Molecular basis of cyclooxygenase enzymes (COXs) selective inhibition

Proceedings of the National Academy of Sciences of the United States of America

Volumn 107, Issue 12, 2010, Pages 5411-5416

  Limongelli, Vittorio ^a,b   Bonomi, Massimiliano ^a   Marinelli, Luciana ^b   Gervasio, Francesco Luigi ^c   Cavalli, Andrea ^d,e   Novellino, Ettore ^b   Parrinello, Michele ^a  

^a UNIVERSITY OF LUGANO   (Switzerland)

^b UNIVERSITY OF NAPLES FEDERICO II   (Italy)

^c Centro Nacional de Investigaciones Oncológicas   (Spain)

^d UNIVERSITY OF BOLOGNA   (Italy)

^e ISTITUTO ITALIANO DI TECNOLOGIA   (Italy)

Author keywords

COX selectivity; Coxibs; Metadynamics; Nonsteroidal anti inflammatory drugs; Path collective variables

Indexed keywords

4 [5 (4 BROMOPHENYL) 3 TRIFLUOROMETHYL 1H PYRAZOL 1 YL]BENZENESULFONAMIDE; CYCLOOXYGENASE 1; CYCLOOXYGENASE 2; PROSTAGLANDIN SYNTHASE;

ANALYTIC METHOD; ARTICLE; CONFORMATIONAL TRANSITION; DISSOCIATION; ENZYME INHIBITION; MOLECULAR DYNAMICS; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN INTERACTION; SIMULATION;

ANTI-INFLAMMATORY AGENTS, NON-STEROIDAL; BINDING SITES; BIOPHYSICAL PHENOMENA; CATALYTIC DOMAIN; CYCLOOXYGENASE 1; CYCLOOXYGENASE 2; CYCLOOXYGENASE INHIBITORS; HUMANS; KINETICS; MODELS, MOLECULAR; PROSTAGLANDIN-ENDOPEROXIDE SYNTHASES; PYRAZOLES; THERMODYNAMICS;

EID: 77950450012     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0913377107     Document Type: Article

References (36)

