, unfractionated) blood. Jak2 vs. Jak3 selectivity as well as "off-target" effects on other cell signaling pathways were measured using a combination of cytokines that target different white blood cell subsets, namely GM-CSF (monocytes/granulocytes), IL-2 (T cells), and CD40L (B cells). The compounds were then rank-ordered by potency and selectivity against the different pathways tested. Notably, SCNP performed in whole unfractionated blood compared to fractionated peripheral blood mononuclear cells (PBMC) from the same donors revealed potency loss for all compounds, with one exception. These studies show that SCNP can be used to efficiently measure a drug candidate's potency and selectivity in a physiologically relevant environment (eg, whole blood) and that robust IC(50) are attainable from rare subpopulations (<100 cells). The ability to generate in vitro IC(50) measurements in whole blood can be used not only for the preclinical selection of lead molecules, but also to determine the target plasma concentration for clinical studies and to measure target coverage after drug administration in early phase clinical trials. Knowledge of the compound plasma concentration necessary to achieve biochemical coverage permits rational design of clinical trials based on biologically active dose vs. the traditional maximum tolerated dose (MTD) design, which is better suited for cytotoxic, nontargeted drugs.

MeSH terms

  • Algorithms
  • Antineoplastic Agents / pharmacology
  • Blood Cells / drug effects*
  • Cells / drug effects
  • Confidence Intervals
  • Drug Delivery Systems / methods*
  • Drug Evaluation, Preclinical / methods*
  • Drug Industry
  • Enzyme Inhibitors / pharmacology
  • Humans
  • In Vitro Techniques
  • Janus Kinases / metabolism
  • Phosphoinositide-3 Kinase Inhibitors
  • Phosphorylation
  • Protein Kinase Inhibitors / pharmacology*
  • Reproducibility of Results
  • STAT1 Transcription Factor / metabolism
  • STAT5 Transcription Factor / metabolism
  • Signal Transduction / drug effects
  • Small Molecule Libraries*
  • Staining and Labeling


  • Antineoplastic Agents
  • Enzyme Inhibitors
  • Phosphoinositide-3 Kinase Inhibitors
  • Protein Kinase Inhibitors
  • STAT1 Transcription Factor
  • STAT1 protein, human
  • STAT5 Transcription Factor
  • Small Molecule Libraries
  • Janus Kinases