Virtual screening of compound libraries using in silico three dimensional pharmacophores to aid the discovery and design of antimalarial and antileishmanial agents

Frontiers in Drug Design and Discovery

Volumn 3, Issue 1, 2007, Pages 257-292

  Bhattacharjee, Apurba K ^a  

^a WALTER REED ARMY INSTITUTE OF RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 53549111542     PISSN: 15740889     EISSN: None     Source Type: Book Series    
DOI: None     Document Type: Article

References (123)

1. World Health Organization. The World Health Report: Reducing Risks, Promoting Healthy Life, 2002.
2. Trigg, P.I.; Kondrachine, A.V. In Malaria Parasite Biology, Pathogenesis and Protection: The current global malaria situation; Sherman, I.W.; Eds; ASM Press: Washington, D.C.; Chapter 2, 1998; pp. 11-22.
3. Vroman, J.A.; Gaston, M.A.; Avery, M.A. Curr. Pharm. Des., 1999, 5, 101-138.
4. Brewer, T.G.; Grate, S.J.; Peggins, J.O.; Weina, P.J.; Petras, J.M.; Levine, B.S.; Heiffer, M.H.; Schuster, B.G. Am. J. Trop. Med. Hyg., 1994, 51, 251-259.
5. Bhattacharjee, A.K.; Karle, J. M. Chem. Res. Toxicol., 1999, 12, 422-428.
6. http://www.who.int/leishmaniasis.
7. Delfín, D.A.; Bhattacharjee, A.K.; Yakovich, A.; Werbovetz, K.A. J. Med. Chem., 2006, 49, 4196-4207.
8. Magill, A. J. Leishmaniasis. In Tropical Medicine and Emerging Infectious Diseases, 8th ed.; Strickland, G.T.; Ed.; W.B. Saunders Co. Philadelphia, PA, 2000; pp. 665-687.
9. Leishmaniasis: Disease Information. www.who.int/tdr/diseases/leishmaniasis.
10. Singh, S.; Sivakumar, R. J. Infect. Chemother., 2004, 10, 317-315.
11. Davis, A. J.; Kedzierski, L. Curr. Opin. Investig. Drugs, 2005, 6(2), 163-169.
12. Ouellette, M.; Drummelsmith, J.; Papadopoulou, B. Drug Resist. Updat., 2004, 7(4-5), 257-266.
13. Croft, S. L.; Vivas, L.; Brooker, S. East Mediterr. Health J., 2003, 9(4), 518-533.
14. Buchwald, P.; Bodor, N. Drug Future, 2002, 27, 577-588.
15. Janseen, D. Drug Disc., 2002, 38, 1.
16. Podlogar, B.L.; Muegge, I.; Brice, L.J. Curr. Opin. Drug Disc., 2001, 12, 102-109.
17. Walters, W. P.; Stahl, M. T.; Murko, M. A. Drug Discov. Today, 1998, 3, 160-178.
18. Lyne, P. D. Drug Discov. Today, 2002, 7, 1047-1055.
19. Wilton, D.; Willett, P. J. Chem. Inf. Comput. Sci., 2003, 43, 469-474.
20. Ehrlich, P. Dtsch. Chem. Ges., 1909, 42, 17.
21. Guner, O.; Ed.; Pharmacophore Perception, Development and Use in Drug Design (IUL Biotechnology Series, 2000).
22. Gund, P. Prog. Mol. Subcell. Biol., 1977, 5, 117-143.
23. Kurogi, Y.; Gunner O.F. Curr. Med. Chem., 2001, 8, 1035-1055.
24. Langer, T. Hoffmanne R.D. Curr. Pharm. Des., 2001, 7, 509-27.
25. Hou, T.; Xu, X. Curr. Pharm. Des., 2004, 10, 1011-1033.
26. Bhattacharjee, A.K. Lett. Drug Des. Discov., 2006, 3, 219-35.
27. Bhattacharjee, A.K.; Geyer, J. A.; Woodard, C.L.; Kathcart, A.K.; Nichols, D.A.; Prigge, S.T.; Li, Z.; Mott, B.T.; Waters, N.C. J. Med. Chem., 2004, 47, 5418-5426.
28. Wernsdorfer, W.; McGregor, I. (Eds.) Malaria: Principles and Practice of Malariology; Churchill Livingstone, New York, 1988; pp. 1818.
29. Thomson, C.; Cory, M.; Zerner, M. Int. J. Qunat. Biol Symp., 1991, 18, 231-245.
30. Bernardinelli, G.; Jefford, C.W.; Maric, D.; Thomson, C.; Weber, J. Int. J. Qunat. Chem. Quant. Biol Symp., 1994, 21, 117-131.
