In silico screening of quadruplex-binding ligands

Methods

Volumn 57, Issue 1, 2012, Pages 106-114

  Ma, Dik Lung ^a   Ma, Victor Pui Yan ^a   Chan, Daniel Shiu Hin ^a   Leung, Ka Ho ^a   Zhong, Hai Jing ^b,c   Leung, Chung Hang ^b,c  

^a HONG KONG BAPTIST UNIVERSITY   (Hong Kong)

^b University of Macau   (Macao)

^c UNIVERSITY OF MACAU   (Macao)

Author keywords

G quadruplex; High throughput; In silico; Ligands; Molecular docking; Virtual screening

Indexed keywords

1H PYRAZOLE 3 CARBOXY 4 METHYL 5 PHENYL (1H INDOL 3 YLMETHYLENE)HYDRAZIDE; DNA; GUANINE QUADRUPLEX; HYDRAZIDE; IMIDAZOLE; RNA; TELOMESTATIN; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; COMPUTER MODEL; DATA BASE; DRUG STRUCTURE; HIGH THROUGHPUT SCREENING; MOLECULAR DOCKING; PHARMACOPHORE; PRIORITY JOURNAL; PROTEIN STRUCTURE; SCREENING TEST;

EID: 84865091468     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2012.02.001     Document Type: Article

References (138)

1. Felsenfeld G., Davies D.R., Rich A. J. Am. Chem. Soc. 1957, 79:2023-2024.
2. Langridge R., Rich A. Nature 1963, 198:725-728.
3. Gehring K., Leroy J.-L., Gueron M. Nature 1993, 363:561-565.
4. Gellert M., Lipsett M.N., Davies D.R. Proc. Natl. Acad. Sci. USA 1962, 48:2013-2018.
5. Davis J.T. Angew. Chem. Int. Ed. 2004, 43:668-698.
6. Burge S., Parkinson G.N., Hazel P., Todd A.K., Neidle S. Nucleic Acids Res. 2006, 34:5402-5415.
7. Phan A.T., Kuryavyi V., Patel D.J. Curr. Opin. Struct. Biol. 2006, 16:288-298.
8. Patel D.J., Phan A.T., Kuryavyi V. Nucleic Acids Res. 2007, 35:7429-7455.
9. Neidle S. Curr. Opin. Struct. Biol. 2009, 19:239-250.
10. Phan A.T. FEBS J. 2010, 277:1107-1117.
11. Parkinson G.N., Lee M.P.H., Neidle S. Nature 2002, 417:876-880.
12. Kankia B.I., Marky L.A. J. Am. Chem. Soc. 2001, 123:10799-10804.
13. Miyoshi D., Nakao A., Sugimoto N. Nucleic Acids Res. 2003, 31:1156-1163.
14. Pedroso I.M., Duarte L.F., Yanez G., Baker A.M., Fletcher T.M. Biochem. Biophys. Res. Commun. 2007, 358:298-303.
15. Gonzalez V., Guo K., Hurley L., Sun D. J. Biol. Chem. 2009, 284:23622-23635.
16. Thakur R.K., Kumar P., Halder K., Verma A., Kar A., Parent J.-L., Basundra R., Kumar A., Chowdhury S. Nucleic Acids Res. 2009, 37:172-183.
17. Phan A.T., Modi Y.S., Patel D.J. J. Am. Chem. Soc. 2004, 126:8710-8716.
18. Ambrus A., Chen D., Dai J., Jones R.A., Yang D. Biochemistry 2005, 44:2048-2058.
19. Dettler Jamie M., Buscaglia R., Le Vu H., Lewis Edwin A. Biophys. J. 2011, 100:1517-1525.
20. Dai J., Dexheimer T.S., Chen D., Carver M., Ambrus A., Jones R.A., Yang D. J. Am. Chem. Soc. 2006, 128:1096-1098.
21. Dexheimer T.S., Sun D., Hurley L.H. J. Am. Chem. Soc. 2006, 128:5404-5415.
22. Guo K., Gokhale V., Hurley L.H., Sun D. Nucleic Acids Res. 2008, 36:4598-4608.
23. Sun D., Liu W.-J., Guo K., Rusche J.J., Ebbinghaus S., Gokhale V., Hurley L.H. Mol. Cancer Ther. 2008, 7:880-889.
24. Sun D., Guo K., Shin Y.-J. Nucleic Acids Res. 2010.
25. Paramasivam M., Membrino A., Cogoi S., Fukuda H., Nakagama H., Xodo L.E. Nucleic Acids Res. 2009, 37:2841-2853.
26. Cogoi S., Paramasivam M., Membrino A., Yokoyama K.K., Xodo L.E. J. Biol. Chem. 2010, 285:22003-22016.
27. Fernando H., Reszka A.P., Huppert J., Ladame S., Rankin S., Venkitaraman A.R., Neidle S., Balasubramanian S. Biochemistry 2006, 45:7854-7860.
28. Phan A.T., Kuryavyi V., Burge S., Neidle S., Patel D.J. J. Am. Chem. Soc. 2007, 129:4386-4392.
29. Todd A.K., Haider S.M., Parkinson G.N., Neidle S. Nucleic Acids Res. 2007, 35:5799-5808.
30. Hsu S.-T.D., Varnai P., Bugaut A., Reszka A.P., Neidle S., Balasubramanian S. J. Am. Chem. Soc. 2009, 131:13399-13409.
31. Kuryavyi V., Phan A.T., Patel D.J. Nucleic Acids Res. 2010, 38:6757-6773.
32. Guo K., Pourpak A., Beetz-Rogers K., Gokhale V., Sun D., Hurley L.H. J. Am. Chem. Soc. 2007, 129:10220-10228.
33. Tong X., Lan W., Zhang X., Wu H., Liu M., Cao C. Nucleic Acids Res. 2011.
34. Dailey M.M., Hait C., Holt P.A., Maguire J.M., Meier J.B., Miller M.C., Petraccone L., Trent J.O. Exp. Mol. Pathol. 2009, 86:141-150.
35. Han H., Hurley L.H. Trends Pharmacol. Sci. 2000, 21:136-142.
