Quantification of binding affinities of essential sugars with a tryptophan analogue and the ubiquitous role of C-H⋯π interactions

Physical Chemistry Chemical Physics

Volumn 13, Issue 14, 2011, Pages 6517-6530

  Kumari, Manju ^a   Balaji, Petety V ^a   Sunoj, Raghavan B ^a  

^a INDIAN INSTITUTE OF TECHNOLOGY BOMBAY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

CARBOHYDRATE; DRUG DERIVATIVE; SKATOLE; TRYPTOPHAN;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; HYDROGEN BOND; MONTE CARLO METHOD; THERMODYNAMICS;

CARBOHYDRATE CONFORMATION; CARBOHYDRATES; HYDROGEN BONDING; MODELS, MOLECULAR; MONTE CARLO METHOD; SKATOLE; THERMODYNAMICS; TRYPTOPHAN;

EID: 79952909685     PISSN: 14639076     EISSN: None     Source Type: Journal    
DOI: 10.1039/c0cp02559c     Document Type: Article

References (91)

1. P. Hobza and K. Müller-Dethlefs, Non-Covalent Interactions: Theory and Experiment, RSC, 2010
2. A. K. Tewari R. Dubey Bioorg. Med. Chem. 2008 16 126 143
3. M. Nishio CrystEngComm 2004 6 130 158
4. P. Tarakeshwar H. S. Choi K. S. Kim J. Am. Chem. Soc. 2001 123 3323 3331
5. N. J. Singh H. M. Lee I. Hwang K. S. Kim Supramol. Chem. 2007 19 321 332
6. E. Lee D. Kim P. JurecÏka P. Tarakeshwar P. Hobza K. S. Kim J. Phys. Chem. A 2007 111 3446 3457
7. N. J. Singh H. M. Lee S. B. Suh K. S. Kim Pure Appl. Chem. 2007 79 1057 1075
8. C. B. Shinisha R. B. Sunoj Org. Biomol. Chem. 2007 5 1287 1294
9. A. Varki, R. D. Cummings, J. D. Esko, H. H. Freez, P. Stanley, C. R. Bertozzi, G. W. Hart and M. E. Etzler, Essentials of Glycobiology, Cold Spring Harbour, New York, 2008
10. P. R. Crocker T. Feiz Curr. Opin. Struct. Biol. 1996 6 679 691
11. R. E. Huber S. Hakda C. Cheng C. G. Cupples R. A. Edwards Biochemistry 2003 42 1796 1803
12. K. Denker F. Orlik B. Schiffler R. Benz J. Mol. Biol. 2005 352 534 550
13. P. V. Gelder F. Dumas I. Bartoldus N. Saint A. Prilipov M. Winterhalter Y. Wang A. Philippsen J. P. Rosenbusch T. Schirmer J. Bacteriol. 2002 184 2994 2999
14. K. Haga R. Kanai O. Sakamoto M. Aoyagi K. Harata K. Yamane J. Biochem. (Tokyo) 2003 134 881 891
15. A. Malik S. Ahmad BMC Struct. Biol. 2007 7 1
16. C. S. Sundari D. Balasubramanian Prog. Biophys. Mol. Biol. 1997 67 183 216
17. M. Nishio Y. Umezawa M. Hirota Y. Takeuchi Tetrahedron 1995 51 8665 8671
18. P. Hobza Z. Havlas Chem. Rev. 2000 100 4253 4264
19. I. Alkorta I. Rozas J. Elguero Chem. Soc. Rev. 1998 27 163 170
20. C. Tatko Nat. Chem. Biol. 2008 4 586 587
21. S. Tsuzuki K. Honda T. Uchimaru M. Mikami K. Tanabe J. Am. Chem. Soc. 2000 122 11450 11458
22. S. Tsuzuki K. Honda T. Uchimaru M. Mikami A. Fujii J. Phys. Chem. A 2006 110 10163 10168
23. A. Fujii K. Shibasaki T. Kazama R. Itaya N. Mikami S. Tsuzuki Phys. Chem. Chem. Phys. 2008 10 2836 2843
24. O. Takahashi Y. Kohno M. Nishio Chem. Rev. 2010 110 6049 6076
25. Y. Kobayashi K. Saigo J. Am. Chem. Soc. 2005 127 15054 15060
26. J. Ran M. W. Wong J. Phys. Chem. A 2006 110 9702 9709
27. M. Brandl M. S. Weiss A. Jabs J. Suhnel R. Hilgenfeld J. Mol. Biol. 2001 307 357 377
28. V. Shanthi K. Ramanathan R. Sethumadhavan Appl. Biochem. Biotechnol. 2010 160 1473 1483
29. M. J. Plevin D. L. Bryce J. Boisbouvier Nat. Chem. 2010 2 466 471
30. M. S. Sujatha P. V. Balaji Proteins 2004 55 44 65
