Complete stereochemistry of tetrafibricin

Article abstract of DOI:10.1021/ol0272895

(Matrix presented) With use of the NMR databases in achiral and chiral solvents, the complete stereochemistry of tetrafibricin (1) has been elucidated without degradation of the carbon framework.

Full text of DOI:10.1021/ol0272895

ORGANIC
LETTERS
2003
Vol. 5, No. 1
93-96
Complete Stereochemistry of
Tetrafibricin
Yoshihisa Kobayashi, Werngard Czechtizky, and Yoshito Kishi*
Department of Chemistry and Chemical Biology, HarVard UniVersity,
12 Oxford Street, Cambridge, Massachusetts 02138
kishi@chemistry.harVard.edu
Received November 15, 2002
ABSTRACT
With use of the NMR databases in achiral and chiral solvents, the complete stereochemistry of tetrafibricin (1) has been elucidated without
degradation of the carbon framework.
In 1993, Kamiyama and co-workers at Nippon Roche
reported the isolation of tetrafibricin (1) from Streptomyces
neyagawaensis.1 Tetrafibricin (1) is the nonpeptidic fibrino-
gen receptor inhibitor, which shows potent antiaggregation
activities on human platelets.2 Although the gross structure
was elucidated through extensive two-dimensional NMR
analysis,3 the stereochemistry still remains to be addressed
(Figure 1). We have developed the concept and logic for a
universal NMR database approach to assign the relative and
absolute configuration of an unknown compound without
degradation and/or derivatization.4 The feasibility, reliability,
and applicability of this approach have been demonstrated
through the stereochemical assignment of the desertomycin/
oasomycin class of natural products,5 as well as the myco-
lactones.6 In this letter, using the NMR database in achiral
and chiral solvents, we report the complete stereostructure
of tetrafibricin (1) without degradation of the carbon
framework.
According to the analytical procedure we have previously
developed, tetrafibricin (1) consists of five independent ste-
reoclusters, i.e., the stereoclusters containing the C11-C12,
C15-C19, C23-C29, C33, and C37 stereogenic centers,
respectively. For assignment of the complete stereochemistry,
it is necessary to establish both the absolute and relative
configuration for the first three stereoclusters and the absolute
(1) Kamiyama, T.; Umino, T.; Fujisaki, N.; Fujimori, K.; Satoh, T.;
Yamashita, Y.; Ohshima, S.; Watanabe, J.; Yokose, K. J. Antibiot. 1993,
46, 1039-1046.
(2) (a) Satoh, T.; Yamashita, Y.; Kamiyama, T.; Watanabe, J.; Steiner,
B.; Hadvary, P.; Arisawa, M. Thromb. Res. 1993, 72, 389-400. (b) Satoh,
T.; Yamashita, Y.; Kamiyama, T.; Arisawa, M. Thromb. Res. 1993, 72,
401-412. (c) Satoh, T.; Kouns, W. C.; Yamashita, Y.; Kamiyama, T.;
Steiner, B. Biochem. J. 1994, 301, 785-791. (d) Satoh, T.; Kouns, W. C.;
Yamashita, Y.; Kamiyama, T.; Steiner, B. Biochem. Biophys. Res. Commun.
1994, 204, 325-332.
(3) Kamiyama, T.; Itezono, Y.; Umino, T.; Satoh, T.; Nakayama, N.;
Yokose, K. J. Antibiot. 1993, 46, 1047-1054.
(4) NMR database for relative stereochemistry: (a) Kobayashi, Y.; Lee,
J.; Tezuka, K.; Kishi, Y. Org. Lett. 1999, 1, 2177-2180. (b) Lee, J.;
Kobayashi, Y.; Tezuka, K.; Kishi, Y. Org. Lett. 1999, 1, 2181-2184. For
absolute stereochemistry: (c) Kobayashi, Y.; Hayashi, N.; Tan, C.-H.; Kishi,
Y. Org. Lett. 2001, 3, 2245-2248. (d) Hayashi, N.; Kobayashi, Y.; Kishi,
Y. Org. Lett. 2001, 3, 2249-2252. (e) Kobayashi, Y.; Hayashi, N.; Kishi,
Y. Org. Lett. 2001, 3, 2253-2255.
Figure 1. Structure of tetrafibricin (1) and 13-dihydro-tetrafibricin
2 and 3.
10.1021/ol0272895 CCC: $25.00 © 2003 American Chemical Society
Published on Web 12/13/2002

