Issue in Honor of Prof. S. Swaminathan ARKIVOC 2005 (xi) 89-101 Ferla, B.; Nicotra, F. Chemtracts Org. Chem. 2001, 14, 481. (p) Schweizer, F.; Hindsgaul, O. Curr. Opin. Chem. Biol. 1999, 3, 291. (q) Drickamer, K.; Dwek, R. A. Curr. Opin. Struct. Biol. 1995, 5, 589. 4. (a) Benedetti, F.; Berti, F.; Miertus, S.; Romeo, D.; Schillani, F.; Tossi, A. Arkivoc 2003 (xiv), 140. (b) Alterman, M.; Bjorsne, M.; Muhlman, A.; Clesson, B.; Kvarnstrom, I.; Danielson, H.; Markgreen, P.; Nillroth, U.; Unge, T.; Hallberg, A.; Samuclsson, B. J. Med. Chem. 1998, 41, 3782. (c) Zuccarello, G.; Bouzide, A.; Kvarnstrom, I.; Niklasson, G.; Svensson, S. C. T.; Brisander, M.; Danielsson, H.; Nillroth, U.; Karlen, A.; Hallberg, A.; Classon, B.; Samuelsson, B. J. Org. Chem. 1998, 63, 4898. (d) Pyring, D.; Lindberg, J.; Rosenquist, Å.; Zuccarello, G.; Kvarnström, I.; Zhang, H.; Vrang, L.; Unge, T.; Classon, B.; Hallberg, A.; Samuelsson. B. J. Med. Chem. 2001, 44, 3083. 5. (a) Pieree, M. E.; Harris, G. D.; Islam, Q.; Radesca, L. A.; Storace, L.; Waltermire, R. E.; Wat, E.; Jadav, P. K.; Emmett, G. C. J. Org. Chem. 1996, 61, 441. (b) Lam, P. Y. S.; Jadav, P. K..; Eyermann, C. J.; Hodge, C. N.; Ru, Y.; Bacheler, L. T.; Meek, J. L.; Otto, M. J.; Rayner, M. M.; Wang, Y. N.; Chang, C. H.; Weber, P. C.; Jacksm, D. A.; Sharpe, T. R.; Erickson, V. Science 1994, 263, 380. 6. (a) Chakraborty, T. K.; Jayaprakash, S.; Srinivasu, P.; Madhavendra, S. S.; Shankar, A. R.; Kunwar, A. C. Tetrahedron 2002, 58, 2853. (b) Chakraborty, T. K.; Ghosh, S.; Jayaprakash, S.; Sharma, J. A. R. P.; Ravikanth, V.; Diwan, P. V.; Nagaraj, R.; Kunwar, A. C. J. Org. Chem. 2000, 65, 6441. (c) Chakraborty, T. K.; Jayaprakash, S.; Diwan, P. V.; Nagaraj, R.; Jampani, S. R. B.; Kunwar, A. C. J. Am. Chem. Soc. 1998, 120, 12962. 7. (a) Adams, P. D.; Chen, Y.; Ma, K.; Zagorski, M. G.; Sönnichsen, F. D.; McLaughlin, M. L.; Barkley, M. D. J. Am. Chem. Soc. 2002, 124, 9278. (b) Kessler, H.; Bats, J. W.; Griesinger, C.; Koll, S.; Will, M.; Wagner, K. J. Am. Chem. Soc. 1988, 110, 1033. (c) Kessler, H. Angew. Chem., Int. Ed. 1982, 21, 512. 8. Protocol used for MD Simulation Studies: Molecular mechanics/dynamics calculations were carried out using Sybyl 6.8 program on a Silicon Graphics O2 workstation. The Tripos force field, with default parameters, was used throughout the simulations. Energy minimizations were first carried out with steepest decent, followed by conjugate gradient method for a maximum of 1000 iterations each or RMS deviation of 0.005 kcal/mol, whichever was earlier. The energy-minimized structures were then subjected to MD. A number of interatomic distances obtained from NMR data were used as constraints. Distance constraints with a force constant of 15 kcal/Å were applied in the form of flat bottom potential well with a common lower bound of 2.0 Å and the upper bound of 2.8, 3.5, and 4.0 Å, in accordance with the NOE intensities for strong (s), medium (m), and weak (w), respectively. Force constant of 5 kcal/Å was employed for dihedral angle constraints. The energy-minimized structures were subjected to constrained MD simulations for duration of 300 ps (50 cycles each of 6 ps period, of the Simulated Annealing protocol). The atomic velocities were applied following Boltzmann distribution about the center of mass, to obtain a starting temperature of 700 K. After simulating for 1 ps at high temperature, the system temperature ISSN 1424-6376 Page 100 ©ARKAT USA, Inc
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