36. Hurley L.H., Wheelhouse R.T., Sun D., Kerwin S.M., Salazar M., Fedoroff O.Y., Han F.X., Han H., Izbicka E., Von Hoff D.D. Pharmacol. Ther. 2000, 85:141-158.
37. Ou T.-m., Lu Y.-j., Tan J.-h., Huang Z.-s., Wong K.-Y., Gu L.-q. ChemMedChem 2008, 3:690-713.
38. Monchaud D., Teulade-Fichou M.-P. Org. Biomol. Chem. 2008, 6:627-636.
39. Balasubramanian S., Neidle S. Curr. Opin. Chem. Biol. 2009, 13:345-353.
40. Balasubramanian S., Hurley L.H., Neidle S. Nat. Rev. Drug Discov. 2011, 10:261-275.
41. Han F.X., Wheelhouse R.T., Hurley L.H. J. Am. Chem. Soc. 1999, 121:3561-3570.
42. Lu Y.-J., Ou T.-M., Tan J.-H., Hou J.-Q., Shao W.-Y., Peng D., Sun N., Wang X.-D., Wu W.-B., Bu X.-Z., Huang Z.-S., Ma D.-L., Wong K.-Y., Gu L.-Q. J. Med. Chem. 2008, 51:6381-6392.
43. Waller Z.A.E., Shirude P.S., Rodriguez R., Balasubramanian S. Chem. Commun. 2008, 1467-1469.
44. Bejugam M., Sewitz S., Shirude P.S., Rodriguez R., Shahid R., Balasubramanian S. J. Am. Chem. Soc. 2007, 129:12926-12927.
45. Thorpe J.H., Teixeira S.C.M., Gale B.C., Cardin C.J. Nucleic Acids Res. 2003, 31:844-849.
46. Neidle S., Parkinson G.N. Biochimie 2008, 90:1184-1196.
47. Kang C., Zhang X., Ratliff R., Moyzis R., Rich A. Nature 1992, 356:126-131.
48. Lim K.W., Amrane S., Bouaziz S., Xu W., Mu Y., Patel D.J., Luu K.N., Phan A.T.n. J. Am. Chem. Soc. 2009, 131:4301-4309.
49. Kuryavyi V., Patel D.J. Structure 2010, 18:73-82.
50. Phan A.T., Kuryavyi V., Luu K.N., Patel D.J. Nucleic Acids Res. 2007, 35:6517-6525.
51. Song J., Rechkoblit O., Bestor T.H., Patel D.J. Science 2011, 331:1036-1040.
52. Harley C.B., Futcher A.B., Greider C.W. Nature 1990, 345:458-460.
53. Kim N., Piatyszek M., Prowse K., Harley C., West M., Ho P., Coviello G., Wright W., Weinrich S., Shay J. Science 1994, 266:2011-2015.
54. Hanahan D., Weinberg R.A. Cell 2000, 100:57-70.
55. Zahler A.M., Williamson J.R., Cech T.R., Prescott D.M. Nature 1991, 350:718-720.
56. Wang Y., Patel D.J. Structure 1993, 1:263-282.
57. Redon S., Bombard S., Elizondo-Riojas M.A., Chottard J.C. Nucleic Acids Res. 2003, 31:1605-1613.
58. Ying L., Green J.J., Li H., Klenerman D., Balasubramanian S. Proc. Natl. Acad. Sci. USA 2003, 100:14629-14634.
59. He Y., Neumann R.D., Panyutin I.G. Nucleic Acids Res. 2004, 32:5359-5367.
60. Qi J., Shafer R.H. Nucleic Acids Res. 2005, 33:3185-3192.
61. Vorlíčková M., Chládková J., Kejnovská I., Fialová M., Kypr J. Nucleic Acids Res. 2005, 33:5851-5860.
62. Li J., Correia J.J., Wang L., Trent J.O., Chaires J.B. Nucleic Acids Res. 2005, 33:4649-4659.
63. Phan A.T., Patel D.J. J. Am. Chem. Soc. 2003, 125:15021-15027.
64. Phan A.T., Luu K.N., Patel D.J. Nucleic Acids Res. 2006, 34:5715-5719.
65. Luu K.N., Phan A.T., Kuryavyi V., Lacroix L., Patel D.J. J. Am. Chem. Soc. 2006, 128:9963-9970.
66. Xu Y., Noguchi Y., Sugiyama H. Bioorg. Med. Chem. 2006, 14:5584-5591.
67. Ambrus A., Chen D., Dai J., Bialis T., Jones R.A., Yang D. Nucleic Acids Res. 2006, 34:2723-2735.
68. Dai J., Carver M., Punchihewa C., Jones R.A., Yang D. Nucleic Acids Res. 2007, 35:4927-4940.
69. Xue Y., Kan Z.-y., Wang Q., Yao Y., Liu J., Hao Y.-h., Tan Z. J. Am. Chem. Soc. 2007, 129:11185-11191.
