The binding mode of petrosaspongiolide M to the human group IIA phospholipase A2: Exploring the role of covalent and noncovalent interactions in the inhibition process

Chemistry - A European Journal

Volumn 15, Issue 5, 2009, Pages 1155-1163

  Monti, Maria Chiara ^a   Casapullo, Agostino ^a   Cavasotto, Claudio N ^b   Tosco, Alessandra ^a   Dal Piaz, Fabrizio ^a   Ziemys, Arturas ^b   Margarucci, Luigi ^a   Riccio, Raffaele ^a  

^a UNIVERSITY OF SALERNO   (Italy)

^b UNIVERSITY OF TEXAS   (United States)

Author keywords

Enzymes; Inhibitors; Natural products; Phospholipases; Protein interactions

Indexed keywords

BINDING ENERGY; CATALYSTS; NITROGEN COMPOUNDS; PERMANENT MAGNETS; PLANTS (BOTANY); PROTEINS;

ACTIVE SITES; AMPHIPHILIC(AP); BINDING MODES; BINDING SURFACES; ENZYME MOLECULES; IMINE FORMATION; INHIBITORS; NATURAL PRODUCTS; NON COVALENT INTERACTIONS; PHOSPHOLIPASE (PLC); PHOSPHOLIPASES; PROTEIN INTERACTIONS; SECRETORY PHOSPHOLIPASE; SUPRAMOLECULAR COMPLEXES;

ENZYMES;

DRUG DERIVATIVE; ENZYME INHIBITOR; LIGAND; OLEANOLIC ACID; PETROSASPONGIOLIDE M; PHOSPHOLIPASE A2;

ARTICLE; CHEMICAL MODEL; CHEMISTRY; CONFORMATION; HUMAN; KINETICS; METABOLISM; PROTEIN BINDING; STRUCTURE ACTIVITY RELATION; SURFACE PLASMON RESONANCE;

ENZYME INHIBITORS; HUMANS; KINETICS; LIGANDS; MODELS, CHEMICAL; MOLECULAR CONFORMATION; OLEANOLIC ACID; PHOSPHOLIPASES A2; PROTEIN BINDING; STRUCTURE-ACTIVITY RELATIONSHIP; SURFACE PLASMON RESONANCE;

EID: 58449114054     PISSN: 09476539     EISSN: 15213765     Source Type: Journal    
DOI: 10.1002/chem.200801512     Document Type: Article

References (55)

