Rational design, synthesis, and X-ray structure of selective noncovalent thrombin inhibitors

Journal of Medicinal Chemistry

Volumn 41, Issue 19, 1998, Pages 3664-3674

  Wagner, Jürgen ^a   Kallen, Jörg ^a   Ehrhardt, Claus ^a   Evenou, Jean Pierre ^a   Wagner, Dieter ^a  

^a NOVARTIS PHARMA AG   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

THROMBIN INHIBITOR;

ARTICLE; CRYSTAL STRUCTURE; DRUG STRUCTURE; DRUG SYNTHESIS; MOLECULAR MODEL; STEREOCHEMISTRY; X RAY CRYSTALLOGRAPHY;

ANIMALS; BICYCLO COMPOUNDS, HETEROCYCLIC; BINDING SITES; CATTLE; CRYSTALLOGRAPHY, X-RAY; DRUG DESIGN; FACTOR XA; GUANIDINES; HUMANS; LIGANDS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; SERINE PROTEINASE INHIBITORS; STEREOISOMERISM; THIAZOLES; THROMBIN; TRYPSIN INHIBITORS;

EID: 0032505172     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm981013e     Document Type: Article

References (60)

1. (a) Hirsh, J. Oral Anticoagulant Drugs. New Engl. J. Med. 1991, 324, 1865-1875.
2. (b) New Antithrombotics: Better Agents are Needed to Prevent Blood Clots. Genet. Technol. News 1996, 16, 8+11.
3. (c) Rihal, C. S.; Flather, M.; Hirsh, J.; Yusuf, S. Advances in Antithrombotic Drug Therapy for Coronary Artery Disease. Eur. Heart J. 1995, 16, 10-21.
4. (a) Tapparelli, C.; Metternich, R.; Ehrhardt, C.; Cook, N. S. Synthetic Low-molecular Weight Thrombin Inhibitors: Molecular Design and Pharmacological Profile. Trends Pharmacol. Sci. 1993, 14, 366-376.
5. (b) Bazan, J. F. Big Rigs in Blood Coagulation. Nature 1996, 380, 21-22.
6. (c) Maraganore, J. M. Thrombin, Thrombin Inhibitors, and the Arterial Thrombotic Process. Thromb. Haemostasis 1993, 70, 208-211.
7. (a) For an excellent review on the various classes of novel direct and indirect thrombin inhibitors, see: Balasubramanian, B. N., Ed. Advances in the Design and Development of Thrombin Inhibitors. Bioorg. Med. Chem. 1995, 3, 999-1156. (b) Kimball, S. D. Thrombin Active Site Inhibitors. Curr. Pharm. Des. 1995, 1, 441-468. (c) Edmunds, J. J.; Rapundalo, S. T.; Siddiqui, M. A. Thrombin and Factor Xa Inhibition. Annu. Rep. Med. Chem. 1996, 31, 51-60.
8. (a) For an excellent review on the various classes of novel direct and indirect thrombin inhibitors, see: Balasubramanian, B. N., Ed. Advances in the Design and Development of Thrombin Inhibitors. Bioorg. Med. Chem. 1995, 3, 999-1156. (b) Kimball, S. D. Thrombin Active Site Inhibitors. Curr. Pharm. Des. 1995, 1, 441-468. (c) Edmunds, J. J.; Rapundalo, S. T.; Siddiqui, M. A. Thrombin and Factor Xa Inhibition. Annu. Rep. Med. Chem. 1996, 31, 51-60.
9. (a) For an excellent review on the various classes of novel direct and indirect thrombin inhibitors, see: Balasubramanian, B. N., Ed. Advances in the Design and Development of Thrombin Inhibitors. Bioorg. Med. Chem. 1995, 3, 999-1156. (b) Kimball, S. D. Thrombin Active Site Inhibitors. Curr. Pharm. Des. 1995, 1, 441-468. (c) Edmunds, J. J.; Rapundalo, S. T.; Siddiqui, M. A. Thrombin and Factor Xa Inhibition. Annu. Rep. Med. Chem. 1996, 31, 51-60.
10. (a) Lefkovits, J.; Topol, E. J. Direct Thrombin Inhibitors in Cardiovascular Medicine. Circulation 1994, 90, 1522-1536.