configuration for the last two. If there were a method
available for assigning the relative configuration at the remote
stereogenic centers, the problem in hand could be simplified
significantly.
In this context, we wondered whether the stereochemical
information of one stereocluster is transferred to the other
through a ketone via a hydrogen-bonding network.7 If a
meaningful degree of communication were detected between
the two stereoclusters, the C11-C19 portion could be
considered as a single stereocluster. With this expectation,
we first studied the NMR behavior of the syn- and anti-1,5-
dihydroxy-3-ketones (Figure 2). Experimentally, however,
Figure 3. NMR databases A and B for elucidation of the relative
configuration of 1,3,5-triols and 1,3-diols.
us to predict its relative configuration. The following
predictions can be made from the NMR data reported for
2.3 The C15 chemical shift (δ ) 67.8 ppm in DMSO-d6) is
typical for syn/syn-1,3,5-triols, suggesting the C13/C15/C17
relative configuration to be syn/syn. Similarly, the C25 (63.9
ppm) and C27 (63.8 ppm) chemical shifts are typical for
anti/anti-1,3,5-triols, predicting the relative configuration of
both C23/C25/C27 and C25/C27/C29-triols to be anti/anti,
respectively, and consequently the relative configuration of
the C23-C29 tetraol to be all anti.
On the contrary, as the reported C17 chemical shift (67.2
ppm) lies between the value expected for typical syn/syn-
and syn/anti-(or anti/syn-)1,3,5-triols, these data alone do not
yield a conclusive assignment. In this connection, the NMR
database we have previously reported provides valuable
information. The chemical shift marked with a dot in NMR
database B is diagnostic for distinguishing syn- from anti-
diols (Figure 3).10 The C19 chemical shift reported for 2 is
69.4 ppm, very close to the value found for the syn-diol (C17/
C19) of NMR database B.11 Thus, the relative configuration
at C15/C17/C19 must be either syn/syn or anti/syn but not
syn/anti. Combined with the C13/C15/C17 relative config-
uration (syn/syn, vide ante), the possibility of anti/syn can
be eliminated, thereby establishing the C15/C17/C19 relative
configuration to be syn/syn. Consistent with this conclusion,
the C15 chemical shift reported for 3 (C13-epimer of 2) is
65.9 ppm, a typical value for a syn/anti-(or anti/syn-)1,3,5-
triol, predicting the C13/C15/C17 relative configuration of
3 to be anti/syn.
Figure 2. Structures of 1,5-dihydroxy-3-ketones.
it was found that the degree of the communication between
the C4 and C8 carbons is negligibly small.8 Thus, we
searched for an alternative method and recognized that, if
the C13 ketone is reduced to the corresponding alcohol(s),
the two independent stereoclusters in question should be
treated as one stereocluster; consequently, the relative
configuration between the original two stereoclusters could
be assigned. Interestingly, Kamiyama and co-workers already
reported the detailed NMR data in DMSO-d6 for two C13
alcohols 2 and 3 derived from 1.3 For this reason,9 we focused
on 2 and 3.
Because of its self-contained nature, the center carbon
indicated by the dot in the five-carbon framework, shown
in the box in Figure 3, exhibits a unique chemical shift, which
is dependent on the relative stereochemistry of substituents
present within this framework but independent from the
stereochemistry of substituents present outside this frame-
work. The chemical shift in NMR databse A for the central
carbon, indicated by the dot (Figure 3), of syn/syn-, syn/
anti- and anti/syn-, and anti/anti-1,3,5-triols was found to
be around 68, 66, and 64 ppm in DMSO-d6, respectively,
but was found to be insensitive to the functionalities present
outside of this carbon framework.10 Thus, a chemical shift
analysis of the central carbon in a 1,3,5-triol moiety allows
As reported previously, the methyl group marked by a dot
in the NMR database C (Figure 4) is a degenerate, self-
contained carbon, and its chemical shift is diagnostic for
assigning the relative configuration of 2-methyl-1,3-diols.12
The C41 chemical shift (δ ) 7.5 ppm in DMSO-d6) reported
for 2 suggests its C11/C12/C13 relative configuration to be
syn/syn as indicated in Figure 1. This assignment is further
supported by the C41 chemical shift (9.8 ppm) reported for
3 (C13-epimer of 2), which indicates the C11/C12/C13
relative configuration to be syn/anti.
(5) (a) Kobayashi, Y.; Tan, C.-H.; Kishi, Y. Angew. Chem., Int. Ed. 2000,
39, 4279-4281. (b) Tan, C.-H.; Kobayashi, Y.; Kishi, Y. Angew. Chem.,
Int. Ed. 2000, 39, 4282-4284. (c) Kobayashi, Y.; Tan, C.-H.; Kishi, Y. J.
Am. Chem. Soc. 2001, 123, 2076-2078.
(6) (a) Benowitz, A. B.; Fidanze, S.; Small, P. L. C.; Kishi, Y. J. Am.
Chem. Soc. 2001, 123, 5128-5129. (b) Fidanze, S.; Song, F.; Szlosek-
Pinaud, M.; Small, P. L. C.; Kishi, Y. J. Am. Chem. Soc. 2001, 123, 10117-
10118.
(7) â-Hydroxycarbonyl compounds are known to form hydrogen-bonds
between the hydroxyl groups and the lone pairs of the carbonyl oxygen in
a solid state by X-ray and in a solution state by IR and 1H NMR. Sharma,
V.; Simard, M.; Wuest, J. D. J. Org. Chem. 1994, 59, 7785-7792.
(8) For details, see Supporting Information.
(9) There are two additional reasons for this decision: (1) DMSO and
MeOH have been extensively tested for the NMR database approach;
however, the NMR data of 1 were reported only in D2O. (2) The chemical
stability of 2 and 3 appears to be better than that of 1 (ref 3).
(10) Kobayashi, Y.; Tan, C.-H.; Kishi, Y. HelV. Chim. Acta 2000, 83,
2562-2571.
(11) By employing this database, the relative configuration at C27/C29
is also assigned as anti (C29 of 2, 67.7 ppm).
(12) Other examples of 2-methyl-1,3-diol for anti/syn (or syn/anti) and
anti/anti are found at 9.8-10.6 ppm and 11.0-12.2 ppm in DMSO-d6,
respectively. For details, see ref 5c.
94
Org. Lett., Vol. 5, No. 1, 2003

