Pharmacophore modeling, docking studies, and synthesis of novel dipeptide proteasome inhibitors containing boron atoms

Journal of Chemical Information and Modeling

Volumn 49, Issue 9, 2009, Pages 2092-2100

  Lei, Meng ^a   Zhao, Xin ^b   Wang, Zhanli ^c   Zhu, Yongqiang ^b  

^a NANJING FORESTRY UNIVERSITY   (China)

^b Jiangsu Key Laboratory of Molecular Targeted Antitumor Drug Research   (China)

^c Technology Center   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ATOMS; BORON; CATALYSTS; PEPTIDES; PHARMACODYNAMICS;

COVALENT INTERACTIONS; DIPEPTIDE BORONIC ACIDS; EXPERIMENTAL VALUES; INFORMATION CONTENTS; PHARMACOPHORE MODELING; POTENT INHIBITOR; PROTEASOME INHIBITORS; THEORETICAL MODELING;

3D MODELING;

BORONIC ACID DERIVATIVE; DIPEPTIDE; PROTEASOME; PROTEINASE INHIBITOR;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; DRUG ANTAGONISM; HUMAN; REPRODUCIBILITY; SYNTHESIS;

BORONIC ACIDS; DIPEPTIDES; HUMANS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; PROTEASE INHIBITORS; PROTEASOME ENDOPEPTIDASE COMPLEX; REPRODUCIBILITY OF RESULTS;

EID: 70349918652     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci900225s     Document Type: Article

References (26)