31. Shukla, K.L.; Gund, T.M.; Meshnick, S.R. J. Mol. Graph., 1995, 13, 215-222.
32. Cheng, F.; Shen, J.; Luo, X.; Zhu, W.; Gu, J.; Ji, R.; Jiang, H.; Chen, K. Bioorg. Med. Chem., 2002, 10, 2883-2891.
33. Bhattacharjee, A.K.; Karle, J.M. Chem. Res. Toxicol., 1999, 12, 422-428.
34. Girones, X.; Gallegos, A.; Carbo-Dorca, R. J. Chem. Inf. Comput. Sci., 2000, 40, 1400-1407.
35. Illapakurthy, A.C.; Sabnis, Y.A.; Avery, B.A.; Avery, M.A.; Wyandt, C.M. J. Pharm. Sci., 2003, 92, 649-655.
36. Hartell, M.G.; Hicks, R.; Bhattacharjee, A.K.; Koser, B.W.; Carvalho, K.; Van Hamont, J.E. J. Pharm. Sci., 2004, 93, 2076-2089.
37. Tonmunphean, S.; Wijitkosoom, A.; Tanitirungrotechai, Y. Bioorg. Med. Chem., 2004, 12, 2005-2012.
38. Bhattacharjee, A.K.; Skanchy, D.J.; Hicks, R.P.; Carvalho, K.A.; Chmurny, G.N.; Klose, J.R.; Scovill, J.P. Internet Electron. J. Mol. Des., 2004, 3, 55-72.
39. Brewer, T.G.; Grate, S.J.; Peggins J.O.; Weina, P.J.; Petras, J.M.; Levine, B.S.; Heiffer, M.H.; Schuster, B.G. Am. J. Trop. Med. Hyg., 1994, 51, 251-259.
40. Bhattacharjee, A. K.; Carvalho, K.A.; Opsenica, D.; Šolaja, B.A. J. Serb. Chem. Soc., 2005, 70, 329-345.
41. Bhattacharjee, A.K.; Karle, J.M. Mol. Engineer., 1999, 8, 391-402.
42. Sweeney, T. R.; Strube, R. E. Antimalarials. In Burger's Medicinal Chemistry, 4th ed.; Wolf, M. E.; Ed.; John Wiley & Sons, Inc.: New York, 1979; pp. 333-413.
43. Karle, J. M.; Karle, I. L.; Gerena, L.; Milhous, W. K. Antimicrob. Agents Chemother., 1992, 36, 1538-1544.
44. Tracy, J. W.; Webster, L. T. Drugs Used in the Chemotherapy of Protozoal Infections: Malaria. In The Pharmacological Basis of Therapeutics, 9th ed.; Hardman, J. G.; Limbird, L. E.; Molinoff, P. B.; Ruddon, R. W. R.; Gilman, A. G.; Eds.; McGraw-Hill: New York, 1995; pp. 965-985.
45. Sweeney, T. R.; Strube, R. E. Med. Res. Rev., 1981, 1, 281-301.
46. Palmer, K. J.; Holliday, S. M.; Brogden, R. N. Drugs, 1993, 45, 430-475.
47. Davidson, M. W.; Griggs, B. G.; Bokyn, D. W.; Wilson, W. D. J. Med. Chem., 1977, 20, 1117-1122.
48. Schlesinger, P. H.; Krogstad, D. G.; Herwaldt, B. L. Antimicrob. Agents Chemother., 1988, 32, 793-801.
49. Ginsburg, H.; Geary, T. G. Biochem. Pharmacol., 1987, 36, 1567-1576.
50. Bhattacharjee, A.K.; Karle, J.M. J. Med. Chem., 1996, 39, 4622-4629.
51. Karle, J.M.; Bhattacharjee, A.K. Bioorg. Med. Chem., 1999, 7,1-6.
52. Go, M.L.; Lee, H.S. Ngiam, T.L. Biol. Pharm. Bull., 1993, 16, 668-674.
53. Bhattacharjee, A.K.; Karle, J.M. Bioorg. Med. Chem., 1998, 6, 1927-1933.
54. Vippagunta, S.R, Dorn, A.; Matile, H.; Bhattacharjee, A.K.; Karle, J.M.; Ellis, W.Y.; Ridley, R.G.; Vennerstrom, J.L. J. Med. Chem., 1999, 42, 4630-4639.