70. Zheng K.-w., Chen Z., Hao Y.-h., Tan Z. Nucleic Acids Res. 2010, 38:327-338.
71. Heddi B., Phan A.T.n. J. Am. Chem. Soc. 2011, 133:9824-9833.
72. Xu L., Feng S., Zhou X. Chem. Commun. 2011, 47:3517-3519.
73. Miyoshi D., Nakao A., Sugimoto N. Biochemistry 2002, 41:15017-15024.
74. Miyoshi D., Karimata H., Sugimoto N. Angew. Chem. Int. Ed. 2005, 44:3740-3744.
75. Bajorath J. Nat. Rev. Drug Discov. 2002, 1:882-894.
76. Shoichet B.K. Nature 2004, 432:862-865.
77. Abagyan R., Totrov M. Curr. Opin. Chem. Biol. 2001, 5:375-382.
78. Campbell M. Curr. Opin. Chem. Biol. 2007, 11:494-502.
79. Cavasotto C.N., Orry A.J.W. Top. Med. Chem. 2007, 7:1006-1014.
80. Ghosh S., Nie A., An J., Huang Z. Curr. Opin. Chem. Biol. 2006, 10:194-202.
81. Kitchen D.B., Decornez H., Furr J.R., Bajorath J. Nat. Rev. Drug Discov. 2004, 3:935-949.
82. Ma D.-L., Chan D.S.-H., Leung C.-H. Chem. Sci. 2011, 2:1656-1665.
83. Shoichet B.K., McGovern S.L., Wei B., Irwin J.J. Curr. Opin. Chem. Biol. 2002, 6:439-446.
84. Sheng-Yong Y. Drug Discov. Today 2010, 15:444-450.
85. Wolber G., Langer T. J. Chem. Inf. Model. 2004, 45:160-169.
86. Chen J., Lai L. J. Chem. Inf. Model. 2006, 46:2684-2691.
87. Ortuso F., Langer T., Alcaro S. Bioinformatics 2006, 22:1449-1455.
88. An J., Totrov M., Abagyan R. Mol. Cell. Proteomics 2005, 4:752-761.
89. Kirchhoff P.D., Brown R., Kahn S., Waldman M., Venkatachalam C.M. J. Comput. Chem. 2001, 22:993-1003.
90. Discovery Studio Version 2.5 (DS 2.5) User Manual, Accelrys Inc., San Diego, CA, 2009.
91. Li H., Sutter J., Hoffman R. HypoGen: An Automated System for Generating 3D Predictive Pharmacophore Models. Pharmacophore Perception, Development and Use in Drug Design 2000, International University Line. O. Guner (Ed.).
92. Barnum D., Greene J., Smellie A., Sprague P. J. Chem. Inf. Comput. Sci. 1996, 36:563-571.
93. Dixon S., Smondyrev A., Knoll E., Rao S., Shaw D., Friesner R. J. Comput. Aided Mol. Des. 2006, 20:647-671.
94. Poptodorov K., Luu T., Hoffmann R.D. Pharmacophore Model Generation Software Tools, Pharmacophores and Pharmacophore Searches 2006, Wiley-VCH Verlag GmbH & Co. KGaA, pp. 15-47.
95. Wallach I. Drug Develop. Res. 2011, 72:17-25.
96. Caporuscio F., Tafi A. Med. Chem. 2011, 18:2543-2553.
97. Kim K.-H., Kim N.D., Seong B.-L. Exp. Opin. Drug Discov. 2010, 5:205-222.
98. Berman H.M., Gelbin A., Westbrook J. Prog. Biophys. Mol. Biol. 1996, 66:255-288.
99. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. Nucleic Acids Res. 2000, 28:235-242.
100. Lee H.-M., Chan D.S.-H., Yang F., Lam H.-Y., Yan S.-C., Che C.-M., Ma D.-L., Leung C.-H. Chem. Commun. 2010, 46:4680-4682.
101. Totrov M., Abagyan R. Curr. Opin. Struct. Biol. 2008, 18:178-184.
102. Teodoro M.L., Kavraki L.E. Curr. Pharm. Des. 2003, 9:1635-1648.
103. Totrov M., Abagyan R. Proteins Struct. Funct. Genet. 1998, 215-220.
104. Abagyan R., Totrov M. J. Mol. Biol. 1994, 235:983-1002.
105. Bissantz C., Folkers G., Rognan D. J. Med. Chem. 2000, 43:4759-4767.
106. Clark R.D., Strizhev A., Leonard J.M., Blake J.F., Matthew J.B. J. Mol. Graphics Modell. 2002, 20:281-295.
107. Miklos F. Drug Discov. Today 2006, 11:421-428.
