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Cyclooxygenase 2 (COX-2)
Domains

Cyclooxygenase (also known as prostaglandin endoperoxide synthase or PGH2 synthase) catalyzes the oxidation and cyclization of arachidonic acid - the committed step in the production of prostaglandins. The enzyme contains three domains. The first domain (shown in red)is similar to the epidermal growth factor (EGF) protein. The second domain consists of four alpha-helices (shown in green) which form the transmembrane region. The third domain (shown in blue)is the catalytic site containing both cyclooxygenase and peroxidase activity.
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Cyclooxygenase 2
Hydrophobic Tunnel

The substrate (arachidonic acid) enters the enzyme through a long, narrow, hydrophobic tunnel. The opening of the tunnel is framed by three of the membrane-domain alpha-helices. The walls of the tunnel (shown in orange) are formed by four alpha-helices.
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Cyclooxygenase 2
Peroxidase Active Site

The peroxidase active site lies at the end of the hydrophobic tunnel. The tyrosine residue at 385 (shown as stick model) is believed to abstract a hydrogen from the subtrate during the peroxidase reaction and form a radical. A heme (shown as ball and stick model) is necessary for the reaction and the formation of the radical.
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Cyclooxygenase 2
Substrate Anchoring

The arginine residue (shown as a ball and stick model) is believed to anchor the carboxylate form of the substrate by an ion-pair.
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Cyclooxygenase 2
Inhibition

The non-steroidal anti-inflammatory drugs (NSAIDS)inhibit the cyclooxygenase enzyme. Some of these drugs inhibit both COX-1 and COX-2 (aspirin, advil, tylenol). Other drugs (like Vioxx) selectively inhibit COX-2 over COX-1.

There are four broad classes of NSAIDS. The first class irreversibly inactivates the enzyme by covalent modification. Acetylsalicylate (aspirin) is an example of this class.

The second class of NSAIDS work by reversible competitive inhibition with the substrate. An example of this second class is ibuprofem (sold as Motrin, Nuprin, and Advil).

The third class of NSAIDS work by forming salt bridges with the enzyme that results in a slow, time-dependent inhibition. Examples include flurbiprofen and indomethacin.

The fourth class of NSAIDS are selective for COX-2 and inhibit in a slow, time-dependent process. Examples of these drugs include Vioxx and Celebrex.
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Cyclooxygenase 2
Aspirin Acetylation Site

The serine residue at position 530 (shown as a ball and stick model) is acetylated by aspirin, blocking the substrate from reaching the catalytic site at the end of the tunnel. Other analgesic agents such as bromoaspirin work similarly by covently modifying the enzyme. These agents comprise the first class of non-steroidal anti-inflammatory drugs (NSAIDS).
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Flurbiprofen
Structure

The structure of flurbiprofen is shown. The phenyl group is shown in blue. The fluorophenyl ring is shown in green with the fluorine atom in orange. The carboxylate group is shown in purple with the oxygen atoms in red.
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Cyclooxygenase 2
Flurbiprofen Inhibition

Flurbiprofen is an example of a class 3 NSAID. It works by binding in the hydrophic tunnel of the enzyme, blocking access to the active site. The carboxylate of flurbiprofen forms a salt bridge with the arginine residue at 120 and a hydrogen bond with the tyrosine residue at 355 (white). The phenyl ring interacts with the glycine residue at 526 and the serine residue at 530 (magenta). The fluorophenyl ring has van der Waals interactions with the valine residue at 349 and the alanine residue at 527 (brown).
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Indomethacin
Structure

The structure of indomethacin is shown. The main features are the benzoyl ring (orange), the benzoyl chlorine atom (green), an indole ring (blue) and a carboxylate group (pink). The oxygen atoms are shown in red.
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Cyclooxygenase 2
Indomethacin Inhibition

Indomethacin is another example of the third class of NSAIDS. It works in the same way as flurbiprofen, binding deep in the hydrophobic tunnel and blocking entrance to the active site. The carboxylate of indomethacin forms a salt bridge with the arginine residue at 120 (brown). The benzoyl group of indomethacin interacts hydrophobically with residues deep in the tunnel (leucine, phenylalanine, tyrosine and tryptophan, all shown in purple). In addition, the indole ring interacts with the valine and serine residues (shown in white).
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SC-558
Structure

The structure of the NSAID SC-558 is shown. It has a central pyrazole ring (grey with orange nitrogens). The bromophenyl ring is shown in cyan blue with a brown bromine atom. The trifluoromethyl group is shown in purple with light purple fluorine atoms. The phenyl ring is shown in green with an attached psulphonamide group in yellow (oxygens in red, nitrogens in orange, and hydrogens in white).
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Cyclooxygenase 2
SC-558 Inhibition

SC-558 is an example of a class 4 NSAID. It functions in a similar manner to class 3 NSAIDs, binding noncovalently to the enzyme in the hydrophobic tunnel and blocking access to the active site. Unlike class 3 NSAIDs however, SC-558 and other class 4 NSAIDs are selective for COX-2 over COX-1 (19,000 fold for SC-558).

The bromophenyl ring and trifluoromethyl group bind simililarly to indomethacin and flurbiprofen. The bromophenyl ring is bound by a hydrophobic cavity formed by Phe 381, Leu 384, Tyr 385, Trp 387, Phe 513, Ser 530, Gly 526 and Ala 527 (shown in brown). The trifuoromethyl group is bound by a pocket formed by Met 113, Val 116, Val 349, Tyr 355, Leu 359 and Leu 531 (shown in magenta).

The binding of the phenylsulphonamide group is responsible for the selectivity of SC-558. It binds in a pocket of COX-2 which is not accessible in COX-1 due to two isoleucine to valine substitutions (shown in pink). The phenyl ring is bound by hydrophobic residue Leu 352, Tyr 355, Phe 518, Val 523 and Ser 353 (shown in white). The sulphonamide group interacts with His 90, Gln 192 and Arg 513 (shown in green).
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References
Kurumbail, RG et al. Structural basis for selective inhibition of cyclooxygenase-2 by anti-inflammatory agents. Nature. Dec 1996. 384: 644-648.

Garrett, RH and Grisham, CM. Biochemistry 3rd ed. Thomson Brooks/Cole; Belmont, CA. 2005.
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