1. O. G. Mouritsen in Life-As a Matter of Fat: The Emerging Science of Lipidomics, Springer, Berlin, 2005.
2. E. A. Dennis, Adv. Exp. Med. Biol. 1978, 101, 165-175.
3. K. Best, A. Ohran, A. Hawes, T. Hazlett, E. Gratton, A. Judd, J. Bell, Biochemistry 2002, 41, 13982-13988.
4. W. V. Winstead, J. Balsinde, E. A. Dennis, Biochim. Biophys. Acta Mol. 2000, 1488, 28-39.
5. S. Bezzine, J. Boiling, A. G. Singer, S. L. Veateh, S. L. Keller, M. H. Gelb, J. Biol. Chem. 2002, 277, 48523-48534.
6. S. Canaan, R. Nielsen, F. Ghomashchi, B. Robinson, M. Gelb, J. Biol. Chem. 2003, 275, 30984-30990.
7. a) F. Dal, Piaz, A. Casapullo, A. Randazzo, R. Riccio, P. Pucci, G. Marino, L. Gomez-Paloma, ChemBioChem 2002, 3, 664-671;
8. b) M. C. Monti, A. Casapullo, R. Riccio, L. Gomez-Paloma, Bioorg. Med. Chem. 2004, 12, 1467-1474;
9. c) M. C. Monti, A. Casapullo, R. Riccio, L. Gomez-Paloma, FEBS Lett. 2004, 578, 269-274;
10. d) M. C. Monti, A. Casapullo, R. Riccio, L. Gomez-Paloma, Rapid Commun. Mass Spectrom. 2005, 19, 303-308;
11. e) M. C. Monti, A. Casapullo, M. V. .D'Auria, R. Riccio, L. Gomez-Paloma, ChemBioChem 2006, 7, 971-980;
12. f) L. Gomez-Paloma, M. C. Monti, S. Terracciano, A. Casapullo, R. Riccio, Curr. Org. Chem. 2005, 9, 1419-1427;
13. g) S. Terracciano, M. Rodriguez, M. Aquino, M. C. Monti, A. Casapullo, R. Riccio, L. Gomez-Paloma, Curr. Med. Chem. 2006, 13, 1947-1969.
14. A. Randazzo, C. Debitus, L. Minale, P. Garcia Pastor, M. J. Alcazar, M. Payà, L. Gomez-Paloma, J. Nat. Prod. 1998, 61, 571-575.
15. 4), and it has been shown to modulate the expression of inducible cyclooxygenase and nitric oxide synthetase (COX2 and iNOS) by interfering with the nuclear factor κB (NF-κB) pathways. For further details, see: a) P. Garcia-Pastor, A. Randazzo, L. Gomez-Paloma, M. J. Alcaraz, M. Payà, J. Pharmacol. Exp. Ther. 1999, 289, 166-167;
16. b) I. Posadas, M. C. Terencio, A. Randazzo, L. Gomez-Paloma, M. Payà, M. J. Alcaraz, Biochem. Pharmacol. 2003, 65, 887-895;
17. c) J. Busserolles, M. Paya, M. V. D'Auria, L. Gomez-Paloma, M. J. Alcaraz, Biochem. Pharmacol. 2005, 69, 1433-1440.
18. a) R. W. Schevitz, N. J. Bach, D. G. Carlson, N. Y. Chirgadze, D. K. Clawson, R. D. Dillaheim, S. E. Draheim, L. W. Hartley, N. D. Jones, E. D. Mihelich, J. L. Olkowski, D. W. Snyder, C. Sommers, J. P. Wery, Nat. Struc. Biol. 1995, 2, 458-465;
19. b) J. Balsinde, M. Balboa, P. Insel, E. A. Dennis, Annu. Rev. Pharmacol. Toxicol. 1999, 39, 175-189;
20. c) K. A. Hansford, R. C. Ried, C. I. Clark, J. D. Tyndall, M. W. Whitehouse, T. Guthrie, R. P. McGeary, K. Schafer, J. L. Martin, D. P. Fairlie, ChemBiochem 2003, 4, 181-185;
21. d) M. D. Guerrero, M. Aquino, I. Bruno, M. C. Terencio, M. Paya, R. Riccio, L. Gomez-Paloma, J. Med. Chem 2007, 50, 2176-2184.
22. Q. Dong, M. Patel, K. F. Scott, G. G. Graham, P. J. Russell, P. Sved, Cancer Lett. 2006, 240, 9-16.
23. a) G. V. Richieri, A. M. Klenfield, Anal. Biochem. 1995, 229, 256-263;
24. b) T. Bayburt, M. Gelb, Biochemistry 1997, 36, 3216-3231.
25. D. C. Wilton, Biochem. J. 1990, 270, 163-166.
26. D. C. Wilton, Biochem. J. 1990, 266, 435-439.
27. A. Shevchenko, M. Wilm, O. Worm, M. Mann, Anal. Chem. 1996, 68, 850-858.
