Conformations of laulimalide in DMSO-d6

Journal of the American Chemical Society

Volumn 127, Issue 37, 2005, Pages 12838-12846

  Thepchatri, Pahk ^a   Cicero, Daniel O ^b   Monteagudo, Edith ^c   Ghosh, Arun K ^d   Cornett, Ben ^a   Weeks, Eric R ^a   Snyder, James P ^a  

^a EMORY UNIVERSITY   (United States)

^b UNIVERSITY OF ROME TOR VERGATA   (Italy)

^c IRBM   (Italy)

^d UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HYDROGEN BONDS;

LAULIMALIDES; NAMFIS DECONVOLUTION; SYNPENTANE INTERACTIONS; TAXOLS;

ORGANIC COMPOUNDS;

CYTOTOXIN; DIMETHYL SULFOXIDE; DISCODERMOLIDE; ELEUTHEROBIN; EPOTHILONE A; LAULIMALIDE; MACROLIDE; PACLITAXEL; PELUROSIDE A; PENTANE; SARCODICTYIN A; UNCLASSIFIED DRUG;

ARTICLE; CHEMICAL INTERACTION; DRUG CONFORMATION; DRUG STRUCTURE; ENERGY TRANSFER; HYDROGEN BOND; STRUCTURE ANALYSIS;

CRYSTALLOGRAPHY, X-RAY; DIMETHYL SULFOXIDE; MODELS, MOLECULAR; MOLECULAR CONFORMATION; TAXOIDS;

EID: 25144481876     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja042890e     Document Type: Article

References (62)

