Convergent synthesis and structural confirmation of phellodonin and Sarcodonin ε

Article abstract of DOI:10.1021/ol400709f

The first synthesis of members of the sarcodonin family, phellodonin and sarcodonin ε, is reported herein. This verifies that the unprecedented and seemingly unstable N,N-dioxide-containing benzodioxazine framework can be constructed in the laboratory and lends further support to the proposed structures. The key step in the synthesis involves a biomimetic hetero-Diels-Alder reaction between a pyrazine N-oxide and an ortho-quinone.

Full text of DOI:10.1021/ol400709f

ORGANIC
LETTERS
2013
Vol. 15, No. 9
2080–2083
Convergent Synthesis and Structural
Confirmation of Phellodonin and
Sarcodonin ε
Ippei Usui,† David W. Lin,‡ Takeshi Masuda,§ and Phil S. Baran*
Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines
Road, La Jolla, California 92037, United States
pbaran@scripps.edu
Received March 16, 2013
ABSTRACT
The first synthesis of members of the sarcodonin family, phellodonin and sarcodonin ε, is reported herein. This verifies that the unprecedented
and seemingly unstable N,N-dioxide-containing benzodioxazine framework can be constructed in the laboratory and lends further support to the
proposed structures. The key step in the synthesis involves a biomimetic hetero-DielsꢀAlder reaction between a pyrazine N-oxide and an ortho-quinone.
Phellodonin (1a) is an alkaloid isolated from the fungus
Phellodon niger in 2010 (Figure 1A)1 and is part of a growing
family of sarcodonin natural products (Figure 1B).2 All of
the members of this family were reported to have a striking
molecular architecture consisting of a tricyclic benzodiox-
azine core and an unprecedented N,N-dioxide ring junc-
tion (see structure 1).3 A series of elegant but inconclusive
NMR and molecular modeling studies were used to establish
the connectivity and relative stereochemistry of the benzo-
dioxazine ring junction. Following the initial report,3a,b two
other research groups3c,d have published similar structural
assignments, although all subsequently disclosed struc-
tures were based on the original assignment. From these
structures, it was postulated that the sarcodonins are bio-
synthetically formed via an unusual [4 þ 2] cycloaddition
between an ortho-quinone (2) and the CdN double bond
of an appropriately oxidized pyrazine (3).
Our laboratory took an interest in the striking molecular
architecture of the sarcodonins as well as its intriguing
bioactivity, and undertook studies toward the total synthe-
sis of this natural product family.4 However, when we
attempted to mimic the proposed biosynthetic [4 þ 2]
cycloaddition, we obtained not the proposed tricyclic
benzodioxazine (with the core structure shown in 1) but
a bicyclic benzodioxanone (with the core of 10) instead, a
result confirmed by X-ray crystallography.4 Because of the
unprecedented nature of the structure of 1 and the spectro-
scopic similarity of the crystalline benzodioxanone to the
natural sarcodonins, we proposed a significant structural
revision of the sarcodonin family members from the
original structure 1 to the structure 10, although no ulti-
mate conclusions were drawn.
Evenwiththisreassignment, several key structural issues
were left unresolved in 10: (1) the E/Z configuration of the
2R oxime, (2) whether the methyl group found in some
members of the natural product family is located on the
hydroxamic acid at 1β or on the 1R oxime, (3) the location
of the biaryl substituent at C1 or C6 of the benzodiox-
anone, and (4) the relative configuration of the 2β aminal
stereocenter. To solve these questions as well as to
† Sirenas Marine Discovery, La Jolla, CA, United States.
‡ Pfizer, Inc., Groton, CT, United States.
§ Daiichi Sankyo Inc., Tokyo, Japan.
(1) Fang, S.-T.; Zhang, L.; Li, Z.-H.; Li, B.; Liu, J.-K. Chem. Pharm.
Bull. 2010, 58, 1176–1179.
(2) See preceding paper: Masubuti, H.; Endo, Y.; Araya, H.; Uekusa,
H.; Fujimoto, Y. Org. Lett. 2013, DOI: 10.1021/ol400595k.
ꢀ
(3) (a) Geraci, C.; Neri, P.; Paterno, C.; Rocco, C.; Tringali, C. J. Nat.
ꢀ
Prod. 2000, 63, 347–351. (b) Cali, V.; Spatafora, C.; Tringali, C. Eur. J.
Org. Chem. 2004, 592–599. (c) Ma, B. J.; Liu, J. K. Z. Naturforsch. B
2005, 60b, 565–568. (d) Hashimoto, T.; Quang, D. N.; Kuratsune, M.;
Asakawa, Y. Chem. Pharm. Bull. 2006, 54, 912–914.
(4) (a) Lin, D. W.; Masuda, T.; Biskup, M. B.; Nelson, J. D.; Baran,
P. S. J. Org. Chem. 2011, 76, 1013–1030. (b) Lin, D. W. Ph. D. Thesis,
The Scripps Research Institute, La Jolla, CA, 2010.
r
10.1021/ol400709f
Published on Web 04/11/2013
2013 American Chemical Society

