In one scenario, a knowledge of the tubulin-binding confor-
mation of paclitaxel would enable the design of simple non-
taxoid compounds with comparable binding affinity and
bioactivity.
A more fruitful approach stems from the electron crystal-
lographic (EC) structure of Râ-tubulin stabilized by Zn2+
and PTX. It provides a detailed view of subunit structure
but at 3.7 Å resolution leaves the PTX conformation un-
resolved.26 A model derived from intersection of PTX NMR
and X-ray conformations with the EC density led to the pro-
posal of T-Taxol as the bound conformation.27 A concurrent
EC refinement28 at 3.5 Å resolution provided additional
confidence in the model. Following these developments, a
T-like conformer with a reorganized C-13 side chain (PTX-
NY) was proposed as an alternative binding model.29,30 How-
ever, this conformer is inconsistent with the EC density.31,32
Although the taxane ring system of paclitaxel is relatively
rigid, the compound has flexible side chains at C2, C4, C10,
and notably C13. As a result, there are many possible
conformations available for binding to tubulin. Two different
paclitaxel models of the tubulin-binding conformation were
proposed on the basis of NMR observables and molecular
modeling. A “nonpolar” conformation was put forth on the
basis of solution NMR investigations in nonpolar solvents,7-9
whereas similar studies in polar solvents were interpreted to
favor a bound “polar” conformation.10-13 Although most of
the reports assumed a single conformation, deconvolution
of PTX in CDCl314 and D2O/DMSO-d615 makes it clear that
the molecule adopts 9-10 conformations, no one of which
achieves a population above 30%.
A second approach focused on tubulin-bound paclitaxel
in the solid state. Application of REDOR NMR provided
F-13C distances of 9.8 and 10.3 Å between the fluorine of
a 2-(p-fluorobenzoyl)PTX and the C3′ amide carbonyl and
C3′ methine carbons, respectively.16 A related examination
reported a distance of 6.5 Å between the fluorines of 2-(p-
fluorobenzoyl)-3′-(p-fluorophenyl)-10-acetyldocetaxel and,
like the first solid state study, proposed the polar form to be
tubulin-bound.17-19
We report here an indirect method to establish the nature
of the tubulin-taxane binding conformation more firmly. As
described in more detail elsewhere,33 we previously designed
and prepared several bridged analogues such as 2 based on
the T-Taxol or butterfly conformation. The latter juxtaposes
the C3′-phenyl and C4-OAc groups and encouraged the
construction of taxanes with bridges linking these positions.
Three of the analogues have tubulin-assembly and cytotoxic
activities superior to those of paclitaxel, providing strong
support for the T-Taxol conformation.33,34 Nonetheless, the
actual improvement in bioactivity is relatively modest,
varying from a 22-fold increase in cytotoxicity in the A2780
bioassay to a factor of 1.4 in the case of the PC3 prostate
cancer cell line.33
The “polar” and “nonpolar” conformations have inspired
several elegant synthetic studies designed to generate con-
strained analogues that maintain these conformations, but
none of these constrained analogues have shown tubulin-
polymerization or cytotoxic activities equal to or greater than
those of PTX itself. Various compounds designed to mimic
the “polar” conformation were either inactive20 or less active
than PTX.21 Analogues based on the “nonpolar” conforma-
tion were also less active than PTX.22-25
(7) Dubois, J.; Guenard, D.; Gueritte-Voeglein, F.; Guedira, N.; Potier,
P.; Gillet, B.; Betoeil, J.-C. Tetrahedron 1993, 49, 6533-6544.
(8) Williams, H. J.; Scott, A. I.; Dieden, R. A.; Swindell, C. S.; Chirlian,
L. E.; Francl, M. M.; Heerding, J. M.; Krauss, N. E. Can. J. Chem. 1994,
72, 252-260.
(19) Mastropaolo, D.; Camerman, A.; Luo, Y.; Brayer, G. D.; Camerman,
N. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 6920-6924.
(20) Boge, T. C.; Wu, Z.-J.; Himes, R. H.; Vander Velde, D. G.; Georg,
G. I. Bioorg. Med. Chem. Lett. 1999, 9, 3047-3052.
(21) Ojima, I.; Lin, S.; Inoue, T.; Miller, M. L.; Borella, C. P.; Geng,
X.; Walsh, J. J. J. Am. Chem. Soc. 2000, 122, 5343-5353.
