The examples of HCS assays referred to in Section 5.4 for compound screening highlight the benefits of cellular over conventional assays. First, they can provide access to targets not amenable to screening in conventional assays. Second, multiplexed assays enable the direct identification of pharmacologically active compounds which can modulate the physiology or morphology of a cell.

These advantages must be reflected knowing that most successful drugs descend from natural products selected in intact biological systems, and many drugs show several biological activities, for example nonsteroidal anti-inflammatory agents, cyclosporine, and antihistamines [108]. Even for the most popular drugs, not all of the targets and signaling pathways influenced in one cell are realized, much less the effects on the whole organism.

The minimization of biological complexity by screening isolated targets or individual pathways causes most emergent properties and all network responses of a cell to be missed. Hence, the future use of complex cell systems in combination with testing of several targets will allow the collection of information covering several disease parameters and pathways by selecting for cell-permeable, nontoxic drug candidates. Here, the studies of Kunkel and colleagues have provided a hint of the possibilities that lie ahead [109], when they assayed the effect of 33 kinase inhibitors on 51 protein readouts in four inflammatory cell systems, and ultimately identified an unexpectedly high number of active drugs [110].

Today, a series of new, more physiologically relevant cell culture methods have become available: tumor cells have been grown to three-dimensional spheroids and tested for their response against cytotoxic agents [111], while embryonic stem (ES) cells [112] allow the effects of compounds to be monitored in complex cell systems.

The microscope has long been recognized as an important instrument in cell biology research, yet today its combination with fluorescence techniques and automation has revealed it to be a very powerful and very sensitive tool. Now, the use of automated fluorescence microscopy allows a small number of cells expressing a low number of biomolecules to be screened. Indeed, the potential of this technique has been well documented by Mitchison's group, in testing 90 compounds for mitotic arrest, differentiation, toxicity, and key signaling pathways [113, 114].

In future, the main challenges for complex cellular screens are threefold, namely the identification of drug target(s), the determination of target-based structure-activity relationships ofthe compounds, and regulatory issues. Moreover, the management and presentation of the growing amount of data, as well as the integration of analyzed cellular parameters into a physiological context, represent a major challenge for cellular bioinformatics.

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