55. Bhattacharjee, A.K. J. Mol. Struct. (Theochem), 2001, 549, 27-37.
56. Bhattacharjee, A.K.; Kyle, D.E.; Vennerstrom, J.L. Antimicrob. Agents Chemother., 2001, 45, 2655-2657.
57. Bhattacharjee, A.K.; Kyle, D.E.; Vennerstrom, J.L.; Milhous, W.K. J. Chem. Info. Comput. Sci., 2002, 42, 1212-1220.
58. Karelson, M.; Lobanov, V.S. Chem. Rev., 1996, 96, 1027-1043.
59. Santanna, C.M.R.D.; Alencastro, R.B.D.; Rodrigues, C.R.; Barreiro, G.; Barreiro, E.J.; Neto, J.D.D.M.N.; Freitas, A.C.C. Intl. J. Quant. Chem: Quant. Biol. Symp., 1996, 23, 111-119.
60. Santos, E.V.M.D.; Carneiro, J.W.M.; Ferreira, V.F. Bioorg. Med. Chem., 2004, 12, 87-93.
61. O'Neill, P.M.; Willock, D.J.; Hawley, S.R.; Bray, P.G.; Storr, R.C.; Ward, S.A.; Park, B.K. J. Med. Chem., 1997, 40, 437-448.
62. Li, R.; Kenyon, G.L.; Cohen, F.E.; Chen, X.; Gong, B.; Dominguez, J.N.; Davidson, E.; Kurzban, G.; Miller, R.E.; Nuzum, E.O.; Rosenthal, P.J.; McKerrow, J.H. J. Med. Chem., 1995, 38, 5031-5037.
63. Liu, M.; Wilairat, P.; Go, M.L. J. Med. Chem., 2001, 44, 4443-4452.
64. Rastelli, G.; Pacchioni, S.; Parenti, M.D. Biorg. Med. Chem. Lett., 2003, 13, 3257-3260.
65. Yuvaniyama, J.; Chitnumsub, P.; Kamchonwongpaisan, S.; Vanichtanankul, J.; Sirawaraporn, W.; Taylor, P.; Walkinshaw, M.D.; Yuthavong, Y. Nat. Struct. Biol., 2003, 1-9.
66. Chang, K.P.; Fong, D.; Bray, R.S. In biology of Leishmania and Leishmaniasis: Elsevier Biomedical Press: Amsterdam, 1985; vol. 1, pp. 1-50.
67. http://www.who.int/inf-fs/en/fact259.html.
68. Alves, L.V.; Canto-Cavalheiro, M.M.; Finelstein, L.C.; Leon, L. Biol. Pharm. Bull., 2003, 26, 453-456.
69. Tewari, N.; Ramesh, Mishra, R.C.; Tripathi, R.P.; Srivastava, V.M.L.; Gupta, S. Bioorg. Med. Chem. Lett., 2004, 14, 4055-4059.
70. Delmas, F.; Avellaneda, A.; Giorgio, C.D.; Robin, M.; Clercq, E.D.; David, P.T.; Galy, J.P. Euro. J. Med. Chem., 2004, 39, 685-690.
71. Bhattacharya, G.; Herman, J.; Delfin, D.; Salem, M.M.; Barszcz, T.; Mollet, M.; Riccio, G.; Brun, R.; Werbovetz, K.A. J. Med. Chem., 2004, 47, 1823-1832.
72. Werbovetz, K.A.; Brendle, J.J.; Sackett, D.L. Mol. Biochem. Parasitol., 1999, 98, 53-65.
73. Ray, S.; Hazra, B.; Mittra, B.; Das, A.; Majumder, H.K. Mol. Pharmacol., 1998, 54, 994-999.
74. Mukhopadhyay, R.; Kapoor, P.; Madhubala, R. Pharmacol. Res., 1996, 33, 67-70.
75. Croft, S.L.; Snowdon, D.; Yardley, V. J. Antimicrob. Chemother., 1996, 38, 1041-1047.
76. Bell, C.A.; Hall, J.E.; Kyle, D.E.; Grogl, M.; Ohemeng, K.A.; Allen, M.A.; Tidwell, R.R. Antimicrob. Agents Chemother., 1990, 34, 1381-1386.
77. Bhattacharjee, A.K. Int. J. Qunat. Chem., 1999, 75, 995-1002.
78. Werbovetz, K.A.; Bhattacharjee, A.K.; Brendle, J.J.; Scovill, J.P. Bioorg. Med. Chem., 2000, 8, 1741-1747.
79. Crucinani, G.; Watson, K.A. J. Med. Chem., 1994, 37, 2589.
80. Waller, C.L.; Opera, T.I.; Giolitti, A.; Marshall, G.R. J. Med. Chem., 1993, 36, 4152.
81. Geladi, P.; Kowalski, B.R. Anal. Chim. Acta, 1986, 185, 1.
82. Cramer, R.D.; Paterson, D.E.; Bunce, J.D. J. Am. Chem. Soc., 1988, 43, 5959-5967.
83. Bobbyer, D.N.A.; Goodford, P.J.; McWhinnie, P.M. J. Med. Chem., 1989, 32, 1083-1094.
84. http://www.accelrys.com.