11. (b) Tadeusz, P.; Cezary, W. Recombinant Hirudin. Biotechnologia 1996, 3, 34-42.
12. (a) Kikumoto, R.; Tonomura, S.; Hara, H.; Ninomiya, K.; Maruyama, A.; Sugano, M.; Tamao, Y. Potent Inhibition of Thrombin by the Newly Synthesized Arginine Derivative No. 805. The Importance of Stereostructure of its Hydrophobic Carboxamide Portion. Biochem. Biophys. Res. Commun. 1981, 101, 440-446.
13. (b) Okamoto, S.; Hijikata-Okunomiya, A. Synthetic Selective Inhibitors of Thrombin. Methods Enzymol. 1993, 222, 328-340.
14. (a) Kaiser, B.; Hauptmann, J.; Weiss, A.; Markwardt, F. Pharmacological Characterization of a New Highly Effective Synthetic Thrombin Inhibitor. Biomed. Biochim. Acta 1985, 44, 1201-1210.
15. (b) Kaiser, B.; Markwardt, F. Experimental Studies on the Antithrombotic Action of a Highly Effective Synthetic Thrombin Inhibitor. Thromb. Haemostasis 1986, 55, 194-196.
16. (a) Turk, D.; Stürzebecher, J.; Bode, W. Geometry of Binding of the Nα-Tosylated Piperidides of m-Amidino, p-Amidino- and p-Guanidino Phenylalanine to Thrombin and Trypsin. FEBS 1991, 287, 133-138.
17. (b) Bode, W.; Turk, D.; Stürzebecher, J. Geometry of Binding of the Benzamidine- and Arginine-based Inhibitors Nα-( 2-naphthyl-sulphonyl-glycyl )-DL-p-amidinophenylalanyl-piperidine (NAPAP) and (2R,4R)-4-methyl-1-[Nα-(3-methyl-1,2,3,4-tetrahydro-8-quinolinesulphonyl)- L-arginyl]-2-piperidine Carboxylic Acid (MQPA) to Human α-Thrombin. Eur. J. Biochem. 1990, 193, 175-182.
18. (c) Brandstetter, H.; Turk, D.; Höffken, H. W.; Grosse, D.; Stürzebecher, J.; Martin, P. D.; Edwards, B. F. P.; Bode, W. Refined 2.3 Å X-ray Crystal Structure of Bovine Thrombin Complexes Formed with the Benzamidine and Arginine-based Thrombin Inhibitors NAPAP, 4-TAPAP and MQPA. J. Mol. Biol. 1992, 226, 1085-1099.
19. (d) Banner, D. W.; Hadváry, P. Crystallographic Analysis at 3.0 Å Resolution of the Binding to Human Thrombin of Four Active Site-directed Inhibitors. J. Biol. Chem. 1991, 266, 20085-20093.
20. Misra, R. N.; Kelly, Y. F.; Brown, B. R.; Roberts, D. G. M.; Chong, S.; Seiler, S. M. Argatroban Analogues: Synthesis, Thrombin Inhibitory Activity and Cell Permeability of Aminoheterocyclic Guanidine Surrogates. Bioorg. Med. Chem. Lett. 1994, 4, 2165-2170.
21. Jendralla, H.; Seuring, B.; Herchen, J.; Kulitzscher, B.; Wunner, J. Efficient Kg-Scale Synthesis of Thrombin Inhibitor CRC 220. Tetrahedron 1995, 51, 12047-12068.
22. Hilpert, K.; Ackermann, J.; Banner, D. W.; Gast, A.; Gubernator, K.; Hadváry, P.; Labler, L.; Müller, K.; Schmid, G.; Tschopp, T. B.; van der Waterbeemd, H. Design and Synthesis of Potent and Highly Selective Thrombin Inhibitors. J. Med. Chem. 1994, 37, 3889-3901.
23. (a) Tucker, T. J.; Lumma, W. C.; Mulichak, A. M.; Chen, Z.; Naylor-Olson, A. M.; Lewis, S. D.; Lucas, R.; Freidinger, R. M.; Kuo, L. C. Design of Highly Potent Noncovalent Thrombin Inhibitors that Utilize a Novel Lipophilic Binding Pocket in the Thrombin Active Site. J. Med. Chem. 1997, 40, 830-832.
24. (b) Tucker, T. J.; Lumma, W. C.; Lewis, S. D.; Gardell, S. J.; Lucas, B. J.; Baskin, E. P.; Weltmann, R.; Lynch, J. J.; Lyle, E. A.; Appleby, S. D.; Chen, I.; Dancheck, K. B.; Vacca, J. P. Potent Noncovalent Thrombin Inhibitors that Utilize the Unique Amino Acid D-Dicyclohexylalanine in the P3 Position. Implications on Oral Bioavailability and Antithrombotic Efficacy. J. Med. Chem. 1997, 40, 1565-1569.
