Combining crystallographic information and an aspherical-atom data bank in the evaluation of the electrostatic interaction energy in an enzyme-substrate complex: Influenza neuraminidase inhibition

Acta Crystallographica Section D: Biological Crystallography

Volumn 65, Issue 5, 2009, Pages 485-499

  Dominiak, Paulina M ^a,b   Volkov, Anatoliy ^a,c   Dominiak, Adam P ^a   Jarzembska, Katarzyna N ^b   Coppens, Philip ^a  

^a UNIVERSITY AT BUFFALO   (United States)

^b UNIVERSITY OF WARSAW   (Poland)

^c MIDDLE TENNESSEE STATE UNIVERSITY   (United States)

Author keywords

Aspherical atom databank; Electrostatic interaction energy; Enzyme substrate complexes; Influenza neuraminidase

Indexed keywords

AMINO ACID; AROMATIC HYDROCARBON; CALCIUM; ENZYME INHIBITOR; GLYCEROL; ION; N ACETYLNEURAMINIC ACID; NA PROTEIN, INFLUENZA A VIRUS; NA PROTEIN, INFLUENZA B VIRUS; SIALIDASE; VIRUS PROTEIN;

AMINO ACID SUBSTITUTION; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CLASSIFICATION; COMPARATIVE STUDY; DRUG ANTAGONISM; DRUG EFFECT; ENZYME ACTIVE SITE; ENZYMOLOGY; GENETICS; HYDROPHOBICITY; INFLUENZA VIRUS A; INFLUENZA VIRUS B; PROTEIN DATABASE; STATIC ELECTRICITY; X RAY CRYSTALLOGRAPHY;

AMINO ACID SUBSTITUTION; AMINO ACIDS; CALCIUM; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; DATABASES, PROTEIN; ENZYME INHIBITORS; GLYCEROL; HYDROCARBONS, AROMATIC; HYDROPHOBICITY; INFLUENZA A VIRUS; INFLUENZA B VIRUS; IONS; MODELS, MOLECULAR; N-ACETYLNEURAMINIC ACID; NEURAMINIDASE; STATIC ELECTRICITY; VIRAL PROTEINS;

SIA;

EID: 65349121892     PISSN: 09074449     EISSN: 13990047     Source Type: Journal    
DOI: 10.1107/S0907444909009433     Document Type: Article

References (76)

1. Armstrong, K. A., Tidor, B. & Cheng, A. C. (2006).J. Med. Chem. 49, 2470-2477.
2. Babu, Y. S., Chand, P., Bantia, S., Kotian, P., Dehghani, A., El-Kattan, Y., Lin, T.-H., Hutchison, T. L., Elliot, A. J, Parker, C. D., Ananth, S. L., Horn, L. L., Laver, W. G. & Montgomery, J A. (2000).J. Med Chem. 43, 3482-3486.
3. Berman, H. M., Westbrook, J, Feng, Z., Gilliland, G, Bhat, T. N., Weissig, H., Shindyalov, I. N. & Bourne, P. E. (2000). Nucleic Acids Res. 28, 235-242.
4. Bonnet, P. & Bryce, R. A. (2004). Protein Sci. 13, 946-957.
5. Bonnet, P. & Bryce, R. A. (2005).J. Mol. Graph. Model. 24, 147-156.
6. Bossart-Whitaker, P., Carson, M., Babu, Y S., Smith, C. D., Laver, W. G & Air, G M. (1993).J. Mol. Biol. 232, 1069-1083.
7. Brouillette, W. J, Atigadda, V. R., Luo, M., Air, G. M, Babu, Y. S. & Bantia, S. (1999). Bioorg. Med. Chem. Lett. 9, 1901-1906.
8. Burmeister, W. P., Cusack, S. & Ruigrok, R. W. (1994). J Gen. Virol. 75, 381-388.
9. Burmeister, W. P., Henrissat, B., Bosso, C, Cusack, S. & Ruigrok, R. W. (1993). Structure, 1, 19-26.
10. Burmeister, W. P., Ruigrok, R. W. & Cusack, S. (1992). EMBO J. 11, 49-56.
11. Carr, J, Ives, J, Kelly, L., Lambkin, R., Oxford, J, Mendel, D., Tai, L. & Roberts, N. (2002). Antivir. Res. 54, 79-88.
12. Chand, P., Kotian, P. L., Morris, P. E., Bantia, S., Walsh, D. A. & Babu, Y. S. (2005). Bioorg. Med. Chem. 13, 2665-2678.
13. Chong, A. K., Pegg, M. S. & von Itzstein, M. (1991). Biochim Biophys. Acta, 1077, 65-71.
14. Colman, P. M. (1994). Protein Sci. 3, 1687-1696.
15. Colman, P. M., Hoyne, P. A. & Lawrence, M. C. (1993).J. Virol. 67, 2972-2980.
16. DeLano, W. L. (2002). The PyMOL Molecular Graphics System.
17. DeLano Scientific, San Carlos, USA. http://www.pymol.org .
18. Dominiak, P. M., Volkov, A., Li, J., Messerschmidt, M. & Coppens, P. (2007).J. Chem. Theory Comput. 3, 232-247.
19. Faerman, C. H. & Price, S. L. (1990).J. Am. Chem. Soc. 112, 4915- 4926.
20. Finley, J B., Atigadda, V. R., Duarte, F., Zhao, J. J., Brouillette, W. J, Air, G. M. & Luo, M. J M. B. (1999). J Mol. Biol. 293, 1107-1119.
21. Fornabaio, M., Cozzini, P., Mozzarelli, A., Abraham, D. J. & Kellogg, G E. (2003).J. Med. Chem. 46, 4487-4500.
22. Gottschalk, A. (1957). Biochim. Biophys. Acta, 23, 645-646.
23. Gubareva, L. V, Robinson, M. J., Bethell, R. C. & Webster, R. G (1997).J. Virol. 71, 3385-3390.
24. Hay, A. J., Gregory, V., Douglas, A. R. & Lin, Y P. (2001). Philos Trans. R. Soc. Lond B, 356, 1861-1870.
25. Hohenberg, P. & Kohn, W (1964). Phys. Rev. 136, B864-B871.
26. International Tables for Crystallography (1992). Vol. C. Dordrecht, The Netherlands: Kluwer Academic Publishers.
27. Itzstein, M. von, Dyason, J. C, Oliver, S. W, White, H. E, Wu, W Y, Kok, G B. & Pegg, M. S. (1996).J. Med. Chem. 39, 388-391.
28. Jano, I. & Hardcastle, J. E. (1999). Anal. Chim. Acta, 390, 267-274.
29. Jedrzejas, M. J., Singh, S., Brouillette, W J., Air, G M. & Luo, M. (1995). Proteins, 23, 264-277.
30. Jedrzejas, M. J., Singh, S., Brouillette, W J., Laver, W G, Air, G M. & Luo, M. (1995). Biochemistry, 34, 3144-3151.
31. Johansson, B. E. & Brett, I. C. (2003).J. Biochem. (Tokyo), 134, 345-352.
32. Johansson, B. E. & Brett, I. C. (2006).J. Biochem. (Tokyo), 139, 439-447.
33. Kati, W M., Montgomery, D, Carrick, R., Gubareva, L., Mating, C, McDaniel, K., Steffy, K., Molla, A., Hayden, F, Kempf, D & Kohlbrenner, W (2002). Antimicrob. Agents Chemother. 46, 1014- 1021.
34. Koritsanszky, T., Volkov, A. & Coppens, P. (2002). Acta Cryst. A58, 464-472.
35. Krissinel, E. & Henrick, K. (2004). Acta Cryst. D60, 2256-2268.
36. Li, X., Volkov, A. V, Szalewicz, K. & Coppens, P (2006). Acta Cryst. D62, 639-647.
37. Liu, Y, Zhang, J. & Xu, W (2007). Curr. Med. Chem. 14, 2872- 2891.
38. Lommer, B. S., Ali, S. M., Bajpai, S. N., Brouillette, W J., Air, G M. & Luo, M. (2004). Acta Cryst. D60, 1017-1023.
39. Maring, C. J. et al. (2005).J. Med. Chem. 48, 3980-3990.
40. Masukawa, K. M., Kollman, P. A. & Kuntz, I. D. (2003).J. Med. Chem. 46, 5628-5637.
41. McKimm-Breschkin, J. L., Sahasrabudhe, A., Blick, T. J, McDonald, M., Colman, P. M., Hart, G J, Bethell, R. C. & Varghese, J. N. (1998).J. Virol. 72, 2456-2462.
42. Meanwell, N. A. & Krystal, M. (1996). Drug Discov. Today, 1, 388-397.
43. Moscona, A. (2005). N. Engl. J. Med. 353, 1363-1373.
44. Palese, P., Tobita, K., Ueda, M. & Compans, R. W (1974). Virology, 61, 397-410.
45. Pegg, M. S. & von Itzstein, M. (1994). Mol. Biol. Int. 32, 851-858.
46. Sangma, C. & Hannongbua, S. (2007). Curr. Comput. Aided Drug Des. 3, 113-132.
47. Smith, B. J., Colman, P. M., von Itzstein, M., Danylec, B. & Varghese, J. N. (2001). Protein Sci. 10, 689-696.
48. Smith, B. J, Huyton, T., Joosten, R. P., McKimm-Breschkin, J. L., Zhang, J.-G, Luo, C. S., Lou, M.-Z., Labrou, N. E. & Garrett, T. P. J. (2006). Acta Cryst. D62, 947-952.
49. Smith, B. J., McKimm-Breshkin, J. L., McDonald, M., Fernley, R. T., Varghese, J. N. & Colman, P M. (2002).J. Med. Chem. 45, 2207- 2212.
50. Steindl, T. & Langer, T. (2004).J. Chem. Inf. Comput. Sci. 44, 1849- 1856.
51. Stoll, V, Stewart, K. D, Maring, C. J., Muchmore, S., Giranda, V, Gu, Y G, Wang, G, Chen, Y, Sun, M., Zhao, C, Kennedy, A. L., Madigan, D L., Xu, Y, Saldivar, A., Kati, W, Laver, G, Sowin, T., Sham, H. L., Greer, J. & Kempf, D (2003). Biochemistry, 42, 718- 727.
52. Sudbeck, E. A., Jedrzejas, M. J, Singh, S., Brouillette, W J, Air, G M., Laver, W G, Babu, Y S., Bantia, S., Chand, P., Chu, N., Montgomery, J. A., Walsh, D A. & Luo, M. (1997).J. Mol. Biol. 267, 584-594.
53. Tai, C. Y, Escarpe, P. A., Sidwell, R. W, Williams, M. A., Lew, W, Wu, H., Kim, C. U. & Mendel, D B. (1998). Antimicrob. Agents Chemother. 42, 3234-3241.
54. Taylor, N. R., Cleasby, A., Singh, O., Skarzynski, T, Wonacott, A. J, Smith, P. W, Sollis, S. L., Howes, P. D, Cherry, P. C, Bethell, R., Colman, P. & Varghese, J. (1998).J. Med. Chem. 41, 798-807.
55. Taylor, N. R. & von Itzstein, M. (1994).J. Med. Chem. 37, 616- 624.
56. Theobald, D L. & Wuttke, D S. (2006). Bioinformatics, 22, 2171- 2172.
57. Varghese, J. N. & Colman, P. M. (1991).J. Mol. Biol. 221, 473-486.
58. Varghese, J. N., Colman, P. M., van Donkelaar, A., Blick, T J, Sahasrabudhe, A. & McKimm-Breschkin, J. L. (1997). Proc. Natl Acad Sci. USA, 94, 11808-11812.
59. Varghese, J. N., Epa, V C. & Colman, P M. (1995). Protein Sci. 4, 1081-1087.
60. Varghese, J. N., McKimm-Breschkin, J. L., Caldwell, J. B., Kortt, A. A. & Colman, P. M. (1992). Proteins, 14, 327-332.
61. Varghese, J. N., Smith, P. W, Sollis, S. L., Blick, T J, Sahasrabudhe, A., McKimm-Breschkin, J. L. & Colman, P. M. (1998). Structure, 6, 735-746.
62. Verma, R. P. & Hansch, C. (2006). Bioorg. Med. Chem. Lett. 14, 982- 996.
63. Volkov, A., King, H. E & Coppens, P. (2006).J. Chem. Theory Comput. 2, 81-89.
64. Volkov, A., Koritsanszky, T & Coppens, P. (2004). Chem. Phys. Lett. 391, 170-175.
65. Volkov, A., Macchi, P., Farrugia, L. J., Gatti, C, Mallinson, P, Richter, T & Koritsanszky, T (2006). JD2006 - A Computer Program for Multipole Refinement, Topological Analysis of Charge Densities and Evaluation of Intermolecular Energies from Experimental or Theoretical Structure Factors, http://xd.chem.buffalo.edu/ .
66. Volkov, A., Messerschmidt, M. & Coppens, P. (2007). Acta Cryst. D63, 160-170.
67. Wall, I. D, Leach, A. R., Salt, D W, Ford, M. G & Essex, J. W (1999). J. Med. Chem. 42, 5142-5152.
68. Wang, G T, Wang, S., Gentles, R., Sowin, T, Maring, C. J, Kempf, D J., Kati, W M., Stoll, V, Stewart, K. D & Laver, G (2005). Bioorg. Med. Chem. Lett. 15 125-128.
69. Wang, T & Wade, R. C. (2001).J. Med. Chem. 44, 961-971.
70. Warshel, A., Sharma, P K., Kato, M. & Parson, W W (2006). Biochim. Biophys. Acta, 1764, 1647-1676.
71. White, C. L., Janakiraman, M. N., Laver, W. G., Phίlι ́ppon, C, Vasella, A., Air, G. M. & Luo, M. (1995).J. Mol. Biol. 245, 623-634.
72. Wilson, V. W J. & Rafelson, M. E. J. (1967). Biochim. Biophys. Acta,146, 160-166.
73. Word, J. M, Lovell, S. C., Richardson, J. S. & Richardson, D. C. (1999).J. Mol. Biol. 29, 1735-1747.
74. Yi, J., Guo, Z. & Chu, F. M. (2003). Bioorg. Med. Chem. 11, 1465- 1474.
75. Zhang, J, Yu, K.-Q., Zhu, W & Jiang, H. (2006). Bioorg. Med. Chem Lett. 16, 3009-3014.
76. Zheng, M, Yu, K., Liu, H., Luo, J., Chen, K., Zhu, W & Jiang, H. (2006).J. Comput. Aided Mol. Des. 20, 549-566.