1. Corley, D. G.; Herb, R.; Moore, R. E.; Scheuer, P. J.; Paul, V. J. J. Org. Chem. 1988, 53, 3644-3646.
2. Ghosh, A. K.; Wang, Y. J. Am. Chem. Soc. 2000, 122, 11027-11028.
3. Ghosh, A. K.; Wang, Y.; Kim, J. T. J. Org. Chem. 2001, 66, 8973-8982.
4. Enev. V. S.; Kaehlig, H.; Mulzer, J. J. Am. Chem. Soc. 2001, 123, 10764-10765.
5. Mulzer, J.; Ohler, E. Angew. Chem., Int. Ed. 2001, 40, 3842-3846.
6. Paterson, I.; De Savi, C.; Tudse, M. Org. Lett. 2001, 3, 3149-3152.
7. Wender, P. A.; Hegde, S. G.; Hubbard, R. D.; Zhang, L. J. Am. Chem. Soc. 2002, 124, 4956-4957.
8. Crimmins, M. T.; Stanton, M. G.; Allwein, S. P. J. Am. Chem. Soc. 2002, 124, 5958-5959.
9. Nelson, S. G.; Cheung, W. S.; Kassick, A. J.; Hilfiker, M. A. J. Am. Chem. Soc. 2002, 124, 13654-13655.
10. Ahmed, A.; Hoegenauer, E. K.; Enev, V. S.; Hanbauer, M.; Kaehlig, H.; Ohler, E.; Mulzer, J. J. Org. Chem. 2003, 68, 3026-3042.
11. Gallagher, B. M., Jr.; Fang, F. G.; Johannes, C. W.; Pesant, M.; Tremblay, M. R.; Zhao, H.; Akasaka, K.; Li, X. Y.; Liu, J.; Littlefield, B. A. Bioorg. Med. Chem. Lett. 2004, 14, 575-579.
12. Mooberry, S. L.; Tien, G.; Hernandez, A. H.; Plubrukarn, A.; Davidson, B. S. Cancer Res. 1999, 59, 653-660.
13. Jiménez-Barbero, J.; Amat-Guerri, F.; Snyder, J. P. Curr. Med. Chem. 2002, 2, 91-122.
14. Pryor, D. E.; O'Brate, A.; Bilcer, G.; Díaz, J. F.; Wang, Y.; Wang, Y.; Kabaki, H.; Jung, M. K.; Andreu, J. M.; Ghosh, A. K.; Giannakakou, P.; Hamel E. Biochemistry 2002, 41, 9109-9115.
15. Gaitanos, T. N.; Buey, R. M.; Diaz, J. F.; Northcote, P. T.; Teesdale-Spittle, P.; Andreu, J. M.; Miller, J. H. Cancer Res. 2004, 64, 5063-5067.
16. Snyder, J. P.; Nettles, J. H.; Cornett, B.; Downing, K. H.; Nogales, E. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 5312-5316.
17. Lowe, J.; Li, H.; Downing, K. H.; Nogales, E. J. Mol. Biol. 2001, 313, 1045-1057.
18. Nettles, J. H.; Li, H.; Cornett, B.; Krahn, J. M.; Snyder, J. P.; Downing, K. H. Science 2004, 305, 866-869.
19. Cornett, B.; Nettles, J. H.; Downing, K. H.; Li, H.; Hamel, E.; Gapud, E. J.; Thepchatri, P.; Ghosh, A. K.; Snyder, J. P., submitted.
20. Cicero, D. O.; Barbato, G.; Bazzo, R. J. Am. Chem. Soc. 1995, 117, 1027-1033.
21. Nevins, N.; Cicero, D.; Snyder, J. P. J. Org. Chem. 1999, 64, 3979-3986.
22. Ami Lakdawala, A.; Wang, M.; Nevins, N.; Liotta, D. C.; Rusinska-Roszak, D.; Lozynski, M. C.; Snyder, J. P. BMC Chem. Biol. 2001, 1, 2; http://www.biomedcentral.com/1472-6769/1/2.
23. Delaglio, F.; Grzesiek, S.; Vuister, G. W.; Zhu, G.; Pfiezfer, J.; Bax, A. J. Biomol. NMR 1995, 6, 277-293.
24. Johnson, B.; Blevins, R. A. J. Biomol. NMR 1994, 4, 603-614.
25. Claridge, T. D. W. High-Resolution NMR Techniques in Organic Chemistry; Pergamon: NY, 1999.
26. Ganesh, T.; Guza R. C.; Bane, S.; Ravindra, R.; Shanker, N.; Lakdawala, A. S.; Snyder, J. P.; Kingston, D. G. I. Proc. Nat. Acad. Sci. U.S.A. 2004, 101, 10006-10011; footnote p. 10009.
27. Jefford, C. W.; Gernardinelli, G.; Tanaka, J.; Higa, T. Tetrahedron Lett. 1996, 37, 159-162.
28. Bruno, I. J.; Cole, C.; Edgington, P. R.; Kessler, M.; Macrae, C. F.; McCabe, P.; Pearson, J.; Taylor, R. Acta Crystallogr. 2002, B58, 289-397.
29. Allen, F. H. Acta Crystallogr. 2002, B58, 380-388; www.ccdc.cam.ac.uk/.
30. Mohamadi, F. R.; Richards, N. G. J.; Guida, W. C.; Liskamp, R.; Lipton, M.; Caufield, C.; Chang, G.; Hendrickson, T.; Still, W. C. J. Comput. Chem. 1990, 11, 440-467; www.schrodinger.com/Products/macromodel.html.
31. Still, W. C. T.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. J. Am. Chem. Soc. 1990, 112, 6127-6129.
