Study on selectin blocker. 8. Lead discovery of a non-sugar antagonist using a 3D-pharmacophore model

Journal of Medicinal Chemistry

Volumn 43, Issue 8, 2000, Pages 1476-1483

  Hiramatsu, Yasuyuki ^a   Tsukida, Takahiro ^a   Nakai, Yoshiyuki ^a   Inoue, Yoshimasa ^a   Kondo, Hirosato ^a  

^a Nippon Organon KK   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ENDOTHELIAL LEUKOCYTE ADHESION MOLECULE 1; SELECTIN; SIALIC ACID DERIVATIVE;

ARTICLE; CHEMICAL BINDING; CHEMICAL STRUCTURE; COMPLEX FORMATION; INHIBITION KINETICS; MOLECULAR MODEL; PHARMACOPHORE;

BENZAMIDES; BENZOIC ACIDS; CARBOHYDRATE SEQUENCE; DATABASES, FACTUAL; E-SELECTIN; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR SEQUENCE DATA; SELECTINS;

EID: 0034692174     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm990342j     Document Type: Article

References (69)

1. 2) on Human Neutrophils. J. Exp. Med. 1991, 173, 1493-1500.
2. (b) Crovello, C. S.; Furie, B. C.; Furie, B. Histidine Phosphorylation of P-selectin upon Stimulation of Human Platelets; A Novel Pathway for Activation Dependent Signal Transduction. Cell 1995, 82, 279-286.
3. Waddell, T. K.; Fialkow, L.; Chan, C. K.; Kishimoto, T. K.; Downey, G. P. Signal Functions of L-selectin. J. Biol. Chem. 1995, 270, 15403-15411.
4. lck Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 15376-15381
5. (e) Weyrich, A. S.; Elstad, M. R.; McEver, R. P.; McIntyre, T. M.; Moore, K. L.; Morrissey, J. M.; Prescott, S. M.; Zimmerman, G. A. Activated Platelets Signal Chemokine Synthesis by Human Monocyte. J. Clin. Invest. 1996, 97, 1525-1534.
6. (f) Zimmerman, G. A.; McIntyre, T. M.; Prescott, S. M. Perspectives Series: Cell Adhesion in Vascular Biology; Adhesion and Signaling in Vascular Cell-Cell Interactions. J. Clin. Invest. 1997, 100, S3-S5.
7. (g) C.-Torabi, E. Selectins and mechanisms of signal transduction. J. Leukoc. Biol. 1998, 63, 1-14.
8. For recent examples of elegant strategies for oligosaccharide synthesis, see: (a) Kondo, H.; Ichikawa, Y.; Wong, C.-H. β-Sialyl Phosphite and Phosphoramidite: Synthesis and Application to the Chemoenzymatic Synthesis of CMP-Sialic Acid and Sialyl Oligosaccharides. J. Am. Chem. Soc. 1992, 114, 8748-8750.
9. (b) Halcomb, R. L.; Huang, H.; Wong, C.-H. Solution- and Solid-Phase Synthesis of Inhibitors of H. Pylori Attachment and E-Selectin-Mediated Leukocyte Adhesion. J. Am. Chem. Soc. 1994, 116, 11315-11322.
10. Mehta, S.; Pinto, B. M. Novel Glycosidation Methodology: The Use of Phenyl Selenoglycosides as Glycosyl Donors and Acceptors in Oligosaccharide Synthesis. J. Org. Chem. 1993, 58, 3269-3276.
11. Raghavan, S.; Kahne, D. A One-Step Synthesis of the Ciclamycin Trisaccharide. J. Am. Chem. Soc. 1993, 115, 1580-1581.
12. (e) Yamada, H.; Harada, T.; Takahashi, T. Synthesis of an Elicitor-Active Hexaglucoside Analogue by a One-Pot, Two-Step Glycosidation Procedure. J. Am. Chem. Soc. 1994, 116, 7919-7920.
13. (f) Kanie, O.; Ito, Y.; Ogawa, T. Orthogonal Glycosylation Strategy in Oligosaccharide Synthesis. J. Am. Chem. Soc. 1994, 116, 12073-12074.
14. (g) Madsen, R.; Udodong, U.; Roberts, C.; Mootoo, D.; Mootoo, U. D. R.; Konradsson, P.; Fraser-Reid, B. Studies related to Synthesis of Glycophosphatidylinositol Membrane-Bound Protein Anchors. 6. Convergent Assembly of Subunits. J. Am. Chem. Soc. 1995, 117, 1554-1565.
