I'm trying to screen natural inhibitors for MMP-1,-8,-13. I have a compound that fits well and exhibits interactions within all three pockets. But, in MMP-1, the ZN interaction is absent while all other residues interact. Can I call it a common inhibitor even if I do not have ZN interactions with my inhibitor in the active site?
Performing a reverse zymography could be the easiest option to give a try for inhibition studies of MMP-1.
Attached paper could be helpful.
An inhibitor does not have to chelate the active site zinc in order to an inhibitor. Competitive inhibitors merely mean that the inhibitor binds to the same enzyme form as the substrate. The inhibitor does not have to bind to the active site necessarily for any type of inhibition nor bind the active site zinc. I would recommend using standard fluorometric assays because then one can determine the type of inhibition, for example, such as competitive, non competitive or uncompetitive. There is the caveat with the fluorescent substrates that you are not using natural substrates, so that the type of inhibition could be somewhat of an artifact. The zymography is a nice alternative as Sree has mentioned. But first, I would stick to the FRET substrates and just see if the inhibitor actually prevents turnover of the substrate. And I would do the reactions under low and high substrate concentrations so that you won't miss if it is a competitive vs. non competitive or uncompetitive inhibitor. The concentrations of substrate used should be above and below its Km.
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