A preliminary in silico lead series of 2-phthaIimidinoglutaric acid analogues designed as MMP-3 inhibitors

Journal of Chemical Information and Modeling

Volumn 46, Issue 5, 2006, Pages 2104-2109

  Amin, Elizabeth A ^a   Welsh, William J ^b  

^a University of Minnesota   (United States)

^b RUTGERS ROBERT WOOD JOHNSON MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALCOHOLS; DISEASES; DRUG PRODUCTS; ENZYME INHIBITION; MEDICAL APPLICATIONS; SYNTHESIS (CHEMICAL); TUMORS; WATER;

METASTASIS; MOLECULAR FIELD ANALYSIS; PHTHAIIMIDINOGLUTARIC ACIDS;

ENZYMES;

GLUTARIC ACID; GLUTARIC ACID DERIVATIVE; PROTEINASE INHIBITOR; STROMELYSIN; THALIDOMIDE;

ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; DRUG ANTAGONISM; METABOLISM; QUANTITATIVE STRUCTURE ACTIVITY RELATION;

BINDING SITES; GLUTARATES; MATRIX METALLOPROTEINASE 3; MODELS, MOLECULAR; PROTEASE INHIBITORS; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; THALIDOMIDE;

EID: 33750323818     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci0601362     Document Type: Article

References (46)