15. (h) Tsukida, T.; Yoshida, M.; Kurokawa, K.; Nakai, Y.; Achiha, T.; Kiyoi, T.; Kondo, H. A Highly Practical Synthesis of Sulfated Lewis X: One-Pot, Two-Step Glycosylation Using "Armed/Disarmed" Coupling and Selective Benzoylation and Sulfation. J. Org. Chem. 1997, 62, 6876-6881.
16. (a) Mulligan, M. S.; Lowe, J. B.; Larsen, R. D.; Paulson, J.; Zheng, Z.; DeFrees, S.; Maemura, K.; Fukuda, M.; Ward, P. Protective Effects of Sialylated Oligosaccharides in Immune Complex-Induced Acute Lung Injury. J. Exp. Med. 1993, 178, 623-631.
17. (b) Springer, T. A.; Lasky, L. A. Sticky sugar for selecting. Nature 1991, 349, 196-197.
18. Fukushima, K.; Ohkura, T.; Kanai, M.; Kuroki, M.; Matsuoka, Y.; Kobata, A.; Yamashita, K. Carbohydrate structures of a normal counterpart of the carcinoembryonic antigen produced by colon epithelial cells of normal adults. Glycobiology 1995, 5, 105-115.
19. Feizi, T.; Larkin, M. AIDS and glycosylation. Glycobiology 1990, 1, 17-23.
20. (e) Nguyen, M.; Eilber, F. R.; DeFrees, S. Novel Synthetic Analogues of Sialyl Lewis X Can Inhibit Angiogenesis in Vitro and in Vivo. Biochem. Biophys. Res. Commun. 1996, 228, 716-723.
21. Varki, A. Selectin ligands; will the real ones please stand up? J. Clin. Invest. 1997, 99, 158-162.
22. (a) Berg, E. L.; Yoshino, T.; Rott, L. S.; Robinson, M. K.; Warnock, R. A.; Kishimoto, T. K.; Picker, L. J.; Butcher, E. C. The cautaneous Lymphocyte Antigen is a Skin Lymphocyte Horming Receptor for the Vascular Lectin Endothelial Cell-Leukocyte Adhesion Molecule 1. J. Exp. Med. 1991, 174, 1461-1466.
23. (b) Picker, L. J.; Kishimoto, T. K.; Smith, C. W.; Warnock, R. A.; Butcher, E. C. ELAM-1 is an Adhesion Molecule for Skin Horming T Cells. Nature 1991, 349, 796-799.
24. Lorant, D. E.; Topham, M. K.; Whatley, R. E.; McEver, R. P.; McIntyre, T. M.; Prescott, S. M.; Zimmerman, G. A. Inflammatory Roles of P-selectin. J. Clin. Invest. 1993, 92, 559-570.
25. Symon, F. A.; Walsh, G. M.; Watson, S. R.; Wardlaw, A. J. Eosinophil Adhesion to Nasal Polyp Endothelium is P-selectin-Dependent. J. Exp. Med. 1994, 80, 371-376.
26. (e) Akbar, A. N.; Salman, M.; Janossy, G. The Synergy Between Naïve and Memory T Cells During Activation, Immunol. Today 1991, 12, 184-188.
27. (f) Duijvestijn, A. M.; Horst, E.; Pals, S. T.; Rous, B. N.; Steere, A. C.; Picker, L. J.; Meijer, C. J. L. M.; Butcher, E. C. High Endothelial Differentiation in Human Lymphoid and Inflammatory Tissue Defined by Monoclonal Antibody HECA-452. Am. J. Pathol. 1988, 130, 147-155.
28. (a) Ohmoto, H.; Nakamura, K.; Inoue, T.; Kondo, N.; Inoue, Y.; Yoshino, K.; Kondo, H.; Ishida, H.; Kiso, M,; Hasegawa, A. Studies on Selectin Blocker 1. Structure-Activity Relationships of Sialyl Lewis X Analogues. J. Med. Chem. 1998, 39, 1339-1343.
29. (b) Wada, Y.; Saito, T.; Matsuda, N.; Ohmoto, H.; Yoshino, K.; Ohashi, M.; Kondo, H.; Ishida, H.; Kiso, M.; Hasegawa, A. Studies on Selectin Blockers 2. Novel Selectin Blocker as Potential Therapeutics for Inflammatory Disorders. J. Med. Chem. 1996, 39, 2055-2059.
30. Hiramatsu, Y.; Tsujishita, H.; Kondo, H. Study on Selectin Blockers 3: Investigation of the Carbohydrate Ligand Sialyl Lewis X Recognition of P-selectin. J. Med. Chem. 1996, 39, 4547-4553.
31. Yoshino, K.; Ohmoto, H.; Kondo, N.; Tsujishita, H.; Hiramatsu, Y.; Inoue, Y.; Kondo, H.; Ishida, H.; Kiso, M.; Hasegawa, A. Studies on Selectin Blockers. 4. Structure-Function Relationships of Sulfated Sialyl Lewis X Hexasaccharide Ceramides toward E-, P-, and L-Selectin Binding. J. Med. Chem. 1997, 40, 455-462.
