Protein-protein interactions as a target for drugs in proteomics

Proteomics

Volumn 3, Issue 4, 2003, Pages 380-391

  Archakov, Alexander I ^a   Govorun, Vadim M ^a   Dubanov, Alexander V ^a   Ivanov, Yuri D ^a   Veselovsky, Alexander V ^a   Lewi, Paul ^b   Janssen, Paul ^b  

^a INSTITUTE OF BIOMEDICAL CHEMISTRY   (Russian Federation)

^b Center for Molecular Design   (Belgium)

Author keywords

Bioinformatics; Dimerizers; Inhibitor of protein dimerization; Protein protein interaction; Review; Target for drugs

Indexed keywords

BIOINFORMATICS; CATALYSIS; COMPLEX FORMATION; COVALENT BOND; DIMERIZATION; DRUG TARGETING; ENZYME ACTIVE SITE; IONIC STRENGTH; NONHUMAN; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN MODIFICATION; PROTEIN PROTEIN INTERACTION; PROTEOMICS; REVIEW;

COMPUTATIONAL BIOLOGY; DRUG DESIGN; PROTEIN BINDING; PROTEINS; PROTEOMICS; TWO-HYBRID SYSTEM TECHNIQUES;

EID: 0037388679     PISSN: 16159853     EISSN: None     Source Type: Journal    
DOI: 10.1002/pmic.200390053     Document Type: Review

References (162)

1. Cohen, F. E., Prusiner, S. B., Annu. Rev. Biochem. 1998, 67, 793-819.
2. Loregian, A., Mardsen, H. S., Palu, G., Rev. Med. Virol. 2002, 12, 239-262.
3. Selkoe, D. J., Trends Cell Biol. 1998, 8, 443-457.
4. Archakov, A. I., Ivanov, Y. D., in: Biophysics of Electron Transfer and Molecular Bioelectronics, Pleum Publication, USA 1999, pp. 173-194.
5. Furukawa, Y., Ishimory, K., Morishima, I., Biochemistry 2002, 41, 9824-9832.
6. Eyster, K. M., Biochem. Pharmacol. 1998, 55, 1927-1938.
7. Klemm, J. D., Schreiber, S. L., Crabtree, G. R., Annu. Rev. Immunol. 1998, 16, 569-592.
8. Markus, M., Benezra, R., J. Biol. Chem. 1999, 274, 1040-1049.
9. Jones, S., Thornton, J. M., in: Kleanthous, C. (Ed.), Protein-protein Recognition, Oxford University Press, New York 2000, pp. 33-59.
10. Tsai, C.-J., Xu, D., Nissinov, R., Protein Sci. 1997, 6, 1797-1809.
11. Dmitriev, D. A., Massino, Y. S., Segal, O. L., Smirnova, M. B. et al., J. Immunol. Methods 2002, 261, 103-118.
12. Jones, S., Thornton, J. M., Proc. Natl. Acad. Sci. USA 1996, 93, 13-20.
13. Stites, W. E., Chem. Rev. 1997, 97, 1233-1250.
14. Davies, D. R., Cohen, G. H., Proc. Natl. Acad. Sci. USA 1996, 93, 7-12.
15. Ivanov, Y. D., Kanaeva, I. P., Kuznetsov, V. Y., Lehnerer, M. et al., Arch. Biochem. Biophys. 1999, 362, 87-93.
16. Ivanov, Y., Kanaeva, I., Archakov, A., Biochem. Biophys. Res. Commun. 2000, 273, 750-752.
17. Tsai, C.-J., Lin, S. L., Wolfson, H. J., Nissinov, R., Protein Sci. 1997, 6, 53-64.
18. Tsai, C.-J., Lin, S. L., Wolfson, H. J., Nissinov, R., Crit. Rev. Biochem. Mol. Biol. 1996, 31, 127-152.
19. Wells, J. A., Proc. Natl. Acad. Sci. USA 1996, 93, 1-6.
20. Lijnzaad, P., Argos, P., Proteins 1997, 28, 333-343.
21. Stevens, J. M., Armstrong, R. N., Dirr, H. W., Biochem. J. 2000, 347, 193-197.
22. Ivanov, Y. D., Kanaeva, I. P., Karuzina, I. P., Archakov, A. I. et al., Arch. Biochem. Biophys. 2001, 391, 255-264.
23. Sheinerman, F. B., Norel, R., Honig, B., Curr. Opin. Struct. Biol. 2000, 10, 153-159.
24. Xu, D., Lin, S. L., Nissinov, R., J. Mol. Biol. 1997, 265, 68-84.
25. Xu, D., Tsai, C.-J., Nissinov, R., Protein Eng. 1997, 10, 999-1012.
26. McCoy, A. J., Chandana, E. V., Colman, P. M., J. Mol. Biol. 1997, 268, 570-584.
27. Camacho, C. J., Weng, Z. P., Vajda, S., Delisi, C., Biophys. J. 1999, 76, 1166-1178.
28. Vijayakumar, M., Wong, K. Y., Schreiber, G., Fersht, A. R. et al., J. Mol. Biol. 1998, 278, 1015-1024.
29. Lo Conte, L., Chothia, C., Janin, J., J. Mol. Biol. 1999, 285, 2177-2198.
30. Janin, J., Structure Fold. Des. 1999, 7, 277-279.
31. Larsen, T. A., Olson, A. J., Goodsell, D. S., Structure 1998, 6, 421-427.
32. Dall'Acqua, W., Goldman, E. R., Lin, W., Teng, C. et al., Biochemistry 1998, 37, 7981-7991.
33. Vaughan, C. K., Buckle, A. M., Fersht, A. R., J. Mol. Biol. 1999, 286, 1487-1506.
34. Betts, M. J., Sternberg, M. J. E., Protein Eng. 1999, 12, 271-283.
35. Kimura, S. R., Brower, R. C., Vajda, S., Camacho, C. J., Biophys. J. 2001, 80, 635-642.
36. McCammon, J. A., Curr. Opin. Struct. Biol. 1998, 8, 245- 249.
37. Sundberg, E. J., Mariuzza, R. A., Structure Fold. Des. 2000, 8, R137-R142.
38. Janin, J., in: Kleanthous, C. (Ed.), Protein-protein Recognition, Oxford University Press, New York 2000, pp. 1-32.
39. Brady, G. P., Sharp, K. A., Curr. Opin. Struct. Biol. 1997, 7, 215-221.
40. Zeden-Lutz, G., Zuber, E., Witz, J., Van Regenmortel, M. H., Anal. Biochem. 1997, 246, 123-132.
41. Schreiber, G., Frisch, C., Fersht, A. R., J. Mol. Biol. 1997, 270, 111-122.
42. Mathews, F. S., Mauk, A. G., Moore, G. R., in: Kleanthous, C. (Ed.), Protein-protein Recognition, Oxford University Press, New York 2000, pp. 60-101.
43. Jiang, L., Lai, L., J. Biol. Chem. 2002, 15, 1-48.
44. Clackson, T., Wells, J. A., Science 1995, 267, 383-386.
45. Davis, S. J., Davies, E. A., Tucknott, M. G., Jones, E. Y., van der Merwe, P. A., Proc. Natl. Acad. Sci. USA 1998, 95, 5490- 5494.
46. Eubanks, S., Nguyen, T. L., Peyton, D., Breslow, E., Biochemistry 2000, 39, 8085-8094.
47. Koltzscher, M., Gerke, V., Biochemistry 2000, 39, 9533- 9539.
48. Lin, C. T., Kuo, T. J., Shaw, J. F., Kao, M. C., J. Agr. Food Chem. 1999, 47, 2944-2949.
49. Martin, C., Hartley, R., Mauguen, Y., FEBS Lett. 1999, 452, 128-132.
50. Mateu, M. G., Fersht, A. R., EMBO J. 1998, 17, 2748-2758.
51. Scott, S., Dong, F. M., Kisterswoike, B., Mullerhill, B., J. Mol. Biol. 2000, 296, 673-684.
52. Thomas, M. C., Ballantine, S. P., Bethell, S. S., Bains, S. et al., Biochemistry 1998, 37, 11629-11636.
53. Zeng, J., Fridman, M., Maruta, H., Treutlein, H. R., Simonson, T., Protein Sci. 1999, 8, 50-64.
54. Bogan, A. A., Thorn, K. S., J. Mol. Biol. 1998, 280, 1-9.
55. Hu, Z. J., Ma, B. Y., Wolfson, H., Nussinov, R., Proteins 2000, 39, 331-342.
56. McInnes, C., Grothe, S., O'Connor-McCourt, M., Sykes, B. D., Protein Eng. 2000, 13, 143-147.
57. von Kries, J. P., Winbeck, G., Asbrand, C., Schwarz- Romond, T. et al., Nat. Struct. Biol. 2000, 7, 800-807.
58. Lebowitz, J., Lewis, M. S., Schuck, P., Protein Sci. 2002, 11, 2067-2079.
59. Veselovsky, A. V., Ivanov, Y. D., Ivanov, A. S., Archakov, A. I., J. Mol. Recognit. 2002, 15, 405-422.
60. Otzen, D. E., Fersht, A. R., Protein Eng. 1999, 12, 41-45.
61. Spinozzi, F., Gazzillo, D., Giacometti, A., Mariani, P., Carsughi, F., J. Biophys. 2002, 82, 2165-2175.
62. Cole, S. T., Brosch, R., Parkhill, J., Garnier, T. et al., Nature 1998, 393, 537-544.
63. Eisenberg, D., Marcotte, E. M., Xenarios, I., Yeates, T. O., Nature 2000, 405, 823-826.
64. Freiberg, C., Drug Discov. Today 2001, 6, S72-S80.
65. Ruettinger, R. T., Wen, L.-P., Fulco, A. J., J. Biol. Chem. 1989, 264, 10987-10995.
66. Marcotte, E. M., Pellegrini, M., Ng, H.-L., Rice, D. W. et al., Science 1999, 285, 751-753.
67. Bansal, K., Bioinformatics 1999, 15, 900-908.
68. Karp, P. D., Krummenacker, M., Paley, S., Wagg, J., Trends Biotech. 1999, 17, 275-281.
69. Gomez, S. M., Rzetsky, A. Pacific Symp. Biocomputing 2002, 413-424.
70. Butte, A. J., Kohane, I. S., Pacific Symp. Biocomputing 2000, 5, 415-426.
71. Deane, C. M., Salvinsky, L., Xenarios, I., Eisenberg, D. Mol. Cell Proteomics 2002, 1, 349-356.
72. Galperin, M. Y., Coonin, E. G., Curr. Opin. Biotech. 1999, 10, 571-578.
73. Gotoh, O., J. Biol. Chem. 1992, 267, 83-90.
74. Ito, T., Chiba, T., Ozawa, R., Yoshida, M. et al., Proc. Natl. Acad. Sci. USA 2001, 98, 4569-4574.
75. Auerbach, D., Thaminy, S., Hottiger, M. O., Stagljar, I., Proteomics 2002, 2, 611-623.
76. Fransen, M., Brees, C., Ghys, K., Amery, L. et al., Mol. Cell Proteomics 2002, 1, 243-252.
77. Drees, B. L., Curr. Opin. Chem. Biol. 1999, 3, 64-70.
78. Zhang, B., Kraemer, B., SenGupta, S., Fields, S., Wickens, M., Methods Enzymol. 1999, 306, 93-113.
79. Vidal, M., in: Bartel, P., Fields, S., (Eds.), The Two-Hybrid System, Oxford University Press, New York 1997, p. 109.
80. Johnsson, N., Varshavsky, A., Proc. Natl. Acad. Sci. USA 1994, 91, 10340-10344.
81. Osborne, M. A., Dalton, S., Kochan, J. P., Biotechnology (NY) 1995, 13, 1474-1478.
82. Kochan, J. P., Volpers, C., Osborne, M. A., Methods Enzymol. 2000, 328, 111-127.
83. Aronheim, A., Engelberg, D., Li, N., al-Alawi, N. et al., Cell 1994, 78, 949-961.
84. Marsolier, M. C., Tanaka, S., Livingstone-Zatchej, M., Grunstein, M. et al., Genes Dev. 1995, 9, 410-422.
85. Yang, M., Wu, Z., Fields, S., Nucleic Acids Res. 1995, 23, 1152-1156.
86. Geyer, C. R., Colman-Lerner, A., Brent, R., Proc. Natl. Acad. Sci. USA 1999, 96, 8567-8572.
87. Norman, T. C., Smith, D. L., Sorger, P. K., Drees, B. L. et al., Science 1999, 285, 591-595.
88. He, M., Taussig, M. J., Nucleic Acids Res. 2001, 29, e73-3.
89. Walter G., Bussow, K., Cahill, D., Lueking, A., Lehrach, H., Curr. Opin. Microbiol. 2000, 3, 298-302.
90. Shevchenko, A., Schaft, D., Roguev, A., Pijnappel, W. W. et al., Mol. Cell Proteomics 2000, 1, 204-212.
91. Ivanov, Y. D., Gara, O. G., Konstantinova, N. I., Moshkovsky, S. A. et al., Vopr. Med. Chem. 2003, in press.
92. Catimel, B., Weinstock, N. M., Domagala, T., Nice, E. C., J. Chromatogr. A 2000, 869, 261-273.
93. Natsume, T., Nakayama, H., Isobe, T., Trends Biotech. 2001, 19, S28-S33.
94. Krone, J. R., Nelson, R. W., Dogruel, D., Williams, P., Granzow, R., Anal. Biochem. 1997, 244, 124-132.
95. Berkowitz, O., Wirtz, V., Wolf, A., Kuhlmann, J., Hell, R., J. Biol. Chem. 2002, 277, 30629-30634.
96. Ivanov, Y. D., Usanov, S. A., Archakov, A. I., Biochem. Mol. Biol. Int. 1999, 47, 327-336.
97. Ivanov, Y. D., Kanaeva, I. P., Karuzina, I. I., Usanov, S. A. et al., J. Inorg. Biochem. 2001, 87, 175-184.
98. Davis, S., Aldrich, T. H., Jones, P. F., Acheson, A. et al., Cell 1996, 87, 1161-1169.
99. Sakano, S., Serizawa, R., Inada, T., Iwama, A. et al., Oncogene 1996, 13, 813-822.
100. Sonksen, C. P., Nordhoff, E., Jansson, O., Malmqvist, M., Roepstorff, P., Anal. Chem. 1998, 70, 2731-2736.
101. Ivanov, Y. D., Panova, N. G., Buneeva, O. A., Medvedev, A. E., Archakov, A. E., Vopr. Med. Chem. 2002, 48, 73-83.
102. Ivanov, Y. D., Gnedenko, O. V., Nikolaeva, L. I., Konev, V. A. et al., Vopr. Med. Chem. 2001, 419-425.
103. Ivanov, Y. D., Gnedenko, O. V., Nikolaeva, L. I., Konev, V. A. et al., J. Microbiol., Immunobiol. Epidemiol. 2003, in press.
104. Hochstrasser, D. F., Sanchez, J. C., Appel, R. D., Proteomics 2002, 2, 807-812.
105. Kathryn, Y., The Biochemist 2001, February, 19-20.
106. Srivastava, A. K., Sauer, R. T., Biochemistry 2000, 39, 8308-8314.
107. Wallace, L. A., Dirr, H. W., Biochemistry 1999, 38, 16686-16694.
108. Austin, D. J., Crabtree, G. R., Schreiber, S. L., Chem. Biol. 1994, 1, 131-136.
109. Clemons, P. A., Curr. Opin. Chem. Biol. 1999, 3, 112-115.
110. Michnick, S. W., Chem. Biol. 2000, 7, R217-R221.
111. Beeley, N. R. A., Drug Discov. Today 2000, 5, 354-363.
112. Cochran, A. G., Chem. Biol. 2000, 7, R85-R94.
113. Cochran, A. G., Curr. Opin. Chem. Biol. 2001, 5, 654-659.
114. Cody, W. L., Lin, Z. W., Panek, R. L., Rose, D. W., Rubin, J. R., Curr. Pharm. Design. 2000, 6, 59-98.
115. Freidinger, R. M., Curr. Opin. Chem. Biol. 1999, 3, 395-406.
116. Way, J. C., Curr. Opin. Chem. Biol. 2000, 4, 40-46.
117. Zutshi, R., Brickner, M., Chmielewski, J., Curr. Opin. Chem. Biol. 1998, 2, 62-65.
118. Belshaw, P. J., Ho, S. N., Crabtree, G. R., Schreiber, S. L., Proc. Natl. Acad. Sci. USA 1996, 93, 4604-4607.
119. Kopytek, S. J., Standaert, R. F., Dyer, J. C. D., Hu, J. C., Chem. Biol. 2000, 7, 313-321.
120. Smith, K. M., Vanetten, R. A., J. Biol. Chem. 2001, 276, 24372-24379.
121. Amara, J. F., Clackson, T., Rivera, V. M., Guo, T. et al., Proc. Natl. Acad. Sci. USA 1997, 94, 10618-10623.
122. Keenan, T., Yaeger, D. R., Courage, N. L., Rollins, C. T. et al., Bioorg. Med. Chem. 1998, 6, 1309-1335.
123. MacCorkle, R. A., Freeman, K. W., Spencer, D. M., Proc. Natl. Acad. Sci. USA 1998, 95, 3655-3660.
124. Blau, A. C., Petrson, K. R., Drachman, J. G., Spencer, D. M., Proc. Natl. Acad. Sci. USA 1997, 94, 3076-3081.
125. Clackson, T., Yang, W., Rozamus, L. W., Hatada, M. et al., Proc. Natl. Acad. Sci. USA 1998, 95, 10437-10442.
126. Yang, W., Rozamus, L. W., Narula, S., Rollins, C. T. et al., J. Med. Chem. 2000, 43, 1135-1142.
127. Aviezer, D., Cotton, S., David, M., Segev, A. et al., Cancer Res. 2000, 60, 2973-2980.
128. Rohrer, S. P., Birzin, E. T., Mosley, R. T., Berk, S. C. et al., Science 1998, 282, 737-740.
129. Parker, S. L., Parker, M. S., Can. J. Physiol. Pharmacol. 2000, 78, 150-161.
130. Marusawa, H., Setoi, H., Kuroda, A., Sawada, A. et al., Bioorg. Med. Chem. 1999, 7, 2635-2645.
131. Fujita, T., Nakajima, M., Inoue, Y., Nose, T., Shimohigashi, Y., Bioorg. Med. Chem. Lett. 1999, 9, 1351-1356.
132. Hoekstra, W. J., Hulshizer, B. L., McComsey, D. F., Andrade-Gordon, P. et al., Bioorg. Med. Chem. Lett. 1998, 8, 1649-1654.
133. Burke, T. R., Yao, Z. J., Gao, Y., Wu, J. X. et al., Bioorg. Med. Chem. 2001, 9, 1439-1445.
134. Davidson, J. P., Martin, S. F., Tetrahedron Lett. 2000, 41, 9459-9464.
135. Fretz, H., Furet, P., Garciaecheverria, C., Rahuel, J., Schoepfer, J., Curr. Pharm. Design 2000, 6, 1777-1796.
136. Niimi, T., Orita, M., Okazawaigarashi, M., Sakashita, H. et al., J. Med. Chem. 2001, 44, 4737-4740.
137. Shakespeare, W. C., Curr. Opin. Chem. Biol. 2001, 5, 409-415.
138. Vu, C. B., Curr. Med. Chem. 2000, 7, 1081-1100.
139. Bouras, A., Boggetto, N., Benatalah, Z., Derosny, E. et al., J. Med. Chem. 1999, 42, 957-962.
140. Morris, M. C., Robert-Hebmann, V., Chaloin, L., Mery, J. et al., J. Biol. Chem. 1999, 274, 24941-24946.
141. Sourgen, F., Maroun, R. G., Frere, V., Bouziane, M. et al., Eur. J. Biochem. 1996, 240, 765-773.
142. Liuzzi, M., Deziel, R., Moss, N., Beaulieu, P. et al., Nature 1994, 372, 695-698.
143. Digard, P., Williams, K. P., Hensley, P., Brooks, I. S. et al., Proc. Natl. Acad. Sci. USA 1995, 92, 1456-1460.
144. Nordhoff, A., Tziatzios, C., van den Broek, J. A., Schott, M. K. et al., Eur. J. Biochem. 1997, 245, 273-282.
145. Eaton, S. R., Cody, W. L., Doherty, A. M., Holland, D. R. et al., J. Med. Chem. 1998, 41, 4329-4342.
146. Schramm, H. J., Derosny, E., Reboudravaux, M., Buttner, J. et al., Biol. Chem. 1999, 380, 593-596.
147. Shultz, M. D., Chmielewski, J., Bioorg. Med. Chem. Lett. 1999, 9, 2431-2436.
148. Sennequier, N., Wolan, D., Stuehr, D. J., J. Biol. Chem. 1999, 274, 930-938.
149. Usui, T., Kondoh, M., Mayumi, T., Osada, H., Biochem. J. 1998, 333, 543-548.
150. Pacofsky, G. J., Lackey, K., Alligood, K. J., Berman, J. et al., J. Med. Chem. 1998, 41, 1894-1908.
151. Findeis, M. A., Biochim. Biophys. Acta 2000, 1502, 76-84.
152. Souroujon, M. C., Mochly-Rosen, D., Nat. Biotechnol. 1998, 16, 919-924.
153. Shultz, M. D., Chmielewski, J., Tetrahedron 1997, 8, 3881- 3886.
154. Ulysse, L. G., Chmielewski, J., Bioorg. Med. Chem. Lett. 1998, 8, 3281-3152.
155. Song, M. C., Rajesh, S., Hayashi, Y., Kiso, Y., Bioorg. Med. Chem. Lett. 2001, 11, 2465-2468.
156. Maroun, R. G., Gayet, S., Benleulmi, M. S., Porumb, H. et al., Biochemistry 2001, 40, 13840-13848.
157. Park, S. H., Raines, R. T., Nat. Biotechnol. 2000, 18, 847-851.
158. Singh, S. K., Maithal, K., Balaram, H., Balaram, P., FEBS Lett. 2001, 501, 19-23.
159. Violette, S. M., Shakespeare, W. C., Bartlett, C., Guan, W. et al., Chem. Biol. 2000, 7, 225-235.
160. Zutshi, R., Chmielewski, J., Bioorg. Med. Chem. Lett. 2000, 10, 1901-1903.
161. Chrunyk, B. A., Rosner, M. H., Cong, Y., Mccoll, A. S. et al., Biochemistry 2000, 39, 7092-7099.
162. Pepys, M. B., Herbert, J., Hutchinson, W. L., Tennent, G. A. et al., Nature 2002, 417, 254-259.