The cyclooxygenase step in the conversion of arachidonic acid is a key point in the biosynthesis of prostanoids, managed by two enzymatic isoforms. In the following study we focused on the mechanism of the inhibitory action of CGP 28238 and structurally-related indanone derivatives using purified enzymes. Consistent with our earlier studies on cell systems, CGP 28238 revealed selective inhibition of cyclooxygenase-2. The process affects the bisoxygenase subunit time-dependently, and is reversible in the early phase of inhibition. From structure-activity relationships, we propose the formation of a Schiff base between the oxo-groups of CGP 28238 and an amino group at the active site providing additional binding forces for an effective inhibition of cyclooxygenase-2.