Figure 4. Structures of NMR database C for elucidation of the
relative configuration of 2-methyl-1,3-diols.
Figure 6. Structure of bidentate chiral NMR solvent, BMBA-p-
Me, and the general trend of ∆δRR-SS for the adjacent carbon
exhibited by isolated alcohols.
Overall, the analysis of the 13C chemical shifts reported
for the 13-dihydrotetrafibricins (2 and 3) allowed us to assign
the relative configuration at C11-C19 and C23-C29 as
indicated (Figure 1). To establish the complete stereostructure
of tetrafibricin (1), it was necessary to establish the absolute
configuration of at least one stereogenic center present in
each of the four stereoclusters C11-C19, C23-C29, C33,
and C37. The NMR database approach in chiral solvents
recently developed in this laboratory is ideally suited for this
purpose.
Our second experiment was to establish the 13C NMR
chemical shift differences (∆δRR-SS) for 3 in perdeuterated
(R)- and (S)-BMBA-p-Me (Figure 6).17,18 As long as both
adjacent carbons are sp3-carbons, a secondary alcohol
exhibits the general trend of ∆δRR-SS for the adjacent carbon
as summarized in the box in Figure 6.13 However, we have
recently observed the opposite trend of ∆δRR-SS for benzyl,
biaryl, and tertiary alcohols.19 Specifically related to the
current case, we synthesized and studied the behavior of
∆δRR-SS of E and F (Figure 7).20,21 Upon comparison with
Two types of chiral solvents, mono- and bidentate solvents,
represented by DMBA (N,R-dimethylbenzylamine)4c and
BMBA-p-Me (vide infra),13 have been developed; the bi-
dentate solvents are powerful for assigning the absolute
configuration of a stereochemically isolated, saturated sec-
ondary alcohol (separated by a two-or-more methylene bridge
from other alcohols), whereas the monodentate solvents are
for assigning the absolute configuration of more than two
alcohol-containing stereoclusters.
Our first experiment was to determine the 13C chemical
shift differences (∆δR-S) for 3 in perdeuterated (R)- and (S)-
DMBA.14,15 Figure 5 shows the significant 13C ∆δR-S
Figure 7. Observed signs and values (in parts per million) of
∆δRR-SS in bidentate chiral NMR solvent, BMBA-p-Me, of NMR
databases E and F for the absolute configuration and compound 3.
these NMR databases, the ∆δRR-SS observed for the C32/
C34 and the C36/C38 carbons of 3 (and 2) suggested the
absolute configurations at C33 and C37 as shown in Figure
7.
(13) Kobayashi, Y.; Hayashi, N.; Kishi, Y. Org. Lett. 2002, 4, 411-
414.
(14) We gratefully acknowledge Dr. Kamiyama at Nippon Roche for a
generous gift of 20 mg of tetrafibricin (1). By following Kamiyama’s
procedure (ref 3), this sample was converted to a mixture (12 mg) of 2 and
3.
(15) For details, see Supporting Information of ref 4c.
(16) For detailed conditions of the measurement, see Supporting Informa-
tion.
Figure 5. Observed signs and values (in parts per million) of ∆δR-S
in chiral NMR solvent, DMBA, of compound 3 and NMR database
A1, C1, and D for elucidation of the absolute configuration.
(17) For preparation of perdeuterated BMBA-p-Me, see Supporting
Information.
(18) 13C NMR data of 2 and 3 were obtained in a 5:2:1 w/w mixture of
perdeuterated BMBA-p-Me (350 mg) and CDCl3 (140 mg)/DMSO-d6 (70
mg).
detected.16 A comparison of these ∆δR-S values with the
∆δR-S values observed for NMR databases A1, C1, and D4d
allowed us to conclude the absolute configuration of the
C10-C30 portion of 3 as indicated.
(19) Kobayashi, Y.; Hayashi, H.; Kishi, Y. Unpublished results.
(20) Compounds E and F were prepared by Brown’s asymmetric
allylation. For details, see Supporting Information.
(21) 13C NMR data of NMR databases E and F were obtained in BMBA-
p-Me (350 mg)/CDCl3 (140 mg) (5:2 w/w).
Org. Lett., Vol. 5, No. 1, 2003
95

Figure 8. Mosher’s esters of degradation products of tetrafibricin
(1).
For the case of a stereocluster containing more than two
groups, more than two independent sets of ∆δR-S can, in
principle, be found for assigning the absolute configuration
of a given stereocluster. In other words, a cross-checking
system is installed for this method. Indeed, the two inde-
pendent sets of ∆δR-S in DMBA were found, to assign the
absolute configuration for both the C11-C19 and C23-C29
stereostructures (Figure 5).
On the other hand, only one set of the ∆δRR-SS is available
for deducing the absolute configuration of a given isolated
alcohol: the absolute configuration at C33 and C37 was
predicted from one set of ∆δRR-SS in BMBA-p-Me (Figure
7).
Figure 9. Reported structures of linearmycin A (10) and lieno-
mycin (11).
and C55/C57 to be syn/syn, syn, anti/anti/anti, and syn,
respectively.25 In the case of lienomycin (11), the partial
stereostructure was deduced by Nakanishi and co-workers
Partly because of this reason and partly because this was
the first example of an application of the BMBA-p-Me
method to an unknown natural product, we decided to
confirm the predicted absolute configuration at C33 and C37
by chemical synthesis. In practice, we first synthesized (R)-
and (S)-Mosher esters 6-9 of (S)-butane-1,2,4-triol (4) and
(R)-diol amide 5 (Figure 8).22 With these authentic samples
in hands, we then subjected a mixture of 2 and 3 to
ozonolysis, reduction, and esterification with Mosher acid
chloride, to furnish the expected degradation products. Upon
comparison of 1H NMR spectra, the two corresponding (R)-
Mosher esters derived from the natural product were found
to be identical to synthetic (R)-Mosher esters 6 and 7 but
different from synthetic (S)-Mosher esters 8 and 9, confirm-
ing the predicted absolute configuration at C33 and C37.
Last, we should comment on the structure of two natural
products, linearmycin A (10)23 and lienomycin (11),24 closely
related to tetrafibricin (1) (Figure 9). There is no stereo-
chemical information available for 10. However, on the basis
of the chemical shifts reported for 10, we predict the relative
configuration at C15/C16/C17, C35/C37, C41/C43/C45/C47,
1
through a combination of degradation, [R]D, H NMR, and
MS analysis (Figure 9).26 We believe that the method
reported here can be extended to establish the complete
stereostructure of both linearmycin A (10) and lienomycin
(11).
In conclusion, we have elucidated the complete stereo-
structure of tetrafibricin (1) via an NMR database approach
in achiral and chiral solvents. This conclusion has been
derived from the analyses of 13C NMR profiles of 13-
dihydrotetrafibricin only. In our view, this example further
illustrates the reliability, applicability, and versatility of the
universal NMR database approach in achiral and chiral
solvents.
Acknowledgment. We gratefully acknowledge Dr. Ka-
miyama at Nippon Roche for a generous gift of tetrafibricin.
Financial support from the National Institutes of Health (NS
12108) is gratefully acknowledged.
Supporting Information Available: Experimental pro-
cedures and data for compounds mentioned herein. This
material is available free of charge via the Internet at
http://pubs.acs.org.
(22) Compound 5 was prepared by acid-catalyzed hydrolysis of the
benzylidene acetal reported in ref 26.
(23) (a) Sakuda, S.; Guce-Bigol, U.; Itoh, M.; Nishimura, T.; Yamada,
Y. Tetrahedron Lett. 1995, 36, 2777-2780. (b) Sakuda, S.; Guce-Bigol,
U.; Itoh, M.; Nishimura, T.; Yamada, Y. J. Chem. Soc., Perkin Trans. 1
1996, 2315-2319.
(24) Gauze, G. F.; Maksimova, T. S.; Olhovatova, O. L.; Kudrina, J. S.;
Iltchenko, G. B.; Kotchetkova, G. V.; Volkava, L. I. Antibiotiki 1971, 5,
387-390.
OL0272895
(25) NMR data of 10 were reported in CD3OD. For the detailed analysis,
see Supporting Information.
(26) Pawlak, J.; Nakanishi, K.; Iwashita, T.; Borowski, E. J. Org. Chem.
1987, 52, 2896-2901.
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