Structure elucidation and total synthesis of kulkenon

Article abstract of DOI:10.1002/anie.201309386

The impressive biological profile of secondary metabolites isolated from strains of Sorangium cellulosum prompted us to initiate synthetic studies on kulkenon, also isolated from Sorangium cellulosum. The synthesis features a syn-selective vinylogous Kobayashi aldol reaction, recently developed by us, and a ring-closing intramolecular Heck reaction as the pivotal transformations. Comparison of the NMR spectra of the authentic and synthetic material revealed that the proposed configuration had to be revised. A combination of molecular modeling and NOE experiments was used to propose the revised configuration, which was confirmed by a new synthesis. Similar but not identical: The related natural products sulfangolid and kulkenon exhibit different configurations, which only became apparent by synthesizing the proposed structure and comparison with the authentic data. A combination of NOE experiments and computational conformational search identified the correct structure of kulkenon. Copyright

Full text of DOI:10.1002/anie.201309386

Angewandte
Chemie
DOI: 10.1002/anie.201309386
Natural Products
Structure Elucidation and Total Synthesis of Kulkenon**
Gerrit Symkenberg and Markus Kalesse*
Abstract: The impressive biological profile of secondary
metabolites isolated from strains of Sorangium cellulosum
prompted us to initiate synthetic studies on kulkenon, also
isolated from Sorangium cellulosum. The synthesis features
a syn-selective vinylogous Kobayashi aldol reaction, recently
developed by us, and a ring-closing intramolecular Heck
reaction as the pivotal transformations. Comparison of the
NMR spectra of the authentic and synthetic material revealed
that the proposed configuration had to be revised. A combi-
nation of molecular modeling and NOE experiments was used
to propose the revised configuration, which was confirmed by
a new synthesis.
Figure 1. Proposed configurations of sulfangolide C and kulkenon.
I
n 1996 and 2001 Hçfle reported the isolation of sulfango-
lides and kulkenon from different strains of Sorangium
cellulosum by screening myxobacteria at the Helmholtz
Centre for Infection Research (HZI).[1] In 2012, Mꢀller and
co-workers reported the relative configuration of sulfangoli-
de C (1) on the basis of 1D and 2D NMR spectroscopic data
as well as molecular modeling studies.[2] We became inter-
ested in kulkenon and the sulfangolides and their biological
potential as these natural products were observed as by-
products during the isolation of the highly active natural
products chivosazol,[3] disorazol,[4] and soraphen.[5]
Scheme 1. Retrosynthetic synthesis of kulkenon.
isovaleraldehyde (6) with Z-N,O-keteneacetal 5 provided
alcohol 7 in 82% yield and d.r. 20:1 (Scheme 2). Next, the
Evans auxiliary was removed with lithium borohydride, the
accrued primary hydroxy group protected as its TBS ether,
and the secondary alcohol transformed to the corresponding
phosphonate 9. The subsequent HWE olefination with
aldehyde 10, which was prepared in a three-step sequence
starting from propargylic alcohol,[9] gave the desired product
as a single isomer (92%). Deprotection with TBAF, allylic
oxidation, and tin–iodide exchange then completed the
synthesis of “eastern” fragment 4 (Scheme 2).
Even though the structure elucidation was performed only
for sulfangolide C, we anticipated that the same configuration
would hold true for kulkenon and was consequently used as
the hypothetical configuration of our synthetic target 2
(Figure 1). Our retrosynthesis disconnects kulkenon between
C5 and C6 and between C20 and C21. These bonds can be
constructed in the synthesis through an intramolecular Heck
reaction[6] and by means of a Horner–Wadsworth–Emmons
(HWE) olefination, respectively.[7] We envisaged that the syn
configuration between C24 and C25 could be generated
through the syn-selective Kobayashi aldol reaction, recently
developed in our group (Scheme 1).[8]
For the synthesis of the “eastern” fragment 4 we
employed our syn-selective variation of Kobayashiꢁs vinyl-
ogous Mukaiyama aldol reaction. The transformation of
[*] Dipl.-Chem. G. Symkenberg, Prof. Dr. M. Kalesse
Institute for Organic Chemistry and Centre of Biomolecular Drug
Research (BMWZ), Leibniz Universitꢀt Hannover
Schneiderberg 1B, 30167 Hannover (Germany)
and
Helmholtz Centre for Infection Research (HZI)
Inhoffenstrasse 7, Braunschweig (Germany)
E-mail: Markus.Kalesse@oci.uni-hannover.de
Scheme 2. Synthesis of the “eastern” fragment. a) 6, TiCl4, CH2Cl2,
ꢀ788C, 84%, d.r. >20:1; b) LiBH4, MeOH, THF, 08C!RT, 95%;
c) TBSCl, imidazole, CH2Cl2, RT, 82%; d) 8, DCC, 4-DMAP, CH2Cl2,
08C!RT, 90%; e) 10, NaH, THF, 08C!RT, 95%; f) TBAF, THF,
08C!RT, 88%; g) MnO2, CH2Cl2, RT, 95%; h) I2, CH2Cl2, RT, 88%.
