I know that the siRNA inhibition is chronic and the small-molecule inhibition is temporary and reversible. Do you have an explanation related to this question?
These methods work on different layers of regulation. While siRNA changes the expression of genes (and depending on the gene also genes downstream of it), small molecule inhibitors target only one protein (ideally at least) or enzyme in a pathway. If you want to look at a specific pathway and have a good and specific inhibitor, I would use it. RNAi is of course a good addition.
Assuming that small molecule inhibitors are selectivity proven, then they provide several advantages: they can be applied directly thus no cloning is required, and provided that they do not bind covalently to their target protein they may be used reversibly. One additional advantage is that if they are membrane permeable, they will diffuse very rapidly inside the cell and provide inhibitory effect with rather precise timing. RNAi on the other hand may take some time to affect as it will need time to build up after induction
Excellent answer George. I like how you emphasized whether the small molecular inhibitor has "proven" specificity, because many inhibitors, such as those for kinases, are quite promiscuous and affect multiple kinase targets.
Some of the advantages of siRNA knockdown are the following:
1. siRNA knockdown is transient, and does not completely reduce the expression of your target protein. This can be useful if your target gene is important for cell survival, or if the time course of protein knockdown is important in your system..
2. siRNA can be specific to particular isoforms of an encoded protein, if that is of interest to you. I study the SRC family of tyrosine kinases, and the best drug inhibitors (PP1, PP2, SU6656) still target most of the nine SRC family members, even though I want to study c-Src specifically.
3. siRNA knockdown is easier to monitor (Western blot of target protein, qRT-PCR of target mRNA) than measuring kinase activity with radiolabeling techniques. Plus, most kinase activity assays are performed in vitro, and don't account for in vivo activity, which is the system your drug is actually being applied.
Overall, both small molecular inhibitors and siRNA knockdown are great complimentary techniques in studying the effects of a particular enzyme. Good luck with your experiments!
I have used a variety of small molecule inhibitors. Whilst they are very simple and inexpensive to use, I have found that they aren't very specific! I found it best to use at least 2 or 3 inhibitors for each pathway to be able to have more confidence in my results (and to validate each inhibitor with a control such as transferrin or CTB). Good luck!
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