Structure-based design: From renin to hiv-1 protease

Structure-based Ligand Design

Volumn 6, Issue , 2008, Pages 37-71

  Lunney, Elizabeth A ^a   Humblet, Christine ^a  

^a PFIZER INC   (United States)

Author keywords

3 (2 amino 4 thiazolyl)alanine; 3 dimensional; Allylglycine; Ethylthioglycine; Rous sarcoma virus

Indexed keywords

VIRUSES;

3-(2-AMINO-4-THIAZOLYL)ALANINE; 3-DIMENSIONAL; ALLYLGLYCINE; ETHYLTHIOGLYCINE; SARCOMA VIRUS;

AMINO ACIDS;

EID: 84956730335     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9783527612178.ch3     Document Type: Chapter

References (84)

1. Verlinde, C. L., and Hoi, W. G., Structure 2,577-587 (1994)
2. Greer, J., Erickson, J. W., Baldwin, J. J., and Varney, M. D., J. Med. Chem. 37,1035-1054 (1994)
3. Reich, S. H., and Webber, S, E., Perspect. Drug Discovery Des. 1, 371-390 (1993)
4. Kunst, I. D., Science 257,1078-1082 (1992)
5. Navia, M. A., and Murcko, M. A., Curr. Opin. Struct. Biol. 2,202-209 (1992)
6. Whittle, P. J., and Blundell, T. L., Annu. Rev. Biomol. Struct. 23,349-375 (1994)
7. Greenlee, W. J., Medicinal Research Reviews 10,173-236 (1990)
8. Bott, R., Subramanian E., and Davies, D. R., Biochemistry 21, 6956-6962 (1982)
9. Pearl, L. H., and Blundell, T. L., FEBS Lett. 174, 96-101 (1984)
10. James, M. N. G., and Sielecki, A., J. Mol. Biol. 163,299-301 (1983)
11. Carlson, W., Karplus M., and Haber, E., Hypertension 7,13-26 (1985)
12. Plattner, J. J., Greer, J., Fung, A. K., Stein, H., Kleinert, H. D., Sham, H. L., Smital, J. R., and Perun, T. J., Biochem. Biophys. Res. Commun. 139, 982-990 (1986)
13. Hutchins, C, and Greer, J., Crit. Rev. Biochem. Mol. Biol. 26,77-127 (1991)
14. Sibanda, B. L., Blundell, T., Hobart, P. M., Fogliano, M., Bindra, J. S., Dominy, B. W., and Chirg-win, J. M., FEBS Lett. 174,102-111 (1984)
15. Blundell, T. L., Jenkins, J. A., Sewell, B. T., Pearl, L. H., Cooper, J. B., Wood, S. P., Veerapandian, B.,J. Mol. Biol. 211, 919-941 (1990)
16. Suguna, K., Padian, E. A., Smith, C. W., Carlson, W. D., Davies, D. R., Proc. Natl Acad. Sci., USA 84,7009-7013 (1987)
17. Lunney, E. A., Hamilton, H. W., Hodges, J. C, Kaltenbronn, J. S., Repine, J. T., Badasso, M., Cooper, J. B., Dealwis, C, Wallace, B. A., Lowther, W. T., Dunn B. M., and Humblet, C, J. Med. Chem. 36, 3809-3820 (1993)
18. Sali, A., Veerapandian, B., Cooper, J. B., Moss, D. S., Hofmann, T., and Blundell, T. L., Proteins: Struct., Funct. Genet. 12,158-170 (1992)
19. Schechter, I., and Berger, A. The 'P' subsite nomenclature relates amino acid residues or mimics in the inhibitor to corresponding residues in the natural substrate angiotensinogen. The'S' nomenclature relates in terms of the enzyme subsites. Biochem. Biophys. Res. Commun. 27,157-162 (1967)
20. Verhoef, J. C, Bodde, H. E., de Boer, A. G., Bouwstra, J. A., Junginger, H. E., Merkus, F. W., and Breimer, D. D., Eur. J. Drug Metab. Pharmacokinet. 15,83-93 (1990)
21. Boger, J., Renin Inhibitors. Design of angiotensin transition-state analogs containing statine. In: Peptides, Structure and Function. Proceedings of the Eighth American Peptide Symposium, Hruby, V. J., and Rich, D. H. (Eds.). Pierce Chemical Co.: Rockford, IL; 569-578 (1983)
22. Boger, J., Payne, L. S., Perlow, D. S., Lohr, N. S., Poe, M., Blaine, E. H., Ulm, E. H., Schorn, T. W., La-Mont, B. I., Lin, T-Y., Kawai, M., Rich, D. H., and Veber, D. F., J. Med Chem. 28,1779-1790 (1985)
23. Hanson, G. J., Baran, J. S., Lowrie, H. S., Russell, M. A., Sarussi, S. J., Williams, K., Babler, M., Bitt-ner, S. E., Papaioannou, S. E., Yang, P-C, and Walsh, G. M., Biochem. Biophys. Res. Commun. 160, 1-5 (1989)
24. Hanson, G. J., Baran, J. S., Clare, M., Williams, K., Babler, M., Bittner, S. E., Russell, M. A., Pa-paioannou, S. E., Yang, P.-C, and Walsh, G. M. Orally active renin inhibitors containing a novel aminoglycol dipeptide (Leu-Val) mimetic. In: Peptides, Chemistry, Structure and Biology, Proceedings of the Eleventh American Peptide Symposium, Rivier, J. E., and Marshall, G. R., (Eds.). ESCOM: Leiden, Netherlands; 396-398 (1989)
25. Luly, J. R., BaMaung, N., Soderquist, J., Fung, A. K. L., Stein, H., Kleinert, H. D., Marcotte, P. A., Egan, D. A., Bopp, B., Merits, I., Bolis, G., Greer, J., Perun, T. J., and Plattner, J. J., J. Med. Chem. 31,2264-2276 (1988)
26. Rosenberg, S. H., Dellaria, J. F., Kempf, D. J., Hutchins, C. W., Woods, K. W., Maki, R. G., de Lara, E., Spina, K. P., Stein, H. H., Cohen, J., Baker, W. R., Plattner, J. J., Kleinert, H. D., and Perun, T. J., J. Med. Chem. 33,1582-1590 (1990)
27. Repine, J. T., Himmelsbach, R. J., Hodges, J. C, Kaltenbronn, J. S., Sircar, I., Skeean, R. W., Bren-nan, S. T., Hurley, T. R., Lunney, E., Humblet, C. C, Weishaar, R. E., Rapundalo, S., Ryan, M. J., Taylor, D. G., Olson, S. C, Michniewicz, B. M., Kornberg, B. E., Belmont, D. T., and Taylor, M. D., J. Med. Chem. 34,1935-1943 (1991)
28. Lunney, E. A., and Humblet, C. C. Comparative molecular modeling analyses of endothiapepsin complexes as renin model templates. In: Peptides: Chemistry, Structure and Biology, Proceedings of the Eleventh American Peptide Symposium, Marshall, G. R., and Rivier, J. E. (Eds.). ESCOM: Leiden, Netherlands; 387-389 (1990)
29. Cooper, J., Quail, W., Frazao, C, Foundling, S. I., Blunder, T. L., Humblet, C, Lunney, E. A., Low-ther, W. T., Dunn, B. M, Biochemistry 31, 8142-8150 (1992)
30. de Laszlo, S. E., Bush, B. L., Doyle, J. J., Greenlee, W. J, Hangauer, D. G., Halgren, T. A., Lynch, R. J., Schorn, T. W., and Siegl, P. K. S., J. Med. Chem. 35,833-846 (1992)
31. Allen, F. H., Kennard, O., and Taylor, R., Ace. Chem. Res. 16,146-153 (1983)
32. Allen, F. H., Bellard, S., Brice, M. D., Cartwright, B. A., Doubleday, A., Higgs, H., Hummelink, T., Hummelink-Peters, B. G., Kennard, O., Motherwell, W. D. S., Rodgers, J. R., and Watson, D. G., Acta Crystal-logr. B35,2331-2339 (1979)