31. K. Ramrez-Gualito R. Alonso-Rios B. Quiroz-Garcia A. Rojas-Aguilar D. Diaz J. Jimenez-Barbero G. Cuevas J. Am. Chem. Soc. 2009 131 18129 18138
32. L. Bautista-Ibanez K. Ramirez-Gualito B. Quiroz-Garcia A. Rojas-Aguilar G. Cuevas J. Org. Chem. 2008 73 849 857
33. J. Screen E. C. Stanca-Kaposta D. P. Gamblin B. Liu N. A. Macleod L. C. Snoek B. G. Davis J. P. Simons Angew. Chem. 2007 119 3718 3722 Angew. Chem., Int. Ed. 2007 46 3644 3648
34. E. C. Stanca-Kaposta D. P. Gamblin J. Screen B. Liu L. C. Snoek B. G. Davis J. P. Simons Phys. Chem. Chem. Phys. 2007 9 4444 4451
35. G. Terraneo D. Potenza A. Canales J. Jimenez-Barbero K. K. Baldridge A. Bernardi J. Am. Chem. Soc. 2007 129 2890 2900
36. S. Vandenbussche D. Diaz M. C. Fernandez-Alonso W. Pan S. P. Vincent G. Cuevas F. J. Canada J. Jimnez-Barbero K. Bartik Chem.-Eur. J. 2008 14 7570 7578
37. S. Tsuzuki K. Honda T. Uchimaru M. Mikami K. Tanabe J. Am. Chem. Soc. 2000 122 3746 3753
38. V. Spiwok P. Lipovova T. Skalova E. Buchtelova J. Hasekb B. Kralova Carbohydr. Res. 2004 339 2275 2280
39. A. L. Ringer M. S. Figgs M. O. Sinnokrot C. D. Sherril J. Phys. Chem. A 2006 110 10822 10828
40. M. C. Fernandez-Alonso F. J. Canada J. Jimenez-Barbero G. Cuevas J. Am. Chem. Soc. 2005 127 7379 7386
41. S. Tusuzki T. Uchimaru M. Mikami J. Phys. Chem. A 2009 113 5617 5621
42. K. E. Riley P. Hobza J. Phys. Chem. A 2007 111 8257 8263
43. R. K. Raju A. Ramraj M. A. Vincent I. H. Hillier N. A. Burton Phys. Chem. Chem. Phys. 2008 10 6500 6508
44. R. K. Raju A. Ramraj I. H. Hillier M. A. Vincent N. A. Burton Phys. Chem. Chem. Phys. 2009 11 3411 3416
45. M. S. Sujatha Y. U. Sasidhar P. V. Balaji Protein Sci. 2004 13 2502 2514
46. M. S. Sujatha Y. U. Sasidhar P. V. Balaji Biochemistry 2005 44 8554 8562
47. M. S. Sujatha Y. U. Sasidhar P. V. Balaji J. Mol. Struct. (THEOCHEM) 2007 814 11 24
48. M. W. Schmidt K. K. Baldridge J. A. Boatz S. T. Elbert M. S. Gordon J. H. Jensen S. Koseki N. Matsunaga K. A. Nguyen S. Su T. L. Windus M. Dupuis J. A. Montgomery J. Comput. Chem. 1993 14 1347 1363
49. M. J. Frisch, et al., Gaussian 09, Revisions A.02, Gaussian, Inc., Wallingford CT, 2009
50. M. J. Frisch, et al., Gaussian 03, Revisions C.02 and E.01, Gaussian, Inc., Wallingford CT, 2004
51. F. Biegler-König J. Schönbohm J. Comput. Chem. 2002 23 1489 1494
52. AIM2000 (Version 2.0), The Buro fur Innovative Software, SBK-Software, Bielefeld, Germany
53. MacroModel, version 9.5, Schrödinger, LLC, New York, NY, 2007
54. J. B. Houseknecht P. R. McCarren T. L. Lowary C. M. Hadad J. Am. Chem. Soc. 2001 123 8811 8824
55. P. R. McCarren M. T. Gordon T. L. Lowary C. M. Hadad J. Phys. Chem. A 2001 105 5911 5922
56. M. P. DeMatteo S. Mei R. Fenton M. Morton D. M. Baldisseri C. M. Hadad M. W. Peczuh Carbohydr. Res. 2006 341 2927 2945
57. Y. Zhao D. G. Truhlar Acc. Chem. Res. 2008 41 157 167
58. S. Grimme J. Comput. Chem. 2004 25 1463 1473
59. L. Sobczyk S. J. Grabowski T. M. Krygowski Chem. Rev. 2005 105 3513 3560
60. S. F. Boys F. Bernardi Mol. Phys. 1970 19 553 556
61. K. S. Kim P. Tarakeshwar J. Y. Lee Chem. Rev. 2000 100 4145 4185
62. K. S. Kim J. Y. Lee H. S. Choi J. Kim J. H. Jang Chem. Phys. Lett. 1997 265 497 502
63. J. Y. Lee S. J. Lee H. S. Choi S. J. Cho K. S. Kim T. Ha Chem. Phys. Lett. 1995 232 67 71