TBSCl=tert-butyl(chloro)dimethylsilane, DCC=N,N’-dicyclohexylcarbo-
diimide, 4-DMAP=4-(dimethylamino)pyridine, THF=tetrahydrofuran,
TBAF=tetrabutylammonium fluoride.
[**] We thank Dr. R. Jansen, Helmholtz Centre for Infection Research
(HZI), for providing a sample of authentic kulkenon. This work was
supported by the DFG (Ka 913/22-1).
Supporting information for this article is available on the WWW
under http://dx.doi.org/10.1002/anie.201309386.
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Scheme 3. Synthesis of the “western” fragment. a) PCC, CH2Cl2, RT;
b) 12, TiCl4, iPr2NEt, CH2Cl2, ꢀ508C, 80% over two steps, d.r. 10:1;
c) MeO(Me)NH·HCl, Me3Al, CH2Cl2, ꢀ208C!RT, 90%; d) TBSOTf,
2,6-lutidine, CH2Cl2, 08C!RT, 92%; e) EtMgBr, Et2O, ꢀ788C!RT,
86%; f) (+)-Ipc2BOTf, iPr2NEt, CH2Cl2, ꢀ788C!ꢀ208C, 54%, d.r.
12:1; g) TBSOTf, 2,6-lutidine, CH2Cl2, 08C!RT, 92%; h) CSA, MeOH,
CH2Cl2, ꢀ208C, 69%; i) DMP, NaHCO3, CH2Cl2, RT, 92%; j) 18, nBuLi,
THF, ꢀ788C, 79%; k) DMP, NaHCO3, CH2Cl2, RT, 95%. PCC=pyridi-
nium chlorochromate, TBSOTf=tert-butyldimethylsilyl trifluorometha-
nesulfonate, (+)-Ipc2BOTf=(+)-diisopinocampheylborane trifluorome-
thanesulfonate, CSA=camphor sulfonic acid, DMP=Dess–Martin
periodinane.
Scheme 4. Endgame of the kulkenon synthesis. a) Ba(OH)2, THF, RT,
73%, E/Z>20:1; b) Pd(OAc)2, K2CO3, Bu4NCl, DMF, 608C; c) TAS-F,
DMF, RT, 22% over two steps. DMF=dimethylformamide, TAS-
F=tris(dimethylamino)sulfonium difluorotrimethylsilicate.
lished transformations, it became apparent that we had to
determine the configuration of kulkenon independently.
Unfortunately, neither of the gene clusters for the kulkenon
and the sufangolide C biosynthesis were available and we,
therefore, had to rely solely on NMR data in combination
with computational methods.
We employed the Murata method to confirm the relative
configuration of C14 and C15 as well as of C24 and C25.[12]
The measurement of the required heteronuclear coupling
constants (2,3JC,H) relied on the analysis of HSQC-HECADE
spectra. The homo- and heteronuclear coupling constants for
the two respective regions of kulkenon are shown in Figure 2.
The “western” fragment 3 was constructed by joining
together ketone 14 and aldehyde 15 through an Ipc2BOTf-
mediated aldol reaction (Scheme 3).[10] To achieve this,
alcohol 11 was oxidized with PCC and directly used in
a Nagao aldol reaction, which provided 13 in 80% yield over
two steps. Subsequent transformation to the corresponding
Weinreb amide, TBS protection of the secondary hydroxy
group, and a Grignard reaction with EtMgBr gave ketone 14.
Aldehyde 15 was synthesized according to a four-step
sequence reported by Paterson et al.[11]
Ketone 14 and aldehyde 15 could now be joined through
an aldol reaction with (+)-Ipc2BOTf, which provided 16 in
54% yield and a diastereomeric ratio of 12:1. Furthermore,
the undesired isomers could be separated by column chro-
matography. The newly generated secondary hydroxy group
was protected as a TBS ether, the primary TBS group cleaved
with CSA, and subsequently oxidized using DMP to yield
aldehyde 17. Finally, treatment with lithiated 18 and oxidation
gave “western” fragment 3.
The endgame of kulkenon started with a HWE olefina-
tion[7] of the “western” and the “eastern” segment with
Ba(OH)2 as the base, and provided the precursor for the
subsequent Heck reaction[6] (Scheme 4). Finally, the intra-
molecular Heck reaction provided the macrocyclic backbone
of kulkenone. After removal of the TBS protecting groups
with TAS-F, compound 2 was isolated in 25% yield over two
steps.