25. (a) Préville, P.; He, J. X.; Tarazi, M.; Siddiqui, M. A.; Cody, W. L.; Doherty, A. M. An Efficient Preparation of the Potent and Selective Pseudopeptide Thrombin Inhibitor, Inogatran. Bioorg. Med. Chem. Lett. 1997, 7, 1563-1566.
26. (b) Teger-Nilsson, A.-C.; Bylund, R.; Gustafsson, D.; Gyzander, E.; Eriksson, U. In Vitro Effects of Inogatran, a Selective Low Molecular Weight Thrombin Inhibitor. Thromb. Res. 1997, 85, 133-145.
27. (a) Obst, U.; Gramlich, V.; Diederich, F.; Weber, L.; Banner, D. W. Design of Novel Nonpeptidic Thrombin Inhibitors and Structure of a Thrombin-Inhibitor Complex. Angew. Chem., Int. Ed. Engl. 1995, 34, 1739-1742.
28. (b) Obst, U.; Banner, D. W.; Weber, L.; Diederich, F. Molecular Recognition at the Thrombin Active Site: Structure-based Design and Synthesis of Potent and Selective Thrombin Inhibitors and the X-ray Crystal Structure of Two Thrombin-Inhibitor Complexes. Chem. Biol. 1997, 4, 287-295.
29. Böhm, H.-J.; Klebe, G. What Can we Learn from Molecular Recognition in Protein-Ligand Complexes for the Design of New Drugs? Angew. Chem., Intl. Ed. Engl. 1996, 35, 2588-2614 and references therein.
30. (a) Stewart, D. E.; Sarkar, A.; Wampler, J. E. Occurrence and Role of Cis Peptide Bonds in Protein Structures. J. Mol. Biol. 1990, 214, 253-260.
31. (b) Eberhardt, E. S.; Loh, S. N.; Raines, R. T. Thermodynamic Origin of Prolyl Peptide Bond Isomers. Tetrahedron Lett. 1993, 34, 3055-3056.
32. (a) Nagai, U.; Sato, K. Synthesis of a Bicyclic Dipeptide with the Shape of a β-Turn. Pept. Chem. 1984, 207-210.
33. (b) Nagai, U.; Sato, K. Synthesis of a Bicyclic Dipeptide with the Shape of a β-Turn Central Part. Tetrahedron Lett. 1985, 26, 647-650.
34. (c) Nagai, U.; Sato, K.; Nakamura, R.; Kato, R. Bicyclic Turned Dipeptide (BTD) as a β-Turn Mimetic; its Design, Synthesis and Incorporation into Bioactive Peptides. Tetrahedron 1993, 49, 3577-3592.
35. (a) Sato, K.; Nagai, U. Synthesis and Antibiotic Activity of a Gramicidin S Analogue Containing Bicyclic β-Turn Dipeptides. J. Chem. Soc., Perkin Trans. 1 1986, 1231-1234.
36. (b) Bach, A. C., II; Markwalder, J. A.; Ripka, W. C. Synthesis and NMR Conformational Analysis of a β-Turn Mimic Incorporated into Gramicidin S. Int. J. Pept. Protein Res. 1991, 38, 314-323.
37. (c) Sato, K.; Hotta, M.; Dong, M.-H.; Hu, H.-Y.; Taulene, J. P.; Goodman, M.; Nagai, U.; Ling, N. Solid-Phase Synthesis of Human Growth Hormone-Releasing Factor Analogues Containing a Bicyclic β-Turn Dipeptide. Int. J. Pept. Protein Res. 1991, 38, 340-345.
38. (d) Etzkorn, F. A.; Guo, T.; Lipton, M. A.; Goldberg, S. D.; Bartlett, P. A. Cyclic Hexapeptides and Chimeric Peptides as Mimics of Tendamistat. J. Am. Chem. Soc. 1994, 116, 10412-10425.
39. (e) Rishton, G. M.; Harn, N. K.; Cripps, S. J.; Chiang, S.-L.; Mikos, C.; Cardarelli, P.; Lobl, T. J.; Gorcsan, F.; Moscinski, M.; Delaet, N. G. J.; Walker, S. M. A β-Turn Mimic and a Thiomethylene Dipeptide Surrogate Employed in the Study of Cyclic Peptide RGD and RCD Cell-Adhesion Inhibitors. Lett. Pept. Sci. 1996, 3, 37-44.