32. Lakdawala, A.; Wang, M.; Nevins, N.; Liotta, D. C.; Rusinska-Roszak, D.; Lozynski, M. C.; Snyder, J. P. BMC Chem. Biol. 2001, 1, 2; http://www. biomedcentral.com/1472-6769/1/2.
33. Shenkin, P. S.; McDonald, D. Q. J. Comput. Chem. 1994, 15, 899-916.
34. Kabsch, W. A. Acta Crystallogr. 1976, A32, 922-923.
35. Kabsch, W. A. Acta Crystallogr. 1978, A34, 827-828
36. Landis, C.; Allured, V. S. J. Am. Chem. Soc. 1991, 113, 9493-9499.
37. Landis, C. R.; Luck, L. L.; Wright, J. M. J. Magn. Reson., Ser. B 1995, 109, 44-59.
38. Wright, J. M.; Landis, C. R.; Ros, M. A. M. P.; Horton, A. D. Organometallics 1998, 17, 5031-5040.
39. Nikiforovich, G. V.; Vesterman, B. G.; Betins, J. Biophys. Chem. 1988, 31, 101-106.
40. Nikiforovich, G. V.; Kover, K. E.; Kolodziej, S. A.; Nock, B.; George, C.; Deschamps, J. R.; Flippen-Anderson, J. L.; Marshall, G. R. J. Am. Chem. Soc. 1996, 118, 959-969.
41. Nikiforovich, G. V.; Kover, K. E.; Zhang, W.-J.; Marshall, G. R. J. Am. Chem. Soc. 2000, 122, 3262-3273.
42. Mierke, D. F.; Kurz, M.; Kessler, H. J. Am. Chem. Soc. 1994, 116, 1042-1049.
43. Cuniasse, P.; Raynal, I.; Yiotakis, A. J. Am. Chem. Soc. 1997, 119, 5239-5248.
44. Numerical Algorithms Group (NAG) libraries: http://www.nag.co.uk/numeric/ fl/FLdescription.asp.
45. Haasnoot, C. A. G.; De Leeuw, F. A. A. M.; Altona, C. Tetrahedron 1980, 36, 2783-2792.
46. Becke, A. D. Phys. Rev. A. 1988, 38, 3098-3100.
47. Frisch, M. J. T.; G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Zakrzewski, V. G.; Montgomery, J. A., Jr.; Stratmann, R. E.; Burant, J. C.; Dapprich, S.; Millam, J. M.; Daniels, A. D.; Kudin, K. N.; Strain, M. C.; Farkas, O.; Tomasi, J.; Barone, V.; Cossi, M.; Cammi, R.; Mennucci, B.; Pomelli, C.; Adamo, C.; Clifford, S.; Ochterski, J.; Petersson, G. A.; Ayala, P. Y.; Cui, Q.; Morokuma, K.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Cioslowski, J.; Ortiz, J. V.; Baboul, A. G.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Gonzalez, C.; Challacombe, M.; Gill, P. M.; Johnson, B.; Chen, W.; Wong, M. W.; Andres, J. L.; Gonzalex, C.; Head-Gordon, M.; Replogle, E. S.; Pople, J. A. Gaussian 98, revision A.7.; Gaussian Inc: Pittsburgh, PA, 1998.
48. (a) Halgren, T. A.; Nachbar, R. B. J. Comput. Chem. 1996, 17, 587-615.
49. (b) Halgren, T. A. J. Comput. Chem. 1999, 20, 730-748.
50. cf. www.schrodinger.com/macromodel2.html.
51. Perola, E.; Charifson, P. S. J. Med. Chem. 2004, 47, 2499-2510.
52. Hoffmann, R. W. Angew. Chem., Int. Ed. Engl. 1992. 31, 1124-1134.
53. Taylor, R. E.; Zajicek, J. J. Org. Chem. 1999, 64, 7224-7228.
54. Taylor, R. E.; Chen, Y.; Galvin, G. M.; Pabba, P. K. Org. Biomol. Chem. 2004, 2, 127-132.
55. DeLano, W. L. The PyMOL Molecular Graphics System; DeLano Scientific: San Carlos, CA, USA, 2002. http://pymol.sourceforge.net/.
56. Maestro 7.0 Schrodinger, LLC, New York, 1999-2005. http://www. schrodinger.com/.
57. The mole fraction of 0.27 (27% population) differs from the value of 0.34
58. (34%) recorded in Table 5 because the former refers to the original 22 NAMFIS conformers, while the latter refers to the final 15 conformers following the post-NAMFIS energy analysis.
59. See the Supporting Information for further discussion on errors, error propagation, and interpretation of the NAMFIS matching curves.
60. Snyder, J. P.; Nevins, N.; Cicero, D. O.; Jansen, J. J. Am. Chem. Soc. 2000, 122, 724-725.
61. Monteagudo, E.; Cicero, D. O.; Cornell, B.; Myles, D. C.; Snyder, J. P. J. Am. Chem. Soc. 2001, 123, 6929-6930.
62. Cornett, B.; Monteagudo, E.; Cicero, D. O.; Cinel, B.; Anderson, R. J.; Roberge, M.; Milanesio, M.; Liotta, D. C.; Snyder, J. P., submitted.