Unfortunately, after completion of its synthesis, the NMR
spectra of the authentic and the synthetic material were not
identical and exhibited significant differences, so we had to
conclude that at least one configuration was not correctly
installed (see the Supporting Information). After careful
inspection of all our stereoselective transformations and
confirmation of the stereochemical outcome even of estab-
Figure 2. Conformations and configurations determined for the C14/
C15 subunit (20) and the C24/C25 subunit (21) of kulkenon; coupling
3
constants JH,H and 2,3JH,C [Hz] in parentheses.
A rather small 3JH,H coupling constant between H14 and H15
indicates a gauche conformation of these protons. A large
2JC,H coupling constant between H14 and C15 and a small 3JC,H
coupling constant between H15 and C31 also support the
gauche conformation. These results lead to configuration 20
and confirmed the syn-configuration between the methyl
3
group at C14 and the hydroxy group at C15. The small JH,H
coupling constant between H24 and H25 supports a gauche
2
conformation of these two protons. A large JC,H coupling
3
constant between H24 and C25 and a small JC,H coupling
constant between H25 and C34 also support a gauche
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conformation for each case. Overall, this results in a syn
configuration for the methyl group at C24 and the ester
oxygen atom at C25, as shown in structure 21 (Figure 2).
Consequently, we concluded that the relative configura-
tion at C14 and C15 as well as of C25 and C26 was identical to
that proposed for sufangolide C (1). Unfortunately, the
different clusters of chiral centers cannot be correlated with
each other by the Murata method. On the other hand,
inspection of the NMR data of authentic kulkenon and
compound 2 clearly showed different but indicative NOESY
correlations (Figure 3). Both molecules exhibit a transannular
Figure 4. C18–C24 region of authentic kulkenon (22) and compound
2.
Figure 3. Significant NOESY correlations for authentic kulkenon and
compound 2.
NOESY contact between H3 and H33. However, different
NOE interactions were identified in the C18 to C25 region.
For authentic kulkenon, we observed NOE interactions
between H18 and H21, H20 and H32, as well as between
H23 and H24. These NOESY contacts were not detected for
compound 2. On the other hand, 2 exhibited NOESY
correlations between H18 and H20 as well as between H23
and H34.
Scheme 5. Revised synthesis of kulkenon. a) 6, TiCl4, CH2Cl2, ꢀ788C,
82%, >20:1 d.r.; b) 3HF·NEt3, MeCN, 408C, 25% over two steps.
DMF=dimethylformamide.
With the knowledge of a syn configuration for C14/C15
and C24/C25, the complexity of the configurational assign-
ment was reduced to only four independent regions and
a total of eight possible diastereomers. A Monte Carlo search
using MacroModel (version9.9) was performed for all eight
diastereomers (see the Supporting Information). The so-
obtained conformations were then inspected to identify those
that were in accordance with the experimentally observed
NOESY correlations. Remarkably, only isomer 22 exhibited
a conformation that would be consistent with the NMR data
of authentic kulkenon. The opposite configuration at C24 and
C25 in isomer 22, compared to the originally proposed
configuration, leads to a conformational change in the C18 to
C24 region of kulkenon (Figure 4) and provides a rationale
for the observed NOE contacts.
With this knowledge, we aimed at a revised synthesis of
kulkenon, in which only the configuration of the two chiral
centers established in the vinylogous Mukaiyama aldol
reaction had been changed (Scheme 5). In contrast to the
synthesis of the non-natural diastereomer 2, the final TBS
deprotection was achieved with 3HF·NEt3, since TAS-F led
to significant decomposition of the starting material. After
completion of the second synthesis, we gratifyingly realized
that the spectroscopic data were identical with the data
originating from the authentic sample.
The subsequent total synthesis finally confirmed the proposed
absolute and relative configuration. The pivotal transforma-
tions used in this synthesis are a syn-selective vinylogous
Kobayashi aldol reaction and an intramolecular Heck reac-
tion, which serves as a valuable alternative to established
cyclization strategies. Our efforts to also confirm the pro-
posed configuration of sulfangolide C will be reported in due
course.
Received: October 28, 2013
Published online: January 13, 2014
Keywords: Kobayashi aldol reaction · kulkenon ·
.
macrolactones · structure elucidation · total synthesis
[1] a) G. Hçfle in Scientific Annual Report of the GBF: Biological
active secondary metabolites from Myxobacteria-Isolation, Struc-
ture Elucidation and Chemistry (Ed.: H.-J. Walsdorff), Gesell-
schaft fꢀr Biotechnologische Forschung, Braunschweig, 1996,
pp. 109 – 113; b) G. Hçfle in Scientific Annual Report of the
GBF: Biological active secondary metabolites from Myxobac-
teria-Isolation, Structure Elucidation and Chemistry (Ed.: H.-J.