1. Cuzick J, et al. (2009) Aspirin and non-steroidal anti-inflammatory drugs for cancer prevention: An international consensus statement. Lancet Oncol 10:501-507.
2. Smith W-L, Borgeat P, Fitzpatrick F-A (1991) Biochemistry of Lipids, Lipoproteins and Membranes, eds D-E Vance and J Vance (Elsevier Science, Amsterdam; London), pp 297-3253.
3. Scheen A-J (2004) [Withdrawal of rofecoxib (Vioxx): What about cardiovascular safety of COX-2 selective non-steroidal anti-inflammatory drugs?]. Revue médicale de Liège 59:565-569.
4. Kearney P-M, et al. (2006) Do selective cyclo-oxygenase-2 inhibitors and traditional non-steroidal anti-inflammatory drugs increase the risk of atherothrombosis? Meta-analysis of randomised trials. BMJ 332:1302-1308.
5. Chen L-C, Ashcroft D-M (2007) Risk of myocardial infarction associated with selective COX-2 inhibitors: Meta-analysis of randomised controlled trials. Pharmacoepidemiol Drug Saf 16:762-772.
6. Kurumbail R-G, et al. (1996) Structural basis for selective inhibition of cyclooxygenase-2 by anti-inflammatory agents. Nature 384:644-648. (Pubitemid 27021518)
7. Copeland R-A, et al. (1994) Mechanism of selective inhibition of the inducible isoform of prostaglandin G/H synthase. Proc Natl Acad Sci USA 91:11202-11206.
8. Lanzo C-A, Sutin J, Rowlinson S, Talley J, Marnett L-J (2000) Fluorescence quenching analysis of the association and dissociation of a diarylheterocycle to cyclooxygenase-1 and cyclooxygenase-2: Dynamic basis of cyclooxygenase-2 selectivity. Biochemistry-US 39:6228-6234. (Pubitemid 30327100)
9. Walker M-C, et al. (2001) A three-step kinetic mechanism for selective inhibition of cyclo-oxygenase-2 by diarylheterocyclic inhibitors. Biochem J 357:709-718.
10. Yuan C, Rieke C-J, Rimon G, Wingerd B-A, Smith W-L (2006) Partnering between monomers of cyclooxygenase-2 homodimers. Proc Natl Acad Sci USA 103:6142-6147.
11. Prusakiewicz J-J, Duggan K-C, Rouzer C-A, Marnett L-J (2009) Differential sensitivity and mechanism of inhibition of COX-2 oxygenation of arachidonic acid and 2-arachidonoylglycerol by ibuprofen and mefenamic acid. Biochemistry-US 48:7353-7355.
12. Barducci A, Bussi G, Parrinello M (2008) Well-tempered metadynamics: A smoothly converging and tunable free-energy method. Phys Rev Lett 100:020603.
13. Laio A, Parrinello M (2002) Escaping free-energy minima. Proc Natl Acad Sci USA 99:12562-12566.
14. Picot D, Loll P-J, Garavito R-M (1994) The x-ray crystal structure of the membrane protein prostaglandin H2 synthase-1. Nature 367:243-249. (Pubitemid 24051139)
15. Selinsky B-S, Gupta K, Sharkey C-T, Loll P-J (2001) Structural analysis of NSAID binding by prostaglandin H-2 synthase: Time-dependent and time-independent inhibitors elicit identical enzyme conformations. Biochemistry-US 40:5172-5180. (Pubitemid 32373999)
16. So O-Y, Scarafia L-E, Mak A-Y, Callan O-H, Swinney D-C (1998) The dynamics of prostaglandin H synthases - Studies with prostaglandin H synthase 2 Y355F unmask mechanisms of time-dependent inhibition and allosteric activation. J Biol Chem 273:5801-5807.
17. Gear C-W, Kevrekidis I-G, Theodoropoulos C (2002) 'Coarse' integration/bifurcation analysis via microscopic simulators: Micro-Galerkin methods. Comput Chem Eng 26:941-963.
18. Hummer G, Kevrekidis I-G (2003) Coarse molecular dynamics of a peptide fragment: Free energy, kinetics, and long-time dynamics computations. J Chem Phys 118:10762-10773.
19. Parrinello M (2008) Physical Biology from Atoms to Medicine, ed AH Zewail (Imperial College Press, London), pp 247-265.
20. Luong C, et al. (1996) Flexibility of the NSAID binding site in the structure of human cyclooxygenase-2. Nat Struct Biol 3:927-933. (Pubitemid 26398325)
21. Branduardi D, Gervasio F-L, Parrinello M (2007) From A to B in free energy space. J Chem Phys 126:054103.
22. Bonomi M, Branduardi D, Gervasio F-L, Parrinello M (2008) The unfolded ensemble and folding mechanism of the C-terminal GB1 beta-hairpin. J Am Chem Soc 130:13938-13944.
23. Gervasio F-L, Laio A, Parrinello M (2005) Flexible docking in solution using metadynamics. J Am Chem Soc 127:2600-2607. (Pubitemid 40327822)
24. Masetti M, Cavalli A, Recanatini M, Gervasio F-L (2009) Exploring complex protein-ligand recognition mechanisms with coarse metadynamics. J Phys Chem B 113:4807-4816.
25. Soliva R, Almansa C, Kalko S-G, Luque F-J, Orozco M (2003) Theoretical studies on the inhibition mechanism of cyclooxygenase-2. Is there a unique recognition site?. J Med Chem 46:1372-1382. (Pubitemid 36512701)
26. Price M-L-P, Jorgensen W-L (2000) Analysis of binding affinities for celecoxib analogues with COX-1 and COX-2 from combined docking and Monte Carlo simulations and insight into the COX-2/COX-1 selectivity. J Am Chem Soc 122:9455-9466.
27. Morris G-M, et al. (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 19:1639-1662.
28. Huey R, Morris G-M, Olson A-J, Goodsell D-S (2007) A semiempirical free energy force field with charge-based desolvation. J Comput Chem 28:1145-1152.
29. Gierse J-K, et al. (1996) A single amino acid difference between cyclooxygenase-1 (COX-1) and -2 (COX-2) reverses the selectivity of COX-2 specific inhibitors. J Biol Chem 271:15810-15814.
30. Dogne J-M, Hanson J, Supuran C, Pratico D (2006) Coxibs and cardiovascular side-effects: From light to shadow. Curr Pharm Des 12:971-975.
31. Wang J, Cieplak P, Kollman P-A (2000) How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?. J Comput Chem 21:1049-1074.
32. Cornell W-D, et al. (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 117:5179-5197.
33. Phillips J-C, et al. (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26:1781-1802.
34. Humphrey W, Dalke A, Schulten K (1996) VMD: Visual molecular dynamics. J Mol Graphics 14:33-38.
35. DeLano W-L (2002) The PyMOL Molecular Graphics System (DeLano Scientific, San Carlos, CA).
36. Rimon G, et al. (2010) Coxibs interfere with the action of aspirin by binding tightly to one monomer of cyclooxygenase-1. Proc Natl Acad Sci USA 107:28-33.