1. Morgunova, E.; Tuuttila, A.; Bergmann, U.; Isupov, M.; Lindqvist, Y.; Schneider, G.; Tryggvason, K. Structure of human pro-matrix metalloproteinase-2: Activation mechanism revealed. Science 1999, 284, 1667-1670.
2. Whittaker, M.; Floyd, C.; Brown, P.; Gearing, A. Design and therapeutic application of matrix metalloproteinase inhibitors. Chem. Rev. 1999, 99, 2735-2776.
3. Pikul, S.; Dunham, K.; Almstead, N.; De, B.; Natchus, M.; Anastasio, M.; McPhail, S.; Snider, C.; Taiwo, Y.; Chen, L.; Dunaway, C.; Gu, F.; Mieling, G. Design and synthesis of phosphinamide-based hydroxamic acids as inhibitors of matrix metalloproteinases. J. Med. Chem. 1999, 42, 87-94.
4. Fichter, M.; Korner, U.; Schomburg, J.; Jennings, L.; Cole, A.; Mollenhauer, J. Collagen degradation products modulate matrix metalloproteinase expression in cultured articular chondrocytes. J. Orthop. Res. 2006, 24, 63-70.
5. Kanesaka, T.; Mori, M.; Hattori, T.; Oki, T.; Kuwabara, S. Serum matrix metalloproteinase-3 levels correlate with disease activity in relapsing-remitting multiple sclerosis. J. Neural. Neurosurg. Psychiatry 2006, 77, 185-188.
6. Evio, S.; Tarkkila, L.; Sorsa, T.; Furuholm, J.; Valimaki, M.; Ylikorkala, O.; Tiitinen, A.; Meurman, J. Effects of alendronate and hormone replacement therapy, alone and in combination, on saliva, periodontal conditions and gingival crevicular fluid matrix metallo-proteinase-8 levels in women with osteoporosis. Oral Dis. 2006, 12, 187-193.
7. Mendes, O.; Kim, H.; Stoica, G. Expression of MMP2, MMP9 and MMP3 in breast cancer brain metastasis in a rat model. Clin. Exp. Metastasis 2005, 22, 237-246.
8. Bachmeier, B.; Albini, A.; Vene, R.; Benelli, R.; Noonan, D.; Weigert, C.; Weiler, C.; Lichtinghagen, R.; Jochum, M.; Nerlich, A. Cell density-dependent regulation of matrix metalloproteinase and TIMP expression in differently tumorigenic breast cancer cell lines. Exp. Cell Res. 2005, 505, 83-98.
9. Malemud, C. Matrix metalloproteinases (MMPs) in health and disease: An overview. Front. Biosci. 2006, 11, 1696-1701.
10. Bokarewa, M.; Dahlberg, L.; Tarkowski, A. Expression and functional properties of antibodies to tissue inhibitors of metalloproteinases (TIMPs) in rheumatoid arthritis. Arthritis Res. Ther. 2005, 7, 1014-1022.
11. Lohmander, L.; Brandt, K.; Mazzuca, S.; Katz, B.; Larsson, S.; Struglics, A.; Lane, K. Use of the plasma stromelysin (matrix metalloproteinase 3) concentration to predict joint space narrowing in knee osteoarthritis. Arthritis Rheum. 2005, 52, 3160-3167.
12. Li, M.; Yamamoto, H.; Adachi, Y.; Maruyama, Y.; Shinomura, Y. Role of matrix metalloproteinase-7 (matrilysin) in human cancer invasion, apoptosis, growth, and angiogenesis. Exp. Biol. Med. 2006, 231, 20-27.
13. Przybylowska, K.; Kluczna, A.; Zadrozny, M.; Krawczyk, T.; Kulig, A.; Rykala, J.; Kolacinska, A.; Morawiec, Z.; Drzewoski, I.; Blasiak, J. Polymorphisms of the promoter regions of matrix metalloproteinases genes MMP-1 and MMP-9 in breast cancer. Breast Cancer Res. Treat. 2006, 95, 65-72.
14. Vihinen, P.; Ala-aho, R.; Kahari, V. Matrix metalloproteinases as therapeutic targets in cancer. Curr. Cancer Drug Targets 2005, 5, 203-220.
15. Chen, X.; Su, Y.; Fingleton, B.; Acuff, H.; Matrisian, L.; Zent, R.; Pozzi, A. Increased plasma MMP9 in integrin alpha 1-null mice enhances lung metastasis of colon carcinoma cells. Int. J. Cancer 2005, 116, 52-61.
16. Tas, F.; Duranyildiz, D.; Oguz, H.; Disci, R.; Kurul, S.; Yasaseyer, V.; Topuz, E. Serum matrix metalloproteinase-3 and tissue inhibitor of metalloproteinase-1 in patients with malignant melanoma. Med. Oncol. (Totawa, NJ, U.S.) 2005, 22, 39-44.
17. Kerkela, E.; Saarialho-Kere, U. Matrix metalloproteinases in tumor progression: Focus on basal and squamous cell skin cancer. Exp. Dermatol. 2003, 12, 109-125.
18. Becker, J.; Matey, A.; Rokosz, L.; Axel, M.; Burbaum, J.; Fitzgerald, P.; Cameron, P.; Esser, C.; Hagmann, W.; Hermes, J.; Springer, J. Stromelysin-1: Three-dimensional structure of the inhibited catalytic domain and of the C-truncated proenzyme. Protein Sci. 1995, 4, 1966-1976.
19. Gooley, P.; O'Connell, J.; Marcy, A.; Cuca, G.; Axel, M.; Caldwell, C.; Hagmann, W.; Becker, J. Comparison of the structure of human recombinant short form stromelysin by multidimensional heteronuclear NMR and X-ray crystallography. J. Biomol. NMR 1996, 7, 8-28.
20. Corral, L. G.; Kaplan, G.; Stirling, D.; Wu, M.; Chen, Y.; Moreira, A.; Muller, G. Selection of novel analogs of thalidomide with enhanced tumor necrosis factor-alpha inhibitory activity. Mol. Med. 1996, 2, 506-515.
21. Minchinton, A.; Fryer, K.; Wendt, K.; Clow, K.: Hayes, M. The effect of thalidomide on experimental tumors and metastases. Anti-Cancer Drugs 1996, 7, 339-343.
