Journal of Computer-Aided Molecular Design

, Volume 19, Issue 1, pp 17–31 | Cite as

Free energy perturbation approach to the critical assessment of selective cyclooxygenase-2 inhibitors



The discovery of selective cyclooxygenase-2 (COX-2) inhibitors represents a major achievement of the efforts over the past few decades to develop therapeutic treatments for inflammation. To gain insights into designing new COX-2-selective inhibitors, we address the energetic and structural basis for the selective inhibition of COX isozymes by means of a combined computational protocol involving docking experiment, force field design for the heme prothetic group, and free energy perturbation (FEP) simulation. We consider both COX-2- and COX-1-selective inhibitors taking the V523I mutant of COX-2 to be a relevant structural model for COX-1 as confirmed by a variety of experimental and theoretical evidences. For all COX-2-selective inhibitors under consideration, we find that free energies of binding become less favorable as the receptor changes from COX-2 to COX-1, due to the weakening and/or loss of hydrogen bond and hydrophobic interactions that stabilize the inhibitors in the COX-2 active site. On the other hand, COX-1-selective oxicam inhibitors gain extra stabilization energy with the change of residue 523 from valine to isoleucine because of the formations of new hydrogen bonds in the enzyme-inhibitor complexes. The utility of the combined computational approach, as a valuable tool for in silico screening of COX-2-selective inhibitors, is further exemplified by identifying the physicochemical origins of the enantiospecific selective inhibition of COX-2 by α-substituted indomethacin ethanolamide inhibitors.


cyclooxygenase inhibitors force field design free energy perturbation molecular dynamics simulation selectivity 


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Copyright information

© Springer 2005

Authors and Affiliations

  1. 1.School of Chemistry and Molecular Engineering, and Center for Molecular CatalysisSeoul National UniversitySeoulSouth Korea

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