HostDesigner: A program for the de novo structure-based design of molecular receptors with binding sites that complement metal ion guests

Inorganic Chemistry

Volumn 41, Issue 21, 2002, Pages 5502-5512

  Hay, Benjamin P ^a   Firman, Timothy K ^a  

^a PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DRUG RECEPTOR; METAL; METAL ION;

ALGORITHM; ARTICLE; BINDING AFFINITY; BINDING SITE; CATALYSIS; CHEMICAL BINDING; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; HOST; HYDROGEN BOND; METABOLISM; METAL BINDING; MOLECULAR DYNAMICS;

ALGORITHMS; BINDING SITES; HYDROGEN BONDING; METALS; MODELS, MOLECULAR; RECEPTORS, DRUG;

EID: 0037152393     PISSN: 00201669     EISSN: None     Source Type: Journal    
DOI: 10.1021/ic0202920     Document Type: Article

References (73)

1. (a) Hancock, R. D.; Martell. A. E. Comments Inorg. Chem. 1988, 6, 237.
2. (b) Hancock, R. D.; Martell, A. E. Chem. Rev. 1989, 89, 1875.
3. (c) Martell, A. E.; Hancock, R. D. Coord. Chem. Rev. 1994, 133, 39.
4. (d) Martell, A. E.; Hancock, R. D. In Metal Complexes Aqueous Solution; Fackler, J. P., Ed.; Plenum Press: New York, 1996.
5. Schneider, H.-J.; Yatsimirsky, A. Principles and Methods in Supramolecular Chemistry; John Wiley and Sons: New York, 2000.
6. Martell, A. E.; Smith, R. D. Critical Stability Constants; Plenum Press: New York, 1974-1988; Vol. 1-6.
7. (a) Chistensen, J. J.; Eatough, D. J.; Izatt, R. M. Chem. Rev. 1974, 74, 351.
8. (b) Izatt, R. M.; Bradshaw, J. S.; Nielson, S. A.; Lamb, J.D.; Christensen, J. J. Chem. Rev. 1985, 85, 271.
9. (c) Izatt, R. M.; Pawlak, K.; Bradshaw, J. S.; Bruening, R. L. Chem. Rev. 1991, 91, 1721.
10. (d) Izatt, R. M.; Pawlak, K.; Bradshaw, J. S.; Bruening, R. L. Chem. Rev. 1995, 95, 2529.
11. Hay, B. P.; Hancock, R. D. Coord. Chem. Rev. 2001, 212, 61.
12. (a) Busch. D. H.; Farmery, K.; Goedken, V.; Katovic, V.; Melnyk, A. C.; Sperati, C. R.; Tokel, N. Adv. Chem. Ser. 1971, 100, 44.
13. (b) McDougall, G. J.; Hancock, R. D.; Boeyens, J. C. A. J. Chem. Soc., Dalton Trans. 1978, 1438.
14. (c) Anicini, A.; Fabbrizzi, L.; Paoletti, P.; Clay, R. M. J. Chem. Soc., Dalton Trans. 1978, 577.
15. (d) Cram, D. J.; Kaneda, T.; Helgeson, R. C; Brown, S. B.; Knobler, C. B; Maverick, E.; Trueblood, K. N. J. Am. Chem. Soc. 1985, 107, 3645.
16. (e) Stack, T. D. P.; Hou, Z.; Raymond, K. N. J. Am. Chem. Soc. 1993. 115, 6466.
17. (a) Hay, B. P.; Zhang, D.; Rustad, J. R. Inorg. Chem. 1996, 35, 2650.
18. (b) Hay, B. P. In Metal-Ion Separation and Preconcentration, Progress and Opportunities; Bond, A. H., Dietz, M. L., Rogers, R. D., Eds.; ACS Symposium Series 716; American Chemical Society: Washington, DC, 1999; pp 102-113.