(22) Ojima, I.; Geng, X.; Lin, S.; Pera, P.; Bernacki, R. J. Bioorg. Med.
Chem. Lett. 2002, 12, 349-352.
(9) Cachau, R. E.; Gussio, R.; Beutler, J. A.; Chmurny, G. N.; Hilton,
B. D.; Muschik, G. M.; Erickson, J. W. Supercomput. Appl. High Perform.
Comput. 1994, 8, 24-34.
(10) Vander Velde, D. G.; Georg, G. I.; Grunewald, G. L.; Gunn, C.
W.; Mitscher, L. A. J. Am. Chem. Soc. 1993, 115, 11650-11651.
(11) Paloma, L. G.; Guy, R. K.; Wrasidlo, W.; Nicolaou, K. C. Chem.
Biol. 1994, 1, 107-112.
(23) Geng, X.; Miller, M. L.; Lin, S.; Ojima, I. Org. Lett. 2003, 5, 3733-
3736.
(24) Querolle, O.; Dubois, J.; Thoret, S.; Dupont, C.; Gue´ritte, F.;
Gue´nard, D. Eur. J. Org. Chem. 2003, 542-550.
(25) Querolle, O.; Dubois, J.; Thoret, S.; Roussi, F.; Montiel-Smith, S.;
Gue´ritte, F.; Gue´nard, D. J. Med. Chem. 2003, 46, 3623-3630.
(26) Nogales, E.; Wolf, S. G; Downing, K. H. Nature 1998, 391, 199-
203.
(27) Snyder, J. P.; Nettles, J. H.; Cornett, B.; Downing, K. H.; Nogales,
E. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 5312-5316.
(28) Lowe, J.; Li, H.; Downing, K. H.; Nogales, E. J. Mol. Biol. 2001,
313, 1045-1057.
(29) Geney, R.; Sun, L.; Pera, P.; Bernacki, R. J.; Xia, S.; Horwitz, S.
B.; Simmerling, C. L.; Ojima, I. Chem. Biol. 2005, 12, 339-348.
(30) The T-Taxol conformer proposed by Geney, Ojima, and colleagues
was named “REDOR-Taxol”.29 However, since there are upwards of 100
PTX conformations that meet the REDOR constraints including T-Taxol,31,32
we refer to the Geney-Ojima model as New York paclitaxel (PTX-NY).
(31) Johnson, S. A.; Alcaraz, A.; Snyder, J. P. Org. Lett. 2005, 7, 5549-
5552.
(12) Ojima, I.; Chakravarty, S.; Inoue, T.; Lin, S.; He, L.; Horwitz, S.
B.; Kuduk, S. C.; Danishefsky, S. J. Proc. Natl. Acad. Sci. U. S.A. 1999,
96, 4256-4261.
(13) Ojima, I.; Kuduk, S. D.; Chakravarty, S.; Ourevitch, M.; Begue,
J.-P. J. Am. Chem. Soc. 1997, 119, 5519-5527.
(14) Snyder, J. P.; Nevins, N.; Cicero, D. O.; Jansen, J. J. Am. Chem.
Soc. 2000, 122, 724-725.
(15) Snyder, J. P.; Nevins, N.; Jimenez-Barbero, Cicero, D.; Jansen, J.
M. Unpublished work.
(16) Li, Y.; Poliks, B.; Cegelski, L.; Poliks, M.; Gryczynski, Z.; Piszczek,
G.; Jagtap, P. G.; Studelska, D. R.; Kingston, D. G. I.; Schaefer, J.; Bane,
S. Biochemistry 2000, 39, 281-291.
(17) Ojima, I.; Inoue, T.; Chakravarty, S. J. Fluorine Chem. 1999, 97,
3-10.
(18) The X-ray crystal structure of polar PTX (ref 19) utilized in ref 16
shows an F‚‚‚F distance of 4.8 Å when the para-hydrogens of the phenyl
rings at the C-2 and C-3′ positions are replaced with fluorines (r(C-F)
1.33 Å).
)
(32) Alcaraz, A. A.; Mehta, A. K.; Johnson, S. A.; Snyder, J. P. J. Med.
Chem. 2006, 49, 2478-2488.
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