28. M. J. Cannon, G. A. Papalia, I. Navratilova, R. J. Fisher, L. R. Roberts, K. M. Worthy, A. G. Stephen, G. R. Marchesini, E. J. Collins, D. Casper, H. Qiu, D. Satpaev, S. F. Liparoto, D. A. Rice, I. I. Gorshkova, R. J. Darling, D. B. Bennett, M. Sekar, E. Hommema, A. M. Liang, E. S. Day, J. Inman, S. M. Karlicek, S. J. Ullrich, D. Hodges, T. Chu, E. Sullivan, J. Simpson, A. Rafique, B. Luginbühl, S. N. Westin, M. Bynum, P. Cachia, Y. J. Li, D. Kao, A. Neurauter, M. Wong, M. Swanson, D. G. Myszka, Anal. Biochem. 2004, 330, 98-113.
29. C. N. Cavasotto, A. J. Orry, N. J. Murgolo, M. F. Czarnicki, S. A. Kocsi, B. E. Hawes, K. A. O'Neill, H. Hine, M. S. Burton, J. H. Voight, R. A. Abagyan, M. L. Bayne, F. J. Monsma, J. Med. Chem. 2008, 51, 581-588.
30. C. N. Cavasotto, R. A. Abagyan, J. Mol. Biol. 2004, 337, 209-225.
31. C. N. Cavasotto, G. Liu, S. Y. James, P. D. Hobbs, V. J. Peterson, A. A. Bhattacharya, S. K. Kolluri, X. K. Zhang, M. Leid, R. A. Abagyan, R. C. Liddington, M. I. Dawson, J. Med. Chem. 2004, 47, 4360-4372.
32. C. N. Cavasotto, A. J. W. Orry, R. A. Abagyan, Proteins Struct. Funct. Bioinf. 2003, 51, 423-433.
33. M. C. Monti, A. Casapullo, C. N. Cavasotto, A. Napolitano, R. Riccio, ChemBioChem 2007, 8, 1585-1591.
34. The different chromatographic profile of PM when it is submitted in the presence or absence of DOPG micelles to low-resolution sizeexclusion chromatography supported this hypothesis (data not shown). Actually, after preincubation with the micelles, PM was recovered coeluting with the DOPG vesicles in a unique chromatographic fraction.
35. a) G. V. Richieri, A. M. Kleinfield, Anal. Biochem. 1995, 229, 256-263;
36. b) A. Kinkaid, D. C. Wilton, Biochem. J. 1991, 278, 843-848.
37. A. Buckland, D. C. Wilton, Biochim. Biophys. Acta 1998, 1391, 367-376.
38. U. K. Laemmli, Nature 1970, 227, 680-685.
39. A. Shevchenko, M. Wilm, O. Worm, M. Mann, Anal. Chem. 1996, 68, 850-858.
40. R. Abagyan, M. Totrov, D. Kuznetsov, J. Comput. Chem. 1994, 15, 488-506.
41. F. A. Momany, R. F. McGuire, A. W. Burgess, H. A, Scheraga, J. Phys. Chem. 1975, 79, 2361-2381.
42. G. Nemethy, K. D. Gibson, K. A. Palmer, C. N. Yoon, M. G. Paterlini, A. Zagari, S. Rumsey, H. A. Scheraga, J. Phys. Chem. 1992, 96, 6472-6484.
43. T. Ooi, M. Oobatake, G. Nemethy, H. A. Scheraga, Proc. Natl. Acad. Sci, USA 1987, 84, 3086-3090.
44. M. Totrov, R. Abagyan, Biopolymers 2001, 60, 124-133.
45. R. Abagyan, M. Totrov, J. Mol. Biol. 1994, 235, 983-1002.
46. a) Z. Li, H. A. Scheraga, Proc. Natl. Acad. Sci. USA 1987, 84, 6611-6615;
47. b) N. A. Metropolis, A. W. Rosenbluth, N. M. Rosenbluth, A. H. Teller, E. Teller, J. Chem. Phys. 1953, 21, 1087-1092.
48. R. Abagyan, P. Argos, J. Mol. Biol. 1992, 225, 519-532.
49. M. Totrov, R. Abagyan in Drug-receptor thermodynamics: Introduction and experimental applications (Ed.: R. B. Raffa), Wiley, New York, 2001.
50. A. D. MacKerell, D. Bashford, M. Bellott, R.L. Dunbrack, J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, M. Karplus, J. Phys. Chem. B 1998, 102, 3586-3616.
51. M. Schlenkrich, J. Brickmann, A. D. MacKerell, M. Karplus, Biological Membranes: A Molecular Perspective from Computation and Experiment (Eds.: K. M. Merz, B. Roux), Birkhauser, Boston, 1996, p. 31.
52. Z. Cournia, J. C. Smith, G. M. Ullmann, J. Comput. Chem. 2005, 26, 1383-1399.
53. J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kale, K. Schulten, J. Comput. Chem. 2005, 26, 1781-1802.
54. S. Feller, Y. H. Zhang, R. W. Pastor, B. R. Brooks, J. Chem. Phys. 1995, 103, 4613-4621.
55. T. Darden, D. York, L. Pedersen, J. Chem. Phys. 1993, 98, 10089-10092.