Walsdorff), Gesellschaft fꢀr Biotechnologische Forschung,
Braunschweig, 2001, pp. 102 – 105 available at http://www.
helmholtz-hzi.de/en/news_public_relation/media/publications/
archive.
In summary, we used a combination of computational and
NMR experiments to propose the configuration of kulkenon.
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[2] W. Zander, H. Irschick, H. Augustiniak, M. Herrmann, R.
Jansen, H. Steinmetz, K. Gerth, W. Kessler, M. Kalesse, G.
Hçfle, R. Mꢀller, Chem. Eur. J. 2012, 18, 6264 – 6271.
[3] a) H. Irschik, R. Jansen, K. Gerth, G. Hçfle, H. Reichenbach,
Antibiotics 1995, 48, 962 – 966; b) D. Janssen, D. Albert, R.
Jansen, R. Mꢀller, M. Kalesse, Angew. Chem. 2007, 119, 4985 –
4988; Angew. Chem. Int. Ed. 2007, 46, 4898 – 4901; c) T.
Brodmann, D. Janssen, M. Kalesse, J. Am. Chem. Soc. 2010,
132, 13610 – 13611.
Chem. Soc. 2007, 129, 6100 – 6101; c) D. Menche, J. Hassfeld, J.
Li, K. Mayer, S. Rudolph, J. Org. Chem. 2009, 74, 7220 – 7229;
d) P. Li, J. Li, F. Arikan, W. Ahlbrecht, M. Dieckmann, D.
Menche, J. Am. Chem. Soc. 2009, 131, 11678 – 11679; e) P. Li, J.
Li, F. Arikan, W. Ahlbrecht, M. Dieckmann, D. Menche, J. Org.
Chem. 2010, 75, 2429 – 2444.
[7] I. Paterson, K.-S. Yeung, J. B. Smaill, Synlett 1993, 774 – 776.
[8] a) G. Symkenberg, M. Kalesse, Org. Lett. 2012, 14, 1608 – 1611;
b) S.-i. Shirokawa, M. Kamiyama, T. Nakamura, M. Okada, A.
Nakazaki, S. Hosokawa, A. Kobayashi, J. Am. Chem. Soc. 2004,
126, 13604 – 13605.
[4] H. Irschik, R. Jansen, K. Gerth, G. Hçfle, H. Reichenbach, J.
Antibiot. 1995, 48, 31 – 35.
[5] a) K. Gerth, N. Bedorf, H. Irschik, G. Hçfle, H. Reichenbach, J.
Antibiot. 1994, 47, 23 – 31; b) S. Abel, D. Faber, O. Hꢀter, B.
Giese, Angew. Chem. 1994, 106, 2522 – 2523; Angew. Chem. Int.
Ed. Engl. 1994, 33, 2466 – 2468; c) B. M. Trost, J. D. Sieber, W.
Qian, R. Dhawan, Z. T. Ball, Angew. Chem. 2009, 121, 5586 –
5589; Angew. Chem. Int. Ed. 2009, 48, 5478 – 5481; d) H.-H. Lu,
A. Raja, R. Franke, D. Landsberg, F. Sasse, M. Kalesse, Angew.
Chem. 2013, 125, 13791 – 13795; Angew. Chem. Int. Ed. 2013, 52,
13549 – 13552.
[9] M. Altendorfer, A. Raja, F. Sasse, H. Irschik, D. Menche, Org.
Biomol. Chem. 2013, 11, 2116 – 2139.
[10] I. Paterson, J. M. Goodman, M. A. Lister, R. C. Schumann, C. K.
McClure, R. D. Norcross, Tetrahedron 1990, 46, 4663 – 4684.
[11] I. Paterson, F. A. Mꢀhlthau, C. J. Cordier, M. P. Housden, P. M.
Burton, O. Loiseleur, Org. Lett. 2009, 11, 353 – 356.
[12] a) N. Matsumori, D. Kaneno, M. Murata, H. Nakamura, K.
Tachibana, J. Org. Chem. 1999, 64, 866 – 876; b) D. Menche, Nat.
Prod. Rep. 2008, 25, 905 – 918.
[6] a) D. Menche, P. Li, H. Irschik, Bioorg. Med. Chem. Lett. 2010,
20, 939 – 941; b) D. Menche, J. Hassfeld, J. Li, S. Rudolph, J. Am.
1798
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