Crystallographic determination of the structures of human α-thrombin complexed with BMS-186282 and BMS-189090

Protein Science

Volumn 5, Issue 2, 1996, Pages 221-228

  Malley, Mary F ^a   Tabernero, Lydia ^a,b   Chang, Chiehying Y ^a   Ohringer, Shari L ^a   Roberts, Daniel G M ^a   Das, Jagabandhu ^a   Sack, John S ^a  

^a BRISTOL MYERS SQUIBB   (United States)

^b PURDUE UNIVERSITY   (United States)

Author keywords

crystallography; human thrombin inhibitor complexes; structure based drug design

Indexed keywords

1 AMINOIMINOMETHYL N [[1 [N (2 NAPHTHALENYLSULFONYL)SERYL] 2 PYRROLIDINYL]METHYL] 3 PIPERIDINECARBOXAMIDE; 4 AMINOIMINOMETHYLAMINO N [[1 [3 HYDROXY 2 (2 NAPHTHALENYLSULFONYLAMINO) 1 OXOPROPYL] 2 PYRROLIDINYL]METHYL]BUTANAMIDE; BMS 186282; BMS 189090; HIRUGEN; THROMBIN; THROMBIN INHIBITOR; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; CRYSTALLOGRAPHY; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS;

EID: 0030040580     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560050205     Document Type: Article

References (36)