64. E. R. Davidson S. J. Chakravorty Chem. Phys. Lett. 1994 217 48 53
65. E. R. Davidson S. J. Chakravorty Chem. Phys. Lett. 1995 241 146 148
66. S. Maity R. Sedlak P. Hobza G. N. Patwari Phys. Chem. Chem. Phys. 2009 11 9738 9743
67. R. F. W. Bader, Atoms in Molecules: A Quantum Theory, Clarendon Press, Oxford, 1990
68. J. J. Novoa F. Mota Chem. Phys. Lett. 2000 318 345 354
69. The preferred chair conformation for saccharides with their a- and b-face is provided in Fig. S1 in ESI
70. Refer to Fig. S1b (ESI) for three different rotameric forms of saccharides
71. C-H⋯N interaction is considered as belonging to the C-H⋯π interaction, as the N atom is one of the members of the aromatic ring
72. G. R. Desiraju and T. Steiner, The Weak Hydrogen Bond in Structural Chemistry and Biology, Oxford, 1999
73. Complete details of weak interactions identified with other complexes can be found in Fig. S2 in ESI
74. The Laplacians of the electron densities at bcps are provided in Table S1 (ESI)
75. In as many as seven complexes N-H of the aromatic ring is found to remain out-of-plane with an angle of up to 27° to facilitate optimum N-H⋯O interaction. The distances and angles of N-H⋯O are found to be in the range from 1.96 to 2.44 and from 102° to 154° respectively
76. F. A. Quiocho J. C. Spurlino L. E. Rodseth Structure (London) 1997 5 997 1015
77. H. M. Berman J. Westbrook Z. Feng G. Gilliland T. N. Bhat H. Weissig I. N. Shindyalov P. E. Bourne Nucleic Acids Res. 2000 28 235 242
78. The optimized geometries of 2c and rest of the complexes are provided in Fig. S3 (ESI). The N-H of the aromatic ring is found to remain out-of-plane bending with an angle of up to 29° and the distances and angles of N-H⋯O are found to be in the range from 2.01 to 2.90 and from 94° to 152° respectively
79. The Laplacians of the electron densities at bcps are provided in Table S2 (ESI)
80. 2OH. This further results in an increase in the apolar patch of the b-face
81. Interestingly, the C-H⋯π contact distance is found to be 2.33 . A full description of the type of interactions as identified by the AIM analyses is provided in Table S3 in ESI
82. A more detailed representation of key intermolecular interactions for the additional complexes is provided in Fig. S4 in ESI
83. bcp values obtained through AIM analyses are provided in Table S4 in ESI
84. The optimized geometries of complexes other than those provided in Fig. 5 are given in Fig. S5 in ESI
85. The optimized geometries of complexes other than those provided in Fig. 6 are given in Fig. S6 in ESI
86. bcp values for several other interactions noticed for all the binary complexes of α-l-fucose with 3-MeIn is provided in Table S5 in ESI
87. Other complexes such as 5d and 5e are also identified to display similar geometries
88. The optimized geometries of complexes other than those provided in Fig. 7 are given in Fig. S7 in ESI
89. bcp values for several other interactions noticed for all binary complexes of β-l-fucose with 3-MeIn is provided in Table S6 in ESI
90. The computed interaction energies are provided in Table S7 in ESI
91. The scatter plots for comparison of the interaction energies obtained using basis sets with and without diffuse functions are provided in Fig. S8 in ESI