1. Ciechanover, A. The ubiquitin-proteasome pathway: on protein death and cell life. EMBO J. 1998, 17, 7151-7160.
2. Rock, K. L.; Goldberg, A. L. Degradation of cell proteins and the generation of MHC class I- presented peptides. Annu. J. Rev. Immunol. 1999, 17, 739-779.
3. Prösch, S.; Priemer, C.; HÖflich, C.; Liebenthal, C.; Babel, N.; Kriüger, D. H.; Volk, H. D. Proteasome inhibitors: a novel tool to suppress human cytomegalovirus replication and virus-induced immune modulation. Antiviral Ther. 2003, 8, 555-567.
4. Mitch, W. E.; Goldberg, A. L. Mechanisms of muscle wasting. The role of the ubiquitin-proteasome pathway. New. Engl. J. Med. 1996, 335, 1897-1905.
5. Hampton, R. Y.; Gardner, R. G.; Rine, J. Role of 26S proteasome and HRD genes in the degradation of 3-hydroxy-3-methylglutaryl- CoA reductase, an integral endoplasmic reticulum membrane protein. Mol. Biol. Cell 1996, 7, 2029-2044.
6. Murakami, Y.; Matsufuji, S.; Kameji, T.; Hayashi, S.; Igarashi, K.; Tamura, T.; Tanaka, K.; Ichihara, A. Ornithine decarboxylase is degraded by the 26S proteasome without ubiquitination. Nature 1992, 360, 597-599.
7. Turner, G. C.; Du, F.; Varshavsky, A. Peptides accelerate their uptake by activating a ubiquitin-dependent proteolytic pathway. Nature 2000, 405, 579-583.
8. Naidoo, N.; Song, W.; Hunter-Ensor, M.; Sehgal, A. A role for the proteasome in the light response of the timeless clock protein. Science 1999, 285, 1737-1741.
9. Chain, D. G.; Schwartz, J. H.; Hegde, A. N. Ubiquitin-mediated proteolysis in learning and memory. Mol. Neurobiol. 1999, 20, 125-142.
10. Richardson, P. G.; Sonneveld, P.; Schuster, M. W.; Irwin, D.; Stadtmauer, E. A.; Facon, T.; Harousseau, J. L.; Ben-Yehu, D.; Lonial, S.; Goldschmidt, H. Bortezomib or high-dose dexamethasone for relapsed multiple myeloma. New Engl. J. Med. 2005, 352, 2487-2498.
11. Adams, J. Proteasome inhibition: a novel approach to cancer therapy. Trends Mol. Med. 2002, 8 (Suppl.), S49-S54. (Pubitemid 34297079)
12. Adams, J.; Palombella, V. J.; Sausville, E. A.; Johnson, J.; Destree, A.; Lazarus, D. D.; Maas, J.; Pien, C. S.; Prakash, S.; Elliott, P. J. Proteasome inhibitors: a novel class of potent and effective antitumor agents. Cancer Res. 1999, 59, 2615-2622.
13. Pham, L.; Tamayo, A.; Lo, P.; Yoshimura, L.; Ford, R. J. Antitumor activity of the proteasome inhibitor PS-341 in mantle cell lymphoma B cells. Blood 2001, 98, 1945 (abstr 1945a, suppl).
14. Groll, M.; Berkers, C. R.; Ploegh, H. L.; Ovaa, H. Crystal structure of the boronic acid-based proteasome inhibitor bortezomib in complex with the yeast 20S proteasome. Structure 2006, 14, 451-456.
15. Adams, J.; Behnke, M.; Chen, S. W.; Cruickshank, A. A.; Dick, L. R.; Grenie, L.; Klunder, J. M.; Ma, Y. T.; Plamondon, L.; Stein, R. L. Potent and selective inhibitors of the proteasome: dipeptidyl boronic acids. Bioorg. Med. Chem. Lett. 1998, 8, 333-338.
16. Adams, J. Potential for proteasome inhibition in the treatment of cancer. Drug Discov. Today 2003, 8, 307-315.
17. Zhu, Y. Q.; Pei, J. F.; Liu, Z. M.; Lai, L. H.; Cui, J. R.; Li, R. T. 3D-QSAR studies on tripeptide aldehyde inhibitors of proteasome using CoMFA and CoMSIA methods. Bioorg. Med. Chem. 2006, 14, 1483-1496.
18. Zhu, Y. Q.; Lei, M.; Lu, A. J.; Zhao, X.; Yin, X. J.; Gao, Q. Z. 3D- QSAR studies of boron-containing dipeptides as proteasome inhibitors with CoMFA and CoMSIA methods. Eur. J. Med. Chem. 2009, 44, 1486-1499.
19. Zhu, Y. Q.; Zhao, X.; Zhu, X. R.; Wu, G.; Li, Y. J.; Ma, Y. H.; Yuan, Y. X.; Yang, J.; Hu, Y.; Ai, L.; Gao, Q. Z. Design, Synthesis, biological evaluation, and structure-activity relationship (SAR) discussion of dipeptidyl boronate proteasome inhibitors, Part I: comprehensive understanding of the SAR of α-amino acid boronates. J. Med. Chem. 2009, 52, 4192-4199.
20. Catalyst, 4. 11; Accelrys Inc. : San Diego, CA, USA.
21. Adams, J.; Ma, Y. T.; Stein, R.; Baevsky, M.; Grenier, L.; Plamonda, L. Boronic ester and acid compounds, synthesis and uses. PCT Int. Appl. 1995, WO 1996013266.
22. Insight II, 2005; Accelrys Inc. : San Diego, CA, USA.
23. Johnsamuel, J.; Byun, Y.; Jones, T. P.; Endo, Y.; Tjarks, W. A new strategy for molecular modeling and receptor-based design of carborane containing compounds. J. Organomet. Chem. 2003, 680, 223-231.
24. Johnsamuel, J.; Byun, Y.; Jones, T. P.; Endo, Y.; Tjarks, W. A convenient method for the computer-aided molecular design of carborane containing compounds. Bioorg. Med. Chem. Lett. 2003, 13, 3213-3216.
25. Borissenko, L.; Groll, M. 20S proteasome and its inhibitors: crystallographic knowledge for drug development. Chem. Rev. 2007, 107, 687-717.
26. Klausner, Y. S.; Bodansky, M. Coupling reagents in peptide synthesis. Synthesis 1972, 453-463.