40. (f) Haubner, R.; Schmitt, W.; Hölzemann, G.; Goodman, S. L.; Jonczyk, A.; Kessler, H. Cyclic RGD Peptides Containing β-Turn Mimetics. J. Am. Chem. Soc. 1996, 118, 7881-7891.
41. (g) Doyle, P. M.; Harris, J. C.; Moody, C. M.; Sadler, P. J.; Martin, S.; Thornton, J. M.; Uppenbrink, J.; Viles, J. H. Solution Structure of a Biologically Active LDV Peptide Analogue Containing a Type II' β-Turn Mimetic. Int. J. Pept. Protein Res. 1996, 47, 427-436.
42. (h) Alberg, D. G.; Schreiber, S. L. Structure-Based Design of a Cyclophilin-Calcineurin Bridging Ligand. Science 1993, 262, 248-250.
43. 2. J. Med. Chem. 1993, 36, 2356-2361.
44. 3 Bicyclic Lactam Moiety. Bioorg. Med. Chem. Lett. 1997, 7, 331-336.
45. 3 Peptidomimetic Class of Interleukin-1β-Converting Enzyme Inhibitor. J. Med. Chem. 1997, 40, 1941-1946.
46. Osano, Y. T.; Nagai, U.; Matsuzaki, T. Crystal Structure of a β-Turn Model Dipeptide, (3S,6S, 9R)-2-Oxo-3-tert-butyloxycarboxylamino-7-thia-1-aza-bicyclo-[4.3.0]nonane-9- carboxylic Acid. Anal. Sci. 1989, 5, 625-626. The data of the X-ray structure of S-BTD are found in the Cambridge Structural Databank (Code SEYZUR).
47. For the original procedure, see ref 16. A second approach was published by Bartlett et al., see ref 17d. Very recently, the Fmoc-protected S-BTD became commercially available from Neosystem.
48. 7a.
49. Prepared according to Bergeron, R. J.; McMarris, J. S. Total Synthesis of (±)15-Deoxyspergualin. J. Org. Chem. 1987, 52, 1700-1703.
50. Compound 18 is unstable and cyclizes to 18a even at low temperatures: (Matrix Presented)
51. 3 of the major diastereoisomer has been determined to be trans by NOE measurements in DMSO. The stereochemistry has been confirmed by X-ray crystallography of the ligand 15 bound to thrombin.
52. The programs CHARMM 23 and Quanta 4.0 were developed by MSI: Molecular Simulation Inc., San Diego, CA 92121-3752.
53. Fenton, J. W., II; Fasco, M. J.; Stackrow, A. B.; Aronson, D. L.; Young, A. M.; Finlayson, J. S. Human Thrombins: Production, Evaluation, and Properties of α-Thrombin. J. Biol. Chem. 1977, 252, 3587-3598.
54. Skrzypczak-Jankun, E.; Carperos, V. E.; Ravichandran, K. G.; Tulinsky, A.; Westbrook, M.; Maraganore, J. M. Structure of the Hirugen and Hirulog 1 Complexes of α-Thrombin. J. Mol. Biol. 1991, 221, 1379-1393.
55. Messerschmidt, A.; Pflugrath, J. W. Crystal Orientation and X-ray Pattern Prediction Routines for Area Detector Diffractometer Systems in Macromolecular Crystallography. Appl. Crystallogr. 1987, 20, 306-315.
56. Jones, T. A.; Zou, J.-Y.; Cowan, S. W.; Kjeldgraad, M. Improved Methods for Building Protein Models in Electron Density Maps and the Location of Errors in these Models. Acta Crystallogr. 1991, A47, 110-119.
57. Brünger, A. T. X-PLOR Manual 3.1; Yale University: New Haven, CT, 1992.
58. Engh, R. A.; Huber, R. Accurate Bond and Angle Parameters for X-ray Protein Structure Refinement. Acta Crystallogr. 1991, A47, 392-400.
59. Stone, S. R.; Hofsteenge, J. Kinetics of the Inhibition of Thrombin by Hirudin. Biochemistry 1986, 25, 4622-4628.
60. Dixon, M. The Determination of Enzyme Inhibition Constants. Biochem. J. 1953, 55, 170-171.