I performed virtual screening of the natural products from the ZINC library with the aim to identify compounds against the b5 active site of the proteasome. Carfilzomib and epoxomicin were positive controls. The best two ligands, with the lowest estimated binding affinity, were selected for biological evaluation using in vitro assays of purified chymotrypsin-like 20S proteasome. The standard assay lab method was performed in triplicate and to measure b5 activity Suc-LLVY-AMC was used. So far I plotted AFU vs time curve of the average of that two compounds in 8 different concentrations; I calculated % inhibitor remaining activity and IC50.
Which test should I perform to compare these two inhibitors and use my data further? I'm thinking about doing SE and t-test.
I would appreciate any suggestions. Thank you!
Measure the IC50 for each inhibitor. Make the measurements 3 times, at least, if you want to use a t-test to see of there is a statistically significant difference between the IC50s.
You can compare IC50 values indeed. Be aware though that epoxomicin and carfilzomib are covalently binding, irreversible inhibitors of the proteasome and therefore will display a time dependent IC50 value (the longer you pre-incubate, the more will bind, the lower the IC50; hence better to speak of an "apparent IC50). If your other molecules are reversible binders, a direct comparison is a bit tricky, because the inhibitory mechanism will be different.
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