85. Guner, O.A. Pharmacophore, Perception, Development, and Use in Drug Design. 2000, San Diego: University International Line.
86. Koide, Y.; Tatasui, A.; Hasegawa, T.; Nurakami, A.; Satoh, S.; Yamada, H.; Kazayama, S.; Takahashi, A. Biorg. Med. Chem. Lett., 2003, 13, 25-29.
87. Singh, J.; van Vlijimen, H.; Liao, Y.S.; Lee, W.C.; Cornebise, M.; Harris, M.; Shu, I.; Gill, A.; Cuervo, J.H.; Abraham, W.M.; Adams, S.P. J. Med. Chem., 2002, 45, 2988-93.
88. Koide, Y.; Hasegawa, T.; Takahashi, A.; Endo, A.; Mochizudi, N.; Nakagawa, M.; Nishida, A. J. Med. Chem., 2002, 45, 4629-4638.
89. Kurogi, Y.; Miyata, K.; Okamura, T.; Hashimoto, K.; Tsutsumi, K.; Nasu, M.; Moriyasu, M. J. Med. Chem., 2001, 44, 2304-2307.
90. Chen, G.S.; Chang, C.S.; Kan, W.M.; Chang, C.L.; Wang, K.C, Chern, J.W. J. Med. Chem., 2001, 44, 3759-3763.
91. Kurogi, Y.; Guner, O.F. Curr. Med. Chem., 2001, 8, 1035-1055.
92. Schuster, D.; Maurer, E.M.; Laggner, C.; Nashev, L.G.; Wilckens, T.; Langer, T.; Odermatt, A. J. Med. Chem., 2006, 49, 3454-66.
93. Schuster, D.; Laggner, C.; Steindl, T.M.; Palusczak, A.; Hartmann, R.W.; Langer T. J. Chem. Inf. Model., 2006, 46, 1301-11.
94. Chemical Information System; Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, MD. U.S.A.
95. Riel, M.A.; Kyle, D.E.; Bhattacharjee, A.K.; Milhous, W.K. Antimicrob. Agents Chemother., 2002, 46, 2627-2632.
96. Bhattacharjee, A.K.; Hartell, M.G.; Nichols, D.; Hicks, R.P.; Stanton, B.; van Hamont, J. E.; Milhous, W. K. Eur. J. Med. Chem., 2004, 39, 59-67.
97. Hicks, R.P.; Nichols, D.A.; DiTusa, C.A.; Sullivan, D.J.; Hartell, M.G.; Koser, B.W.; Bhattacharjee, A.K. Internet Electron. J. Mol. Design, 2005, 4, 751-764.
98. Bhattacharjee, A.K.; Geyer, J. A.; Woodard, C.L.; Kathcart, A.K.; Nichols, D.A.; Prigge, S.T.; Li, Z.; Mott, B.T.; Waters, N.C. J. Med. Chem., 2004, 47, 5418-5426.
99. Klayman, D.L. Science, 1985, 228, 1049-1055.
100. Borstnik, K.; Paik, I-H.; Shapiro, T.A.; Posner, G. H. Int. J. Parasitol., 2002, 32, 1661-1667.
101. Todorović, N.M.; Stefanović, M.; Tinant, B.; Declercq, J.-P.; Makler, M.T.; Šolaja, B.A. Steroids, 1996, 61, 688-696.
102. Opsenica, D.; Pocsfalvi, G.; Juranić, Z.; Tinant, B.; Declercq, J.-P.; Kyle, D.E.; Milhous, W.K.; Šolaja, B.A. J. Med. Chem., 2000, 43, 3274-3282.
103. Šolaja, B.A.; Terzić, N.; Pocsfalvi, G.; Gerena, L.; Tinant, B.; Opsenica, D.; Milhous, W.K. J. Med. Chem., 2002, 45, 3331-3336.
104. Opsenica, D.; Pocsfalvi, G.; Milhous, W.K.; Šolaja, B.A. J. Serb. Chem. Soc., 2002, 67, 465-471.
105. Opsenica, D.; Kyle, D.E.; Milhous, W.K.; Šolaja, B.A. J. Serb. Chem. Soc., 2003, 68, 291-302.
106. Opsenica, D.; Angelovski, G.; Pocsfalvi, G.; Juranić, Z.; Žižak, Ž.; Kyle, D.E.; Milhous, W.K.; Šolaja, B.A. Bioorg. Med. Chem., 2003, 11, 2761-2768.
107. Bhattacharjee, A. K.; Carvalho, K.A.; Opsenica, D.; Šolaja, B.A. J. Serb. Chem. Soc., 2005, 70, 329-345.
108. Gutteridge, C.E.; Nichols, D.A.; Curtis, S.M.; Thota, D.S.; Vo, J.V.; Gerena, L.; Montip, G.; Asher, C.O.; Diaz, D.S.; DiTusa, C.A.; Smith, K.S.; Bhattacharjee, A. K. Bioorg. Med. Chem. Lett., 2006, 16, 5682.
109. Bhattacharjee, A.K.; Nichols, D.A.; Gerena, L.; Roncal, N.; Gutteridge, C.E. Med. Chem., 2007, in press.
110. Gutteridge, C.E.; Vo, J.V.; Tillet, C.B.; Vigilante, J.A.; Dettmer, J.R.; Patterson, S.L.; Werbovetz, K.A.; Capers, J.; Nichols, D.A.; Bhattacharjee, A.K.; Gerena, L. Med. Chem., 2007, in press.
111. Bhattacharjee, A.K.; Skanchy, D.J.; Jennings, B.; Hudson, T.H.; Brendle, J.J.; Werbovetz, K.A. Bioorg. Med. Chem., 2002, 10, 1979-1989.
112. Werbovetz, K. A.; Sackett, D. L.; Delfín, D.; Bhattacharya, G.; Salem, M.; Obrzut, T.; Rattendi, D.; Bacchi, C. Mol. Pharmacol., 2003, 64, 1325-1333.
113. Bhattacharya, G.; Salem, M.; Werbovetz, K.A. Bioorg. Med. Chem. Lett., 2002, 12, 2395-2398.
114. Bhattacharya, G.; Herman, J.; Delfín, D.; Salem, M. M.; Barszcz, T.; Mollet, M.; Riccio, G.; Brun, R.; Werbovetz, K. A. J. Med. Chem., 2004, 47, 1823-1832.
115. Delfín, D.A.; Bhattacharjee, A.K.; Yakovich, A.; Werbovetz, K.A. J. Med. Chem., 2006, 49, 4196-4207.
116. SPARTAN version 5.1, Wavefunction, Inc., 18401 Von Karman Ave.; #370, Irvine, CA 92715.
117. Dixon, R.W.; Leonard, J.M.; Hehre, W.J.A. Israel J. Chem., 1993, 33, 427-434.
118. Frisch, M. J, Trucks, G.W.; Schlegel, H.B.; Gill, P.M.W.; Johnson, B.G.; Robb, M.A.; Cheeseman, J.R.; Keith, T.A.; Petersson, G.A.; Montgomery, J.A.; Raghavachari, K.; Al-Laham, M.A.; Zakrzewski, V.G.; Ortiz, J.V.; Foresman, J.B.; Cioslowski, J.; Stefanov, B.B.; Nanayakkara, A.; Challacombe, M.; Peng, C.Y.; Ayala, P.Y.; Chen, W.; Wong, M.W.; Andres, J.L.; Replogle, E.S.; Gomperts, R.; Martin, R.L.; Fox, D.J.; Binkley, J.S.; Defrees, D.J.; Baker, J.; Stewart, J.P.; Head-Gordon, M.; Gonzalez, C.; Pople, J.A. Gaussian 94 (Revision A.1), Gaussian Inc.; Pittsburgh PA. 1995.
119. Grigorov, M.; Weber, J.; Tronchet, M.J.; Jefford, C.W.; Milhous, W.K.; Maric, D. J. Chem. Inf. Comput. Sci., 1995, 35, 285-304.
120. Greenridge, P.A.; Weiser, J. Mini Rev. Med. Chem., 2001, 1, 79-87.
121. Desjardins, R.E.; Canfield, C.J.; Haynes, D.E.; Chulay, J.D. Antimicrob. Agents Chemther., 1979, 16, 710-718.
122. Chulay, J.D.; Haynes, J.D.; Diggs, C.L. Exp. Parasitol., 1983, 55, 138-146.
123. Kyle, D.E.; Oduola, A.M.J.; Martin, S.K.; Milhous, W.K. Trans. Royal Soc. Trop. Med. Hyg., 1990, 84, 474-478.