I've recently conducted/validated a small molecule screen looking for synergy between an RTK inhibitor and a panel of small molecules. I have two strong hits that appear to be targeting the same thing, but there is no immediate clear mechanism between these two compounds and the RTK. Are there any ideas for identifying the mechanism of synergy without individually analyzing each pathway downstream of the RTK?
Generally, there will be something known about these small molecules or they will be structurally similar to other molecules with known targets. Otherwise, you can probably start at the top of the RTK pathway and work your way down. I guess starting at your phenotype and working your way back up to the RTK is also a good strategy. You also might want to consider some of the antibody arrays that are getting more popular.
What was your synergy measurement? Cell death? Pathway activation?
The hit compounds might not target the RTK pathway, but the likelihood of this is determined by how you have measured synergy.
James-
Initial synergy was measured in cell viability, but have since demonstrate synergy in pathway activity downstream of the nuclear kinase.
I would like to come up with a relatively quick and inexpensive way to determine the pathway(s) that get me from the RTK to intersecting with the nuclear kinase pathway without having to individually inhibit each RTK downstream pathway and then look at signaling. I've looked into a phospho-protein/Mass. spec comparison approach, but it is currently outside my available budget.
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