We present a strategy for identifying off-target effects and hidden phenotypes of drugs by directly probing biochemical pathways that underlie therapeutic or toxic mechanisms in intact, living cells. High-content protein-fragment complementation assays (PCAs) were constructed with synthetic fragments of a mutant fluorescent protein ('Venus', EYFP or both), allowing us to measure spatial and temporal changes in protein complexes in response to drugs that activate or inhibit particular pathways. One hundred and seven different drugs from six therapeutic areas were screened against 49 different PCA reporters for ten cellular processes. This strategy reproduced known structure-function relationships and also predicted 'hidden,' potent antiproliferative activities for four drugs with novel mechanisms of action, including disruption of mitochondrial membrane potential. A simple algorithm identified a 25-assay panel that was highly predictive of antiproliferative activity, and the predictive power of this approach was confirmed with cross-validation tests. This study suggests a strategy for therapeutic discovery that identifies novel, unpredicted mechanisms of drug action and thereby enhances the productivity of drug-discovery research.

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Activated Ras, but not Raf, causes transformation of RIE-1 epithelial cells, supporting the importance of Rafindependent pathways in mediating Ras transformation. The p38 and JNK mitogen-activated protein kinase cascades are activated by Ras via Raf-independent effector function. Therefore, we determined whether p38 and JNK activation are involved in Ras transformation of RIE-1 epithelial cells. Rather surprisingly, we found that pharmacologic inhibition of p38, together with Raf activation of ERK, was sufficient to mimic the morphologic and growth transformation caused by oncogenic Ras. p38 inhibition together with ERK activation also caused the same alterations in cyclin D1 and p21 CIP1 expression caused by Ras and induced an autocrine growth factor loop important for transformation. Finally, in contrast to p38, we found that JNK activation promoted Ras transformation, and that Ras deregulation of p38 and JNK was not mediated by activation of the Rac small GTPase. We conclude that a key action of Raf-independent effector pathways important for Ras transformation may involve inhibition of p38 and activation of JNK.

c-Jun N-terminal kinase (JNK) is a member of the mitogenactivated protein kinase family, and its function is critical for signal transduction in tumor and endothelial cells. JNK is a serine/threonine protein kinase that phosphorylates c-Jun, a component of the activator protein-1 transcription factor complex. We hypothesize that inhibiting JNK will lead to the inhibition of tumor growth; therefore, we evaluated the efficacy of the recently described JNK inhibitor SP600125 [anthra[1,9-cd] pyrazol-6 (2H)-one]. SP600125 is an anthrapyrazole that is a reversible, ATP-competitive inhibitor of JNK1/2. SP600125 exhibited broad-based antiproliferative activity in human endothelial and tumor cell lines. SP600125 affects proliferation by arresting cells in the G 2 /M phase of the cell cycle. SP600125 also acts to inhibit endothelial cell migration. In cell lines, a correlation of cell growth inhibition with reduced JNK activity was observed. The systemic administration of SP600125 resulted in the inhibition of DU145 human prostate carcinoma xenografts and murine Lewis lung carcinoma. SP600125 also enhanced the potency of cyclophosphamide in the inhibition of Lewis lung tumor growth. These data indicate the therapeutic antitumor potential of small molecule inhibitors that act to block the cellular activity of JNK.

Cellular signal transduction occurs in the context of dynamic multiprotein complexes in highly ramified pathways. These complexes in turn interact with the cytoskeleton, protein scaffolds, membranes, lipid rafts, and specific subcellular organelles, contributing to the exquisitely tight regulation of their localization and activity. However, these realities of drug target biology are not addressed by currently available drug discovery platforms. In this article, we describe the use of protein-fragment complementation assays (PCAs) to assess drugs and drug targets in the context of their native environment. The PCA process allows for the detection of protein-protein complexes following the expression of full-length mammalian genes linked in-frame to polypeptide fragments of rationally dissected reporter genes. If cellular activity causes the association of two proteins linked to complementary reporter fragments, the interaction of the proteins of interest enables refolding of the fragments, which can then generate a quantifiable signal. Using a PCA based on a yellow fluorescent protein, we demonstrate that functional (p50/p65) complexes of the heterodimeric nuclear factor-kappaB transcription factor, as well as the transcription factor subunit p65 and its modulator IkappaBalpha, can be visualized and monitored in live cells. We observed similar responses of the PCA assays to the activities of the cognate endogenous proteins, including modulation by known agonists and antagonists. A proof-of-concept high throughput screen was carried out using the p50/p65 cell line, and potent inhibitors of this pathway were identified. These assays record the dynamic activity of signaling pathways in living cells and in real time, and validate the utility of PCA as a novel approach to drug discovery.