33. Reily, M. D., Thanabal, V., Lunney, E. A., Repine, J. T., Humblet, C. C, and Wagner, G., FEBS Lett. 302, 97-103 (1992)
34. Weber, A. E., Halgren, T. A., Doyle, J. J., Lynch, R. J., Siegl, P. K. S., Parsons, W. H., Greenlee, W. J., and Patchett, A. A., J. Med. Chem. 34,2692-2701 (1991)
35. Weber, A. E., Steiner, M. G, Krieter, P. A., Colletti, A. E., Tata, J. R., Halgren, T. A., Ball, R. G., Doyle, J. J., Schorn, T. W., Stearns, R. A., Miller, R. R., Siegl, P. K. S., Greenlee, W. J., and Patchett, A. A., J. Med. Chem. 35,3755-3773 (1992)
36. Thaisrivongs, S., Blinn, J. R., Pals, D. T and Turner, S. R., J. Med. Chem. 34,1276-1282 (1991)
37. Greer, J., Hutchins, C., Bolis, G., Fung, A., and Sham, H. Comparative modeling of proteins in the design of novel cyclic renin inhibitors. In: Proteins, Renugoplakrishnan, V. (Ed.). ESCOM: Leiden, Netherlands; 283-289 (1991)
38. Brotherton-Pleiss, C. E., Newman, S. R., Waterbury, L. D., and Schwartzberg, M. S. Design and synthesis of conformationally restricted renin inhibitors. In: Peptides: Chemistry and Biology, Proceedings of the Twelfth American Peptide Symposium, Smith, J. A., and Rivier, J. E. (Eds.). ESCOM: Leiden, Netherlands; 816-817 (1992)
39. Plummer, M., Hamby, J. M., Hingorani, G., Batley, B. L., and Rapundalo, S. T., Bioorg. Med. Chem. Lett. 3,2119-2124 (1993)
40. Motoc, I., Dammkoehler, R. A., Mayer, D., and Labanowski, J., Quant. Struct.-Act. Relat. 5,99-105 (1986)
41. Plummer, M. S., Shahripour, A., Kaltenbronn, J. S., Lunney, E. A., Steinbaugh, B. A., Hamby, J. M., Hamilton, H. W., Sawyer, T. K., Humblet, C, Doherty, A. M., Taylor, M. D., Hingorani, G., Batley, B. L., and Rapundalo, S. T., J. Med. Chem. 38,2893-2905 (1995)
42. Doherty, A. M., Kaltenbronn, J. S., Hudspeth, J. P., Repine, J. T., Roark, W. H., Sircar, I., Tinney, F. J., Connolly, C. J., Hodges, J. C, Taylor, M. D., Batley, B. L., Ryan, M. J., Essenburg, A. D., Rapundalo, S. T, Weishaar, R. E., Humblet, C, and Lunney, E. A., J. Med. Chem. 34, 1258-1271 (1991)
43. Thaisrivongs, S., Pals, D. T., Turner, S. R., and Kroll, L. T., J Med. Chem. 31,1369-1376 (1988)
44. Rahuel, J., Priestle, J., and Gruetter, M. G., J. Struct. Biol. 107,227-236 (1991)
45. Dhanaraj, V., Dealwis, C. G., Frazao, C, Badasso, M., Sibanda, B. L., Tickle, I. J., Cooper, J. B., Driessen, H. P. C, Newman, M., Aguilar, C, Wood, S. P., Blundell, T. L., Hobart, P. M., Geog-hegan, K. F., Ammirati, M. J., Danley, D. E., O'Connor, B. A., and Hoover, D. J., Nature 357, 466-472 (1992)
46. Lim, L. W., Roderick, A. S., Leimgruber, N. K., Gierse, J. K., Abdel-Meguid, S. S.J. Mol. Biol. 210, 239-240 (1989)
47. Sielecki, A. R., Hayakawa, K., Fujinaga, M., Murphy, M. E. P., Fraser, M., Muir, A. K., Carilli, C. T., Lewicki, J. A., Baxter, J. D., and James, M. N. G., Science 243,1346-1351 (1989)
48. Frazao, C, Topham, C, Dhanaraj, V., Blundell, T. L., Pure Appl. Chem. 66,43-50 (1994)
49. Blundell, T. L., Carney, D., Gardner, S., Hayes, F., Howlin, B., Hubbard, T., Overington, J., Singh, D. A., Sibanda, B. L., and Sutcliffe, M. J., Eur. J. Biochem. 172,513-520 (1988)
50. Toh, H., Ono, M., Saigo, K., and Miyata, T., Nature 315,691-692 (1985)
51. Miller, M., Jaskolski, M., Rao, J. K. M., Leis, J., and Wlodawer, A., Nature 337, 576-579 (1989)
52. Katz, R. A, and Skalka, A. M. Annu. Rev. Biochem. 63,133-173 (1994)
53. Kohl, N. E., Emini, E. A., Schleif, W. A., Davis, L. I., Heimbach, J. C, Dixon, R. A., Scolnick, E. M., and Sigal, I. S., Proc. Natl Acad. Sci., USA 85,4686-4690 (1988)
54. McQuade, T. K., Tomasselli, A. G., Liu, L., Karacostas, V., Moss, B., Sawyer, T. K., Heinrikson, R.L., and Tarpley, W. G., Science 247,454-456 (1990)
55. Kaplan, A. H., Zack, J. A., Knigge, M., Paul, D. A., Kempf, D. J., Norbeck, D. W., and Swanstrom, R. J., J. Virol. 67,4050-4055 (1993)
56. Humblet, C. C, Lunney, E. A., Buckheit Jr., R. W., Doggett, C, Wong, R. and Antonucci, T. K., Antiviral Research 21,73-84 (1993)
57. Weber, I. T., Miller, M., Jaskolski, M., Leis, J., Skalka, A. M., and Wlodawer, A., Science 243, 928-931 (1989)
58. Navia, M. A., Fitzgerald, P. M. D., McKeever, B. M., Leu, C.-T., Heimbach, J. C, Herber, W. K., Sigal, I. S., Drake, P. L., and Springer, J. P., Nature 337, 615-620 (1989)
59. Wlodawer, A., Miller, M., Jaskolski, M., Sathyanarayana, B. K., Baldwin, E., Weber, I. T., Selk, L. M., Clawson, L., Schneider, J., and Kent, S. B. H., Science 245,616-621 (1989)
60. Appelt, K., Perspect. Drug Discovery Des. 1,23-48 (1993)
61. Erickson, J. W., Perspect. Drug Discovery Des. 1,109-128 (1993)
62. Kuntz, I. D., Blaney, J. M., Oatley, S. J., Langridge, R., and Ferrin, T. E., J. Mol. Biol. 161,269-288 (1982)
63. DesJarlais, R. L., Seibel, G. L., Kuntz, X D., Furth, P. S., Alvarez, J. C, Ortiz de Montellano, P. R., DeCamp, D. L., Babe, L. M., Craik, C. S., Proc. Natl Acad. Sci., USA 87, 6644-6648 (1990)
64. Rutenber, E., Fauman, E. B., Keenan, R. J, Fong, S., Furth, P. S., Oritz deMontellano, P. R., Meng, E., Kuntz, X D., DeCamp, D. L., Salto, R., Rose, X R., Craik, C. S., and Stroud, R. M., J. Biol. Chem. 268,15343-15346(1993)
65. Appelt, K., 33rd Interscience Conference on Antimicrobial Agents & Chemotherapy, New Or-leans, LA., 1993
66. Kim, E. E., Baker, C. T., Dwyer, M. D., Murcko, M. A., Rao, B. G., Tung, R. D., and Navia, M. A., J. Am. Chem. Soc. 117,1181-1182 (1995)
67. Ramnarayan, S. R., Pan, W., Gulnik, S. V., Burt, S., and Erickson, J. W., Biorg. Med. Chem. Lett. 4, 1247-1252 (1994)
68. Lam, P. Y. S., Jadhav, P. K., Eyermann, C. J., Hodge, C. N., Ru, Y., Bacheler, L. T., Meek, J. L., Otto, M. J., Rayner, M. M., Wong, Y. N., Chang, C.-H., Weber, P. C, Jackson, D. A., Sharpe, T. R., and Erickson-Viitanen, S. K., Science 263,380-383 (1994)
69. DesJarlais, R. L., Sheridan, R. P., Seibel, G. L., Dixon, J. S., Kuntz, X D., and Venkataraghavan, R., J. Med. Chem. 31,722-729 (1988)
70. Chenera, B., DesJarlais, R. L., Finkelstein, J. A., Eggleston, D. S., Meek, T. D., Tomaszek, Jr., T. A., and Dreyer, G. B., Biorg. Med. Chem. Lett. 3, 2717-2722 (1993)
71. Tummino, P. J., Ferguson, D., Hupe, L., and Hupe, D., Biochem. Biophys. Res. Commun. 200, 1658-1664 (1994)
72. Thaisrivongs, S., Tomich, P. K., Watenpaugh, K. D., Chong, K.-T., Howe, W. J., Yang, C.-P., Stroh-bach, J. W., Turner, S. R., McGrath, J. P., Bohanon, M. J., Lynn, J, C, Mulichak, A. M., Spinelli, P. A., Hinshaw, R. R., Pagano, P. J., Moon, J. B., Ruwart, M. J., Wilkinson, K. F., Rush, B. D., Zipp, G. L., Dalga, R. J., Schwende, F. J., Howard, G. M., Padbury, G. E., Toth, L. N., Zhao, Z., Koep-linger, K. A., Kakuk, T. J., Cole, S. L., Zaya, R. M., Piper, R. C, and Jeffrey, P., J. Med. Chem. 37, 3200-3204 (1994)
73. Lunney, E. A., Hagen, S. E., Domagala, J. M., Humblet, C, Kosinski, J., Tait, B. D., Warmus, J. S., Wilson, M., Ferguson, D., Hupe, D., Tummino, P. J., Baldwin, E. T., Bhat, T. N., Liu, B., and Erickson, J. W., J. Med. Chem. 37,2664-2677 (1994)
74. Goodsell, D. S., and Olson, A. J., Proteins: Struct, Fund. Genet. 8,195-202 (1990)
75. Goodford, P. J., J Med. Chem. 28,849-857 (1985)
76. GRID Software Program, Molecular Discovery Ltd., West Way House, Elms Parade, Oxford, OX2 9LL, UK
77. Vara Prasad, J. V. N., Para, K. S., Lunney, E. A., Ortwine, D. F., Dunbar, Jr., J. B., Ferguson, D., Tummino, P. J., Hupe, D., Tait, B. D., Domagala, J. M., Humblet, C, Bhat, T. N., Liu, B., Guerin, D. M. A., Baldwin, E. T., Erickson, J. W., and Sawyer, T. K., J. Am. Chem. Soc. 116, 6989-6990 (1994)
78. Ortwine, D., Dunbar, Jr., J. B., Lunney, E. A., Vara Prasad, J. V. N., Para, K. S., Bhat, T. N., Liu, B., Baldwin, E. T., and Erickson, J. W. A Comparison of Docking Approaches. 10th European Symposium on Structure-Activity Relationships: QSAR and Molecular Modeling, Barcelona, 4-9 September (1994)
79. Ho, C. M. W., and Marshall, G. R., J. Comput.-Aided Molec. Des. 4,337-354 (1990)
80. Vara Prasad, J. V. N., Para, K. S., Tummino, P. J., Ferguson, D., McQuade, T. J., Lunney, E. A., Ra-pundalo, S. T., Batley, B. L., Hingorani, G., Domagala, J. M., Grachek, S. X, Bhat, T. N., Liu, B., Baldwin, E. T., Erickson, J. W., and Sawyer, T. K., J Med. Chem. 38, 898-905 (1995)
81. Tait, B. D. HIV Protease: Non-peptide Leads from Compound Collections. The First Winter Conference on Medicinal and Bioorganic Chemistry, Steamboat Springs, Jan. 29-Feb. 2 (1995)
82. Olson, A. J., and Morris, G. M., Perspect. Drug Discovery Des. 1,329-344 (1993)
83. Blaney, J. M., and Dixon, J. S., Perspect. Drug Discovery Des. 1,301-319 (1993)
84. Erickson, J. W., Neidhardt, D. J., VanDrie, J., Kempf, D. J., Wang, X. C, Norbeck, D. W., Plattner, J. J., Rittenhouse, J. W., Turon, M., Wideburg, N., Kohlbrenner, W. E., Simmer, R., Helfrich, R., Paul, D. A., and Knigge, M., Science 249,527-533 (1990)