19. (c) Hay, B. P. In Metal Separation Technologies Beyond 2000: Integrating Novel Chemistry with Processing; Liddell, K. C., Chaiko, D. J., Eds.; Minerals, Metals, Materials Society: Warrendale, PA, 1999; pp 3-13.
20. (d) Sachleben, R. A.; Moyer, B. A. In Metal-Ion Separation and Preconcentration, Progress and Opportunities; Bond, A. H., Dietz, M. L., Rogers, R. D., Eds.; ACS Symposium Series 716: American Chemical Society: Washington. DC, 1999; pp 114-132.
21. (e) Bond, A. H.; Chiarizia, R.; Huber, V. J.; Dietz M. L.; Herlinger, A. W.; Hay, B. P. Anal. Chem. 1999, 71, 2757.
22. (f) Dietz, M. L., Bond, A. H.; Hay, B. P.; Chiarizia, R.; Huber, V. J.; Herlinger, A. W. Chem, Commun. 1999, 13, 1177.
23. (g) Hay, B. P.; Dixon, D. A.; Vargas, R.; Garza, J.; Raymond, K. N. Inorg. Chem. 2001, 40, 3922.
24. (h) Lumetta, G. J.; Rapko, B. M.; Garza, P. A.; Hay, B. P.; Gilbertson, R. D.; Weakley, T. J. R.: Hutchison, J. E. J. Am. Chem. Soc. 2002, 124, 5644.
25. (a) Comba, P.; Hambley, T. W. Molecular Modeling of Inorganic Compounds, 2nd ed.; VCH: New York, 2001; Chapter 9.
26. (b) Comba, P. Coord. Chem. Rev. 1999, 185-186, 81.
27. (a) Kuntz, I. D.; Meng, E. C.; Shoichet. B. K. Acc. Chem. Res. 1994, 27, 117.
28. (b) lybrand, T. P. Curr. Opin. Struct. Biol. 1995, 5, 224.
29. (c) Böhm, H.-J. Prog. Biophys. Mol. Biol. 1996, 66, 197.
30. (d) Joseph-McCarthy, D. Pharm. Ther. 1999, 84, 179.
31. (a) Nishibata, Y.; Itai, A. Tetrahedron 1991, 47, 8985.
32. (b) Nishibata, Y.; Itai. A. J. Med. Chem. 1993, 36, 2921.
33. (c) Rotstein, S. H.; Murcko, M. A. J. Comput.-Aided Mol. Des. 1993, 7, 23.
34. (d) Bohecek, R. S.; McMartin, C. J. Am. Chem. Soc. 1994, 116, 5560.
35. (e) Gehlhaar, D. K.: Moerder, K. E.; Zichi, D.; Sherman, C. J.; Ogden. R. C.; Freer, S. T. J, Med. Chem. 1995, 38, 466.
36. (f) Luo, Z.; Wang, R.; Lai, L. J. Chem. Inf. Comput. Sci. 1996, 36, 1187.
37. (a) Böhm, H.-J. J. Comput.-Aided Mol. Des. 1992, 6, 61.
38. (b) Lawrence. M. C.; davis, P. C. Proteins: Struct. Funct. Genet. 1992, 12, 3 1.
39. (c) Ho, C. M. W.; Marshall, G. R. J. Comput.-Aided Mol. Des. 1993, 7, 623.
40. (d) Rotstein, S. H.; Murcko, M. K. J. Med. Chem. 1993. 36, 1700.
41. (e) Tschinke, V.; Cohen, N. C. J. Med. Chem. 1993, 36, 3863.
42. (f) Gillet, V. J.; Newell, W.; Mata, P.; Myatt, G. J.; Sike, S.; Zsoldos, Z.; Johnson, A. P. J.; Chem. Inf. Comput. Sci. 1994, 34, 207.
43. (g) Leach, A. R.; Kilvington, S. R. J. Comput.-Aided Mol. Des. 1994, 8, 283.
44. (h) Mata, P.; Gillet, V. J.; Johnson, A. P.; Lampreia, J.; Myatt, G. J.; Sike, S.; Stebbings, A. L. J. Chem. Inf. Comput. Sci. 1995, 35, 470.
45. (i) Roe, D. C.; Kuntz, I. D. J. Comput.-Aided Mol. Des. 1995, 9, 269.
46. (j) Wang, R. X.; Gao, Y.; Lai, L. H. J. Mol. Model. 2000, 6, 498.
47. (a) Murcko, A.; Murcko, M. A. J. Med. Chem. 1995, 38, 4953.
48. (b) Head, R. D.; Smythe, M. L.; Oprea, T. I.; Waller, C. L.; Green, S. M.; Marshall, G. R. J. Am. Chem. Soc. 1996, 118, 3959,
49. (c) Eldridge, M. D.; Murray, C, W.; Auton, T. R.; Paolini, G. V.; Mee, R. P. J. Comput.-Aided Mol. Des. 1997, 11, 425.
50. (d) Baxter, C. A.; Murray, C. W.; Clark, D. E.; Westhead, D. R.; Eldridge, M. D. Proteins: Struct. Funct. Genet. 1998, 33, 367.
51. Wang, R.; Liu, L.; Lai, L.; Tang, Y. J. Mol. Model. 1998, 4, 379.
52. Böhm, H.-J.; Schneider, G. Drug Discuss. Today 2002, 7, 64.
53. HostDesigner, version 1.0, was developed by B. P. Hay and T. K. Firman in the William R. Wiley Environmental Molecular Sciences Laboratory at the Pacific Northwest National Laboratory under partial sponsorship of Chemical Sciences, Office of Basic Energy Sciences, Office of Science, U.S. Department of Energy, under Contract DE-AC06-76RL01830. The software can be obtained at no charge from the following website: http://hostdesigner.emsl.pnl.gov.
54. MM3(96) can be obtained from Tripos Associates, 1699 S. Hanley Road, St. Louis. MO 63144, for commercial users, and it can be obtained from the Quantum Chemistry Program Exchange, Mr. Richard Counts, QCPE, Indiana University, Bloomington, IN 47405, for noncommercial users
55. Hay, B. P.; Yang, L.; Allinger, N. L.; Lii, J.-H. J. Mol. Struct. (THEOCHEM) 1998, 428, 203.
56. (a) Allinger, N. L.; Yuh, Y. H.; Lii, J.-H. J. Am. Chem. Soc. 1989, III, 8551.
57. (b) Lii, J.-H.; Allinger, N. L. J. Am. Chem. Soc. 1989, III, 8566.
58. (c) Lii, J.-H.; Allinger, N. L. J. Am. Chem. Soc. 1989, III, 8576.
59. (d) Allinger, N. L.; Li, F.; Yan, L. J. Comput. Chem. 1990, II, 848.
60. (e) Allinger, N. L.; Li, F.; Yan, L.; Tai, J. C. J. Comput. Chem. 1990, 11,868.
61. Hay, B. P.; Rustad, J. R. J. Am. Chem. Soc. 1994, 116, 6316.
62. Hancock, R. D. Prog. Inorg. Chem. 1989, 37, 187.
63. Hancock, R. D.; Maumela, H.; de Sousa, A. S. Coord. Chem. Rev. 1996, 148, 315.
64. Bernhardt, P. V.; Comba, P. Inorg. Chem. 1992, 31, 2638.
65. Hay, B. P.; Clement, O.; Sandrone, G.; Dixon, D. A. Inorg. Chem. 1998, 37, 5887.
66. (a) Nicholas, J. B.; Dixon, D. A.; Hay, B. P. J. Phys. Chem. A 1999, 103, 1394.
67. (b) Nicholas, J. B.; Hay, B. P. J. Phys. Chem. A 1999, 103. 9815.
68. Hay, B. P.; Nicholas, J. B.; Feller, D. J. Am. Chem. Soc. 2001, 122, 10083.
69. Hodgson, D. J.; Pedersen, E.; Toftlund, H.; Weiss, C. Inorg. Chim. Acta 1986, 120, 177.
70. Thom, V.; Fox, C. C.; Boeyens, J. C. A.; Hancock, R. D. J. Am. Chem. Soc. 1984, 106, 5947.
71. (a) Cooper, C. G., Jr.; Zimmer, M. Struct. Chem. 1999, 10, 17.
72. (b) Donnelly, M. A.; Zimmer, M. Inorg. Chem. 1999, 38, 1650.
73. Sofen, S. R.; Abu-Dari, K.; Freyberg, D. P.; Raymond, K. N. J. Am. Chem. Soc. 1978, 100, 7882.