22. Kling, J. Redeeming thalidomide. Modern Drug Discovery 2000, June, 35-39.
23. Grover, J.; Vats, V.: Gopalakrishna, R.; Ramam, M. Thalidomide: A re-look. Natl. Med. J. India 2000, 13, 132-141.
24. Teo, S.; Stirling, D.; Zeldis, J. Thalidomide as a novel therapeutic agent: new uses for an old product. Drug Discovery Today 2005, 10, 107-114.
25. Moreira, A.; Kaplan. G.; Villahermosa, L.; Fajardo, T.; Abalos, R.; Cellona, R.; Balagon, M. Comparison of pentoxifylline, thalidomide and prednisone in the treatment of ENL. Int. J. Lepr. Other Mycobact. Dis. 1998, 66, 61-65.
26. Shimazawa, R.; Miyachi, H.; Takayama, H.; Kuroda, K.; Kato, F.; Kato, M.; Hashimoto, Y. Antiangiogenic activity of tumor necrosis factor-alpha production regulators derived from thalidomide. Biol. Pharm. Bull. 1999, 22, 224-226.
27. Folkman, J.; Browder, T.; Palmblad, J. Angiogenesis research: Guidelines for translation to clinical application. Thromb. Haemostasis 2001, 86, 23-33.
28. D'Amato, R.; Loughnan, M.; Flynn, E.; Folkman, J. Thalidomide is an inhibitor of angiogenesis. Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 4082-4085
29. Knight, R. IMiDs: A novel class of immunomodulators. Semin. Oncol. 2005, 32, S24-30.
30. Shah, J.; Swartz, G.; Papathanassiu, A.; Treston, A.; Fogler, W.; Madsen, J.; Green, S. Synthesis and enantiomeric separation of 2-phthalimidino-glutaric acid analogues: Potent inhibitors of tumor metastasis. J. Med. Chem. 1999, 42, 3014-3017.
31. Muller, G.; Corral, L.; Shire, M.; Wang, H.; Moreira, A.; Kaplan, G.; Stirling, D. Structural modifications of thalidomide produce analogs with enhanced tumor necrosis factor inhibitory activity. J. Med. Chem. 1996, 39, 3238-3240.
32. SYBYL, 6.7; SYBYL, 7.0; Tripos, Inc., St. Louis, MO.
33. Cramer, R.; Patterson, D.; Bunce, J. Effect of shape on binding of steroids to carrier proteins. J. Am. Chem. Soc. 1988, 110, 5959-5967.
34. Klebe, G.; Abraham, U.; Mietzner, T. Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity. J. Med. Chem. 1994, 37, 4130-4146.
35. Cheng, M.; De, B.; Pikul, S.; Almstead, N.; Natchus, M.; Anastasio, M.; McPhail, S.; Snider, C.; Taiwo, Y.; Chen, L.; Dunaway, C.; Gu, P.; Dowty, M.; Mieling, G.; Janusz, M.; Wang-Weigand, S. Design and synthesis of piperazine-based matrix metalloproteinase inhibitors. J. Med. Chem. 2000, 43, 369-380.
36. Matter, H.; Schwab, W. Affinity and selectivity of matrix metalloproteinase inhibitors: A chemometrical study from the perspective of ligands and proteins. J. Med. Chem. 1999, 42, 4506-4523.
37. Almstead, N.; Bradley, R.; Pikul, S.; De, B.; Natchus, M.; Taiwo, Y.; Gu, F.; Williams, L.; Hynd, B.; Janusz, M.; Dunaway, C.; Mieling, G. Design, synthesis, and biological evaluation of potent thiazine- and thiazepine-based matrix metalloproteinase inhibitors. J. Med. Chem. 1999, 42, 4547-4562.
38. Amin, E.; Welsh, W. Three-dimensional quantitative structure-activity relationship (3D-QSAR) models for a novel class of piperazine-based stromelysin-1 (MMP-3) inhibitors: Applying a "divide and conquer" strategy. J. Med. Chem. 2001, 44, 3849-3855.
39. Amin, E.; Welsh, W. Forthcoming.
40. Matter, H.; Schwab, W.; Barbier, D.; Billen, G.; Haase, B.; Neises, B.; Schudok, M.; Thorwart, W.; Schreuder, H.; Brachvogel, V.; Lonze, P.; Weithmann, K. Quantitative structure-activity relationship of human neutrophil collagenase (MMP-8) inhibitors using comparative molecular field analysis and X-ray structure analysis. J. Med. Chem. 1999, 42, 1908-1920.
41. Kunick, C.; Laurenroth, K.; Wieking, K.; Zie, X.; Schultz, C.; Gussio, R.; Zaharevitz, D.; Leost, M.; Meijer, L.; Weber, A.; Jorgensen, F.; Lemcke, T. Evaluation and comparison of 3D-QSAR CoMSIA models for CDK1, CDK5, and GSK-3 inhibition by paullones. J. Med. Chem. 2004, 47, 22-36.
42. Paula, S.; Tabet, M.; Keenan, S.; Welsh, W.; Ball, W. Three-dimensional structure-activity relationship modeling of cocaine binding to two monoclonal antibodies. J. Mol. Biol. 2003, 325, 515-530.
43. Johnson, T.; Khan, I.; Avery, M.; Grant, J.; Meshnick, S. Quantitative structure-activity relationship studies of a series of sulfa drugs as inhibitors of Pneumocystis carinii dihydropteroate synthetase. Antimicrob. Agents Chemother. 1998, 42, 1454-1458.
44. Rarey, M.; Kramer, B.; Lengauer, T. Multiple automatic base selection: Protein-ligand docking based on incremental construction without manual intervention. J. Comput.-Aided Mol. Des. 1997, 11, 369.
45. Veber, D.; Johnson, S.; Cheng, H.; Smith, B.; Ward, K.; Kopple, K. Molecular properties that influence the oral bioavailability of drug candidates. J. Med. Chem. 2002, 45, 2615-2623.
46. Lipinski, C.; Lombarde, F.; Dominy, B.; Feeney, P. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings, Adv. Drug Delivery Rev. 1997, 23, 3-25.