32. (e) Tsukida, T.; Hiramatsu, Y.; Tsujishita, H.; Kiyoi, T.; Yoshida, M.; Kurokawa, K.; Moriyama, H.; Ohmoto, H.; Wada, Y.; Saito, T.; Kondo, H. Studies on Selectin Blockers. 5. Design, Synthesis, and Biological Profile of Sialyl Lewis x Mimetics Based on Modified Serine-Glutamic Acid Dipeptides. J. Med. Chem. 1997, 40, 3534-3541.
33. (f) Hiramatsu, Y.; Moriyama, H.; Kiyoi, T.; Tsukida, T.; Inoue, Y.; Kondo, H. Studies on Selectin Blockers. 6. Discovery of Homologous Fucose Sugar Unit Necessary for E-Selectin Binding. J. Med. Chem. 1998, 41, 2302-2307,
34. (g) Tsukida, T.; Moriyama, H.; Kurokawa, K.; Achiha, T.; Inoue, Y.; Kondo, H. Studies on Selectin Blocker 7. Structure-Activity Relationships of Sialyl Lewis X Mimetics Based on Modified Ser-Glu Dipeptides. J. Med. Chem. 1998, 41, 4279-4287.
35. (a) Cohen, N. C.; Blaney, J. M.; Humblet, C.; Gund, P.; Barry, D. C. Molecular Modeling Software and Methods for Medicinal Chemistry. J. Med. Chem. 1990, 33, 883-984.
36. (b) Bohm, H.-J.; Klebe, G. What Can We Learn from Molecular Recognition in Protein-Ligand Complexes for the Design of New Drug? Angew. Chem., Int. Ed. Engl. 1996, 35, 2588-2614.
37. Graves, B. J.; Crowther, R. L.; Chandran, C.; Rumberger J. M.; Li, S.; Huang, K. S.; Presky, D. H.; Femilletti, P. C.; Wolitzky, B. A.; Burns, D. K. Insight into E-Selectin/Ligand Interaction from the Crystal Structure and Mutagenesis of the Lec/EGF Domains. Nature 1994, 367, 532-538.
38. (a) Erbe, D. V.; Wolitzky, B. A.; Presta, L. G.; Norton, C. R.; Ramos, R. J.; Burns, D. K.; Rumberger, J. M.; Rao, B. N. N.; Foxall, C.; Brandley, B. K.; Lasky, L. A. Identification of an E-selectin Region Critical for Carbohydrate Recognition and Cell Adhesion. J. Cell Biol. 1992, 119, 215-227.
39. (b) Bajorath, J.; Hollenbaugh, D.; King, G.; Harte, W., Jr.; Eustice, D. C.; Darveau, R. P.; Aruffo, A. CD62/P-Selectin Binding Sites for Myeloid Cells and Sulfatides Are Overlapping. Biochemistry 1994, 33, 1332-1339.
40. Kogan, T. P.; Revelle, B. M.; Tapp, S.; Scott, D.; Beck, P. J. A Single Amino Acid Residue Can Determine the Ligand Specificity of E-Selectin. J. Biol. Chem. 1995, 270, 14047-14055.
41. Erbe, D. V.; Watson, S. R.; Presta, L. G.; Wolitzky, B. A.; Foxall, C.; Brandley, B. K.; Lasky, L. A. P- and E-Selectin Use Common Sites for Carbohydrate Ligand Recognition and Cell Ahesion. J. Cell Biol. 1993, 120, 1227-1235.
42. (e) Hollenbaugh, D.; Bajorath, J.; Stenkamp, R.; Aruffo, A. Interaction of P-Selectin (CD62) and Its Cellular Ligand: Analysis of Critical Residues. Biochemistry 1993, 32, 2960-2966.
43. (a) Tyrrell, D.; James, P.; Rao, N.; Foxall, C.; Abbas, S.; Dasgupta, F.; Nashed, M.; Hasegawa, A.; Kiso, M.; Asa, D.; Kidd, J.; Brandley, B. K. Structural Requirements for the Carbohydrate Ligand of E-selectin. Proc. Natl. Acad. Sci. U.S.A. 1991, 88, 10372-10376.
44. x Oligosaccharide. J. Cell Biol. 1992, 117, 895-902.
45. Brandley, B. K.; Kiso, M.; Abbas, S.; Nikrad, P.; Srivasatava, O.; Foxall, C.; Oda, Y.; Hasegawa, A. Structure-function Studies on Selectin Carbohydrate Ligands. Modifications to Fucose. Sialic Acid and Sulfate as a Sialic Acid Replacement. Glycobiology 1993, 3, 633-639.
46. (a) Cooke, R. M.; Hale, R. S.; Lister, S. G.; Shah, G.; Weir, M. P. The Conformation of the Sialyl Lewis X Ligand Changes upon Binding to E-Selectin. Biochemistry 1994, 33, 10591-10596.