108. Yang J.-M., Chen Y.-F., Shen T.-W., Kristal B.S., Hsu D.F. J. Chem. Inf. Model. 2005, 45:1134-1146.
109. Krejsa C.M., Horvath D., Rogalski S.L., Penzotti J.E., Mao B., Barbosa F., Migeon J.C. Curr. Opin. Drug Discov. Devel. 2003, 6:470-480.
110. Wishart D.S., Knox C., Guo A.C., Cheng D., Shrivastava S., Tzur D., Gautam B., Hassanali M. Nucleic Acids Res. 2008, 36:D901-D906.
111. Wang Y., Bolton E., Dracheva S., Karapetyan K., Shoemaker B.A., Suzek T.O., Wang J., Xiao J., Zhang J., Bryant S.H. Nucleic Acids Res. 2010, 38:D255-D266.
112. Reid D., Sadjad B.S., Zsoldos Z., Simon A. J. Comput. Aided Mol. Des. 2008, 22:479-487.
113. Lipinski C.A., Lombardo F., Dominy B.W., Feeney P.J. Adv. Drug Delivery Rev. 2001, 46:3-26.
114. Tan D.S. Nat. Chem. Biol. 2005, 1:74-84.
115. Haggarty S.J. Curr. Opin. Chem. Biol. 2005, 9:296-303.
116. Smith J.M. Nature 1970, 225:563-564.
117. Koch M.A., Schuffenhauer A., Scheck M., Wetzel S., Casaulta M., Odermatt A., Ertl P., Waldmann H. Proc. Natl. Acad. Sci. USA 2005, 102:17272-17277.
118. Ma D.-L., Lai T.-S., Chan F.-Y., Chung W.-H., Abagyan R., Leung Y.-C., Wong K.-Y. ChemMedChem 2008, 3:881-884.
119. Shin-ya K., Wierzba K., Matsuo K.-i., Ohtani T., Yamada Y., Furihata K., Hayakawa Y., Seto H. J. Am. Chem. Soc. 2001, 123:1262-1263.
120. Kim M.-Y., Gleason-Guzman M., Izbicka E., Nishioka D., Hurley L.H. Cancer Res. 2003, 63:3247-3256.
121. Grand C.L., Han H., Muñoz R.M., Weitman S., Von Hoff D.D., Hurley L.H., Bearss D.J. Mol. Cancer Ther. 2002, 1:565-573.
122. del Toro M., Bucek P., Aviñó A., Jaumot J., González C., Eritja R., Gargallo R. Biochimie 2009, 91:894-902.
123. Phan A.T., Kuryavyi V., Gaw H.Y., Patel D.J. Nat. Chem. Biol. 2005, 1:167-173.
124. Cosconati S., Marinelli L., Trotta R., Virno A., Mayol L., Novellino E., Olson A.J., Randazzo A. J. Am. Chem. Soc. 2009, 131:16336-16337.
125. Cáceres C., Wright G., Gouyette C., Parkinson G., Subirana J.A. Nucleic Acids Res. 2004, 32:1097-1102.
126. Morris G.M., Huey R., Lindstrom W., Sanner M.F., Belew R.K., Goodsell D.S., Olson A.J. J. Comput. Chem. 2009, 30:2785-2791.
127. Chen S.-B., Tan J.-H., Ou T.-M., Huang S.-L., An L.-K., Luo H.-B., Li D., Gu L.-Q., Huang Z.-S. Bioorg. Med. Chem. Lett. 2011, 21:1004-1009.
128. Azzalin C.M., Reichenbach P., Khoriauli L., Giulotto E., Lingner J. Science 2007, 318:798-801.
129. Xu Y., Kaminaga K., Komiyama M. J. Am. Chem. Soc. 2008, 130:11179-11184.
130. Deng Z., Norseen J., Wiedmer A., Riethman H., Lieberman P.M. Mol. Cell 2009, 35:403-413.
131. de Lange T. Gene. Dev. 2005, 19:2100-2110.
132. Kumari S., Bugaut A., Huppert J.L., Balasubramanian S. Nat. Chem. Biol. 2007, 3:218-221.
133. Collie G.W., Sparapani S., Parkinson G.N., Neidle S. J. Am. Chem. Soc. 2011, 133:2721-2728.
134. Martadinata H. J. Am. Chem. Soc. 2009, 131:2570-2578.
135. Arora A., Maiti S. J. Phys. Chem. B 2009, 113:10515-10520.
136. Joachimi A., Benz A., Hartig J.S. Bioorg. Med. Chem. 2009, 17:6811-6815.
137. Xu Y., Suzuki Y., Ito K., Komiyama M. Proc. Natl. Acad. Sci. USA 2010.
138. Ito K., Go S., Komiyama M., Xu Y. J. Am. Chem. Soc. 2011, 133:19153-19159.