I have been doing some research on how Ibuprofen works on COX (prostagladin H2 synthese). So far, I have established, that aspirin (another NSID) inhibits COX by ireversible binding to Ser530 and thereby blocking the substrate from entering the active site.
The only problem is, that it is Ibuprofen we are dealing with. Otherwise it would be all dandy.
The question is therefore:
How does Ibuprofen inhibit COX? Does it inhibit by ireversible binding to Ser530 as Aspirin or is it something else?

Thanks in advance,
Stefan

Cyclooxygenase Structure and Mechanism
How Aspirin and NSAIDs Work

http://cti.itc.virginia.edu/~cmg/Demo/pdb/cycox/cycox.html

I know this does not completely answer your question but this is a very cute site with 3D animation of COX and drug binding events.

I would imagine it is of interest to anyone who works with COX.

It does state that Aspirin (and also bromoaspirin) is the only NSAID which covalently modifies a residue in the tunnel, thus irreversibly inactivating both COX-1 and COX-2.

Ibuprofen acts instead by competing in a reversible fashion for the substrate binding site in the tunnel. It does not state the nature of the non-covalent interactions that it forms and with which residue /s it interacts.

Hi,

I dont know how it works, but I can suggest some other things you can look at.

1. There is an assay ( commercially available) which detects the cox-2 activity ( elisa assay).
2. Also it may so happen that COX-2 promoter /cox mRNA stabilty might be affected by the drugs.

It is worth doing these experiments

If you know how to work with crystal structure files, here is the PDB file "1EQG" which is the 2.6 Angstrom Model of ovine COX-1 complexed with Ibuprofen


http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1EQG

Here is Iboprofen in complex with COX 1

The shortest distance I found was 2.7 Angstroms between the Arginine 120 and the carboxy group of Ibuprofen.



The green molecule is the ibuprofen. The nitrogens from the Arginine are in blue and the oxygens from the ibuprofen are in red.

If the image is not working above click on the link below

http://img125.imageshack.us/my.php?image=ibuprofenincoxpv3.png

Aha! here's your reference.

Structural Analysis of NSAID Binding by Prostaglandin H2 Synthase: Time-Dependent and Time-Independent Inhibitors Elicit Identical Enzyme Conformations

Biochemistry. 2001 May 1;40(17):5172-80

Ibuprofen is the bottom right hand panel

Wow! That is just great. You really have got me going now. Thanks a lot!
But just a single question to montgomj - what software do you use to visualize proteins from pdb-files?

I used PyMOL to create the image I posted for you.

http://pymol.sourceforge.net/

It is open source so just download it and get going. bookmark/download the user manual too. it has some good tutorials to get you going on how to use it.