47. x Complex. Angew. Chem., Int. Ed. Engl. 1995, 34, 1841-1844.
48. Kogan, T. P.; Dupré, B.; Keller, K. M.; Scott, I. L.; Bui, H.; Market, R. V.; Beck, P. J.; Voytus, J. A.; Revelle, B. M.; Scott, D. Rational Design and Synthsis of Small Molecule, Nonoligosaccharide Selectin Inhibitors: (α-D-Mannopyranosyloxy)-biphenyl-Substituted Carboxylic Acids. J. Med. Chem. 1995, 38, 4976-4984.
49. Tsujishita, H.; Hiramatsu, Y.; Kondo, N.; Ohmoto, H.; Kondo, H.; Kiso, M.; Hasegawa, A. Selectin-Ligand Interactions Revealed by Molecular Dynamics Simulation in Solution. J. Med. Chem. 1997, 40, 362-369.
50. (a) Martin, Y. C. 3D Database Searching in Drug Design. J. Med. Chem. 1992, 35, 2145-2154.
51. (b) Christe, B. D.; Henery, D. R.; Guner, O. F.; Moock, T. E. MACCS-3D: A Tool for Three-Dimensional Drug Design. Online Inf. 1990, 90, 11-13.
52. Guner, O. F.; Hughes, D. W.; Dumont, L. M. An Integrated Approach to Three-Dimensional Information Management with MACCS-3D. J. Chem. Inf. Comput. Sci. 1991, 31, 408-414.
53. Hurst, T. Flexible 3D Searching: Directed Tweak Technique. J. Chem. Inf. Comput. Sci. 1994, 34, 190-196.
54. (e) Kunz, I. D.; Meng, E. C.; Shoichet, B. K. Structure-Based Molecular Design. Ace. Chem. Res. 1994, 27, 117-123.
55. (f) Moock, T. E.; Henry, D. R.; Ozkabak, A. G.; Alamgir, M. Conformational Searching in ISIS/3D Databases. J. Chem. Inf. Comput. Sci. 1994, 34, 184-189.
56. (g) Murrall, N. W.; Davies, E. K. Conformational Freedom in 3-D Database. 1. Techniques. J. Chem. Inf. Comput. Sci. 1990, 30, 312-316.
57. (h) Ho, C. M. W.; Marshall, G. R. FOUNDATION: A Program to Retrieve All Possible Structures Containing a User-Defined Minimum Number of Matching Query Elements from Three-Dimensional Databases. J. Comput.-Aided Mol. Des. 1993, 7, 3-22.
58. Böhn, H.-J. On the Use of LUDI to Search the Fine Chemicals Directory for Ligands of Known Three-Dimensional Structure. J. Comput.-Aided Mol. Des. 1994, 8, 623-632.
59. (a) McPhalen, C. A.; Strynadka, N. C. J.; James, M. N. G. Calcium-Binding Sites in Proteins: A Structural Perspective. Adv. Protein. Chem. 1991, 42, 77-144.
60. 2+-binding sites in proteins. Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 817-821.
61. Ferrin, T. E.; Huang, C. C.; Jarvis, L. E.; Langridge, R. The MIDAS display system. J. Mol. Graph. 1988, 6, 13-27.
62. Sybyl version 6.5; September 1998, Tripos Inc.
63. (a) Halgren, T. A. Merk Molecular Force Field. I. Basis, Form, Scope, Parametrization, and Performance of MMFF94. J. Comput. Chem. 1996, 17, 490-519.
64. (b) Halgren, T. A. Merk Molecular Force Field. II. MMFF94 van der Waals and Electrostatic Parameters for Intermolecular Interactions. J. Comput. Chem. 1996, 17, 520-552.
65. Halgren, T. A. Merk Molecular Force Field. III. Molecular Geometries and Vibrational Frequencies for MMFF94. J. Comput. Chem. 1996, 17, 553-586.
66. Halgren, T. A.; Nachbar, R. B. Merk Molecular Force Field. IV. Conformational Energies and Geometries for MMFF94. J. Comput. Chem. 1996, 17, 587-615.
67. Stewart, J. P. P. MOPAC93; distibution by Fujitsu Ltd., Tokyo, Japan, and QCPE, Indiana University.
68. Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. AM1: A New General Purpose Quantum Mechanical Molecular Model. J. Am. Chem. Soc. 1985, 107, 3902-3909.
69. Simanek, E. E.; McGarvey, G. J.; Jablonowski, J. A.; Wong, C.-H. Selectin-Carbohydrate Interactions: From Natural Ligand to Designed Mimics. Chem. Rev. 1998, 98, 833-862.