1. Balasubramanian N, St. Lauret DR, Federicei ME, Meanwell NA, Wright JJ, Schmacher W, Seiler SM. 1993. Active site-directed synthetic thrombin inhibitors: Synthesis, in vitro and in vivo activity profile of BMY44621 and analogs. An examination of the role of the amino group in the D-Phe-Pro-Arg-H series. J Med Chem 36:300-303.
2. Banner DW, Hadváry P. 1991. Crystallographic analysis at 3.0 Å resolution of the binding to human thrombin of four active site-directed inhibitors. J Biol Chem 266:20085-20093.
3. -Banner DW, Hadvȧry P. 1993. Inhibitor binding to thrombin: X-ray Crystallographic studies. In: Claeson G, Scully MF, Kakkar VV, Deadman J, eds. Advances in experimental medicine and biology, vol 340. New York: Plenum Press, pp 27-33.
4. Berliner LJ, ed. 1992. Thrombin structure and function. New York: Plenum Press.
5. Bernstein FC, Koetzle TF, Williams GJB, Meyer EF Jr, Brice MD, Rodgers JR, Kennard O, Shimanouchi R, Tasumi M. 1977. The Protein Data Bank: A computer-based archival file for macromolecular structures. J Mol Biol 112:535-542.
6. Bode W, Mayr I, Baumann U, Huber R, Stone SR, Hofsteenge J. 1989. The refined 1.9 Å crystal structure of human α-thrombin: Interaction with D-Phe-Pro-Arg chloromethylketone and significance of the Tyr-Pro-ProTrp insertion segment. EMBO J 8:3467-3475.
7. Bode W, Turk D, Karshikov A. 1992. The refined 1.9 Å crystal structure of D-Phe-Pro-Arg chloromethylketone-inhibited human α-thrombin: Structure analysis, overall structure, electrostatic properties, detailed active-site geometry, and structure-function relationships. Protein Sci 1:426-411.
8. Brünger AT. 1989. X-PLOR, versions 3.1, a system for xray crystallography and NMR. New Haven, Connecticut: Yale University Press.
9. Brünger AT, Kuriyan J, Karplus M. 1987. Crystallographic R factor refinement by molecular dynamics. Science 235:458-460.
10. 50) of an enzymatic reaction. Biochem Pharm 22:3099-3108.
11. Chirgadze NY, Clawson DK, Gesellchen PD, Hermann RB, Kaiser RE, Olkoeski JL, Sall DJ, Schevitz RW, Smith GF, Shuman RT, Wery JP, Jones ND. 1992. The X-ray structure at 2.2 Å of a ternary complex containing human α-thrombin, a hirudin peptide (54-65) and an active site inhibitor. Am Cystallogr Assoc Annu Meeting 20:116. [Abstr PB311].
12. Claeson G, Scully MF, Kakkar VV, Deadman J, eds. 1993. The design of synthetic inhibitors of thrombin. Advances in experimental medicine and biology, vol 340. New York: Plenum Press.
13. Engh RA, Huber R. 1991. Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallogr A 47:392-400.
14. Fenton JW II. 1986. Thrombin. Ann NY Acad Sci 485:5-15.
15. Fenton JW II, Ofosu FA, Moon DG, Maraganore JM. 1991. Thrombin structure and function: Why thrombin is the primary target for antithrombotics. Blood Coagulation and Fibrinolysis 2:69-75.
16. Fitzgerald PMD. 1988. MERLOT, an integrated package of computer programs for the determination of crystal structures by molecular replacement. J Appl Crystallogr 21:273-278.
17. Grütter MG, Pristle JP, Rahuel J, Grossenbacher H, Bode W, Hofsteenge J, Stone SR. 1990. Crystal structure of the thrombin-hirudin complex: A novel mode of serine protease inhibition. EMBO J 9:2361-2365.
18. Hilpert K, Ackermann JA, Banner DW, Gast A, Gubernator K, Hadvâry P, Labler L, Muller K, Schmid G, Tschopp TB, van de Waterbeemd H. 1994. Design and synthesis of potent and highly selective thrombin inhibitors. J Med Chem 37:3889-3901.
19. Iwanowicz E, Lau WF, Lin J, Roberts D, Seiler SM. 1994. Retro-binding tripeptide thrombin active site inhibitors: Discovery, synthesis, and molecular modelling. J Med Chem 37:2122-2124.
20. Kabsch W. 1988a. Automatic indexing of rotation diffraction parameters. J Appl Crystallogr 21:67-71.
21. Kabsch W. 1988b. Evaluation of single crystal X-ray diffraction data from a position sensitive detector. J Appl Crystallogr 21:916-924.
22. Kimball SD, Das J, Lau WF. 11/9/1994. European Patent 0623596A.
23. Markwardt F. 1991. Hirudin and derivatives as anticoagulant agents. Thromb Hemostatis 66:141-152.
24. Martin PD, Robertson W, Turk D, Huber R, Bode W, Edwards BFP. 1992. The structure of residues 7-16 of the Aa chain of human fibrinogen bound to bovine thrombin at 2 3 Å resolution. J Biol Chem 267:7911-7920.
25. McPherson A. 1982. The growth and preliminary investigation of protein and nucleic acid crystals for X-ray diffraction experiments. In: Glick D, ed. Methods in biochemical analysis. New York: Wiley. pp 249-345.
26. Rossmann MJ. 1972. The molecular replacement method. New York: Gordon and Breach.
27. Rydel TJ, Ravichandran KG, Tulinsky A, Bode W, Huber R, Roitsch C, Fenton JW II. 1990. The structure of a complex of recombinant hirudin and human α-thrombin complex. Science 249:277-280.
28. Rydel TJ, Tulinsky A, Bode W, Huber R. 1991. Refined structure of the hirudin-thrombin complex. J Mol Biol 221:583-601.
29. Sack JS. 1988. Chain-A crystallographic modeling program. J Mol Graphics 6:244-245.
30. Shuman RT, Rothenberger RB, Campbell CS, Smith GF, Gifford-Moore DS, Gesellchen PD. 1993. Highly selective tripeptide thrombin inhibitors. J Med Chem 36:314-319.
31. Skrzypczak-Jankun E, Carpenos V, Ravichandran KG, Tulinsky A, Westbrook M, Maraganore JM. 1991. The structure of hirugen and hirulog 1 complexes of α-thrombin. J Mol Biol 221:1379-1393.
32. 2-α-thrombin crystallization and diffraction data. J Mol Biol 206:755-757.
33. Tabernero L, Chang CY, Ohringer SL, Lau WF, Iwanowicz EJ, Han WC, Wang TC, Seiler SM, Roberts DM, Sack JS. 1995. Structure of a retrobinding peptide inhibitor complexed with human α-thrombin. J Mol Biol 246:14-20.
34. Topol EJ, Bonan E, Jewitt D, Sigwart U, Kakkar VV, Rothman M, deBono D, Fegurson J, Willerson JT, Strony J, Adelman B. 1993. Use of a direct antithrombin, hirulog, in place of heparin during coronary angioplasty. Circulation 87:1622-1629.
35. Vandenbos AA, Deckers JW, Heyndrickx GR, Laarman GJ, Suryapranata H, Zijlstra F, Close P, Rijnierse JJMM, Buller HR, Serruya PW. 1993. Safety and efficacy of recombinant hirudin (CGP-29292) versus heparin in patients with stable angina undergoing coronary angioplasty. Circulation 88:2058-2066.
36. Weber PC, Lee SL, Lewandowski FA, Schadt MC, Chang CH, Kettner CA. 1995. Kinetic and crystallographic studies of thrombin with Ac-(D)Phe-Pro-boroArg-OH and its lysine, amidine, homolysine, and ornithine analogs. Biochemistry 34:3750-3757.