Figure 1. (A) Structures of recently isolated natural products, phellodonin (1a) and sarcodonin ε (1b). (B) Originally published structure
for the sarcodonin family (1) and our recently proposed structure revision (10), both arising from a hypothetical biosynthesis via a
formal [4 þ 2] cycloaddition of ortho-quinone 2 and pyrazine derivative 3.
unambiguously identify the core structure of the sarco-
donin family, it was realized that only determination by
X-ray crystallography would be effective. Recent X-ray
Scheme 1. Preparation of Pyrazine Dienophile 10a
analysis conducted by Fujimoto and co-workers have now
indicated that a benzodioxazine similar to 1 forms the core
structure of the sarcodonins, and that the unprecedented
N,N-dioxide moiety is a stable chemical entity.2 Further-
more, they have isolated a new sarcodonin natural pro-
duct, sarcodonin ε (1b). Herein, we report the first syn-
thesis of phellodonin (1a) and sarcodonin ε (1b) and
acknowledge Fujimoto’s confirmation of the originally
proposed structure3 for this unusual heterocyclic natural
product family.
Aiming for the synthesis of phellodonin (1a), our retro-
synthesis mimics the proposed biosynthesis of the sarco-
donins, with ortho-quinone 2 undergoing a [4 þ 2]
cycloaddition with a suitably oxidized pyrazine 3 to give
the desired benzodioxanone core (see Figure 1). To pursue
this approach, however, a pyrazine bis-N-oxide had to be
prepared as the dienophile, which we had previously been
unable to achieve.4 After further investigation, a synthetic
route was devised, and therefore a diketopiperazine of
L-isoleucine (4) was converted into bis-chloropyrazine 6 in
three steps using known conditions (Scheme 1).5 The first
N-oxidation of 6 was quite facile; however, the resulting
mono-N-oxide 7 was highly deactivated, and vigorous
a Reagents and conditions: (a) POCl3, neat, 100 °C, 10 h, 70% 5 þ 4% 6;
oxidizing conditions were necessary to achieve the second
N-oxidation to give 8 in sufficient quantities.6 After this
difficult second oxidation, preparation of the dien-
ophile 10 was completed without serious incident: nucleo-
philic aromatic substitution of the heteroaryl chlorides
(b) m-CPBA (3.0 equiv), CH2Cl2, 40 °C, 4 h; (c) POCl3, neat, 100 °C, 2 h,
61% from 5; (d) H2O2 (6.0 equiv), TFA, 50 °C, 3 h, 70% 7 þ 1% 8; (e)
H2O2 (6.0 equiv), TFA, 50 °C, 3 h, 25% (52% brsm) from 7; (f) 2-TMS-
ethanol (3.3 equiv), NaOtBu (3.5 equiv), THF, 23 °C, 12 h, 63%; (g)
TBAF (1.0 equiv), then MeI (5.0 equiv), THF, 23 °C, 2 h, 99%.
(5) Ohta, A.; Akita, Y.; Hara, M. Chem. Pharm. Bull. 1979, 27, 2027–
2041.
(6) Blake, K. W.; Sammes, P. G. J. Chem. Soc. C 1970, 1070–1073.
proceeded smoothly, after which careful control of depro-
tection conditions permitted the selective removal of one
Org. Lett., Vol. 15, No. 9, 2013
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Scheme 2. Preparation of ortho-Quinone Heterodiene 20a
a Reagents and conditions: (a) Boronic acid 12, AgNO3 (20 mol %), K2S2O8 (3 equiv), R,R,R-trifluorotoluene, H2O, 23 °C, 10 h, 73%; (b) NaOMe,
MeOH, 23 °C, 1 h, 47%; (c) N-bromosuccinimide (3.0 equiv), MeCN, 70 °C, 3 h, 40ꢀ60%; (d) boronic acid 16 (1.5 equiv), Pd(dppf)Cl2 (2 mol %), CsF
(2 equiv), toluene, 70 °C, 2 h, 88%; (e) aq NaOH, MeOH, 80 °C, 2 h; (f) Na2S2O4 (7.0 equiv), MeOH:H2O (6:1), 23 °C, 1 h; (g) AcCl (30 equiv), Et3N
(27 equiv), DMAP (0.6 equiv), dioxane, 23 °C, 1 h, 69% over three steps; (h) Pb(OAc)4 (2.0 equiv), benzene, 80 °C, 12 h; (i) TFA:MeOH:H2O (1:1:1), 23 °C,
1 h, 51% over two steps; (j) NaIO4 (1.1 equiv), nBu4NBr (1.5 mol %), CH2Cl2, 23 °C, 1 h, 81%.
2-(trimethylsilyl)ethyl (TMSE) group and generation of
methoxy compound 10.
The in situ-generated enol 21 was then immediately treated
withortho-quinone20; gratifyingly, desiredcycloaddition9
adducts 22a and 22b were obtained in 69% yield as a 1:1
mixture that could be chromatographically separated. How-
ever, 22a was actually present as a 2:1 mixture of insepara-
ble epimers, most likely containing an epimer at the 1β
nitrogen atom (1β-epi-22a); likewise, 22b was generated as
a 1:3 mixture of inseparable epimers, most likely containing
an epimer at the 1Rnitrogen atom (1r-epi-22b). Themixtures
22a:1β-epi-22a and 22b:1r-epi-22b were then deprotected
separately: 22a:1β-epi-22a was found to give a deprotection
product whose NMR spectroscopic properties matched
those reported for phellodonin (1a),1 and 22b:1r-epi-22b
gave sarcodonin ε (1b).2 This marks the completion of the
first synthesis of members of the sarcodonin natural product
family.10 Two epimeric sarcodonins 1β-epi-1a and 1r-epi-1b
were synthesized as well, which are quite possibly natural
products themselves.11 To the best of our knowledge, these
compounds represent the most highly oxidized diketopiper-
azine-derived molecules synthesized to date, and this was
achieved by a series of oxidative events on diketopiperazine 4.
The regioselectivity of the pyrazine-quinone formal [4 þ 2]-
cycloaddition merits additional discussion. As originally
observed in our model studies with simple pyrazines,4 the
ortho-quinone underwent reaction exclusively with the enol
double bond, giving rise to a benzodioxanone structure
Preparationofthe otherDielsꢀAlderpartner, the ortho-
quinone moiety, was achieved via a combination of our
previous studies,3 literature precedent7 and our recently
reported conditions8 for quinone arylation with boronic
acids (Scheme 2). To this end, 2,5-dichloro-1,4-benzoqui-
none (11) was first arylated using the reported conditions
for silver-mediated arylation of quinones,8 giving arylqui-
none 13. Chloride displacement, then selective bromina-
tion followed by a Suzuki cross-coupling furnished 17. The
complete terphenyl skeleton now in place, the methoxy
groups were replaced with hydroxyl groups, the central
quinone was reduced,7a and the resulting tetraol was fully
acetylated to give terphenyl 18. Finally, oxidative deprotec-
tion of the catechol7b and oxidation using previously reported
conditions7c gave the desired ortho-quinone 20.
With the two coupling partners in hand, the convergent
assembly of phellodonin began with an acidic deprotection
of the remaining TMSE group on pyrazine 10 (Scheme 3).
(7) (a) Ye, Y. Q.; Koshino, H.; Onose, J.-i.; Negishi, C.; Yoshikawa,
K.; Abe, N.; Takahashi, S. J. Org. Chem. 2009, 74, 4642–4645. (b)
Nicolaou, K. C.Tang, Y.; Wang, J. Angew. Chem., Int. Ed. 2009, 48, 3449–
3453. (c) Pieken, W. A.; Kozarich, J. W. J. Org. Chem. 1989, 54, 510–512.
(8) Fujiwara, Y.; Domingo, V.; Seiple, I. B.; Gianatassio, R.; Del Bel,
M.; Baran, P. S. J. Am. Chem. Soc. 2011, 133, 3292–3295.
(9) For examples of thermal ortho-quinone DielsꢀAlder reactions
before 1996, see the following review: (a) Nair, V.; Kumar, S. Synlett
1996, 1143–1147. For selected examples after 1996, see ref 7b as well as
(10) Natural phellodonin (1a) displays a negative optical rotation
and natural sