A. Kontijevskis et al. / Bioorg. Med. Chem. 17 (2009) 5229–5237
5237
11. Beck, Z. Q.; Morris, G. M.; Elder, J. H. Curr. Drug Targets Infect. Disord. 2002, 2, 37.
12. Prusis, P.; Uhlen, S.; Petrovska, R.; Lapinsh, M.; Wikberg, J. E. S. BMC Bioinform.
2006, 7, 167.
13. Lapinsh, M.; Prusis, P.; Lundstedt, T.; Wikberg, J. E. S. Mol. Pharmacol. 2002, 61,
1465.
hexapeptide inhibitor) was also performed. In total each inhibition
assay experiment comprised of 12 data points.
The kinetic data was analyzed by non-linear fit using GRAFIT pro-
gram and the basic equation for Michaelis-Menten kinetics.41 The
14. Lapinsh, M.; Prusis, P.; Mutule, I.; Mutulis, F.; Wikberg, J. E. S. J. Med. Chem.
2003, 46, 2572.
obtained Michaelis constants Km were converted into lM units be-
fore use in the data analyses. The inhibition assay data was fitted
by non-linear regression analysis using GRAFIT program41 and ob-
tained IC50 values were converted into Ki values according to the
equation of Cheng and Prusoff.42 Each experiment was repeated at
least three times, and the average value was taken as a final result.
15. Prusis, P.; Lundstedt, T.; Wikberg, J. E. S. Protein Eng. 2002, 15, 305–311.
16. Wikberg, J. E.; Mutulis, F.; Mutule, I.; Veiksina, S.; Lapinsh, M.; Petrovska, R.;
Prusis, P. Ann. NY Acad. Sci. 2003, 994, 21.
17. Wikberg, J. E. S.; Lapinsh, M.; Prusis, P. Proteochemometrics—A Tool for
Modelling the Molecular Interaction Space. In Chemogenomics in Drug
Discovery—A Medicinal Chemistry Perspective; Kubinyi, H., Müller, G., Eds.;
Wiley-VCH: Weinheim, 2004; pp 289–309.
A Ki value of 200 lM was set for hexapeptides marked as ‘NI’ in Table
3 for the purpose of testing the log (Ki)/log (Km) correlations.
18. Kontijevskis, A.; Petrovska, R.; Mutule, I.; Uhlen, S.; Komorowski, J.; Prusis, P.;
Wikberg, J. E. S. Proteins 2007, 69, 83.
19. Kontijevskis, A.; Prusis, P.; Petrovska, R.; Yahorava, S.; Mutulis, F.; Mutule, I.;
Komorowski, J.; Wikberg, J. E. S. PLoS Comput. Biol. 2007, 3, e48.
20. Sandberg, M.; Eriksson, L.; Jonsson, J.; Sjöström, M.; Wold, S. J. Med. Chem. 1998,
41, 2481.
21. Gustchina, A.; Weber, I. T. FEBS Lett. 1990, 269, 269.
22. Szeltner, Z.; Polgar, L. J. Biol. Chem. 1996, 271, 32180.
23. Debnath, A. K. Curr. Pharm. Des. 2005, 11, 3091.
24. Kurup, A.; Mekapati, S. B.; Garg, R.; Hansch, C. Curr. Med. Chem. 2003, 10,
1679.
25. Johnson, V. A.; Brun-Vezinet, F.; Clotet, B.; Kuritzkes, D. R.; Pillay, D.; Schapiro,
J. M.; Richman, D. D. Top HIV Med. 2006, 14, 125.
Acknowledgements
We are indebted to Dr. Helena Danielson for the generous gift of
the clones used in expression of the HXB2 and mutant HIV-1 pro-
teases. Financial support was provided by Swedish International
Development Cooperation Agency (HIV-2006-019) and the Swed-
ish Research Council (04X-05957).
26. Ho, D. D.; Toyoshima, T.; Mo, H.; Kempf, D. J.; Norbeck, D.; Chen, C. M.;
Wideburg, N. E.; Burt, S. K.; Erickson, J. W.; Singh, M. K. J. Virol. 1994, 68, 2016.
27. Tozser, J.; Weber, I. T.; Gustchina, A.; Blaha, I.; Copeland, T. D.; Louis, J. M.;
Oroszlan, S. Biochemistry 1992, 31, 4793.
28. Hyland, L. J.; Tomaszek, T. A., Jr.; Meek, T. D. Biochemistry 1991, 30, 8454.
29. Ido, E.; Han, H. P.; Kezdy, F. J.; Tang, J. J. Biol. Chem. 1991, 266, 24359.
30. Polgar, L.; Szeltner, Z.; Boros, I. Biochemistry 1994, 33, 9351.
31. Beck, Z. Q.; Hervio, L.; Dawson, P. E.; Elder, J. H.; Madison, E. L. Virology 2000,
274, 391.
Supplementary data
Supplementary data associated with this article can be found, in
References and notes
32. Jordan, S. P.; Zugay, J.; Darke, P. L.; Kuo, L. C. J. Biol. Chem. 1992, 267, 20028.
33. Simca-P+ 10.0 Manual, Umetrics AB: Umeå, Sweden, 2002.
34. Lundstedt, T.; Seifert, E.; Abramo, L.; Thelin, B.; Nystrom, A.; Pettersen, J.;
Bergman, R. Chemometr. Intell. Lab. Syst. 1998, 42, 3.
1. Erickson, J. W.; Stanley, K. B. Annu. Rev. Pharmacol. Toxicol. 1996, 36, 545.
2. Abdel-Rahman, H. M.; Kimura, T.; Kiso, A.; Nezami, A.; Freire, E.; Hayashi, Y.;
Kiso, Y. Biol. Chem. 2004, 385, 1035.
35. Eriksson, L.; Johansson, E.; Kettaneh-Wold, N.; Trygg, J.; Wikström, C.; Wold, S.
Multi- and Megavariate Data Analysis, 2nd ed.; Umetrics AB: Umeå, Sweden,
2006.
3. Li, M.; Laco, G. S.; Jaskolski, M.; Rozycki, J.; Alexandratos, J.; Wlodawer, A.;
Gustchina, A. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 18332.
4. Ohtaka, H.; Muzammil, S.; Schon, A.; Velazquez-Campoy, A.; Vega, S.; Freire, E.
Int. J. Biochem. Cell Biol. 2004, 36, 1787.
36. Wold, S. Technometrics 1978, 20, 397.
37. Wakeling, I. N.; Morris, J. J. J. Chemometr. 1993, 7, 291.
38. Efron, B. J. Am. Stat. Assoc. 1987, 82, 171.
39. Wilcoxon, F. Biometrics 1945, 1, 80.
40. Danielson, H.; Lindgren, M. T.; Markgren, P. O.; Nillroth, U. Adv. Exp. Med. Biol.
1998, 436, 99.
5. Ohtaka, H.; Freire, E. Prog. Biophys. Mol. Biol. 2005, 88, 193.
6. Wlodawer, A.; Gustchina, A. Biochim. Biophys. Acta 2000, 1477, 16.
7. Dunn, B. M.; Goodenow, M. M.; Gustchina, A.; Wlodawer, A. Genome Biol. 2002,
3, 3006. 1.
8. Freire, E. Nat. Biotechnol. 2002, 20, 15.
41. Bardsley, WG.; McGinlay, P. B. J. Theor. Biol. 1989, 139, 85.
42. Cheng, Y.; Prusoff, W. H. Biochem. Pharmacol. 1973, 22, 3099.
9. Randolph, J. T.; DeGoey, D. A. Curr. Top. Med. Chem. 2004, 4, 1079.
10. Dash, C.; Kulkarni, A.; Dunn, B.; Rao, M. Crit. Rev. Biochem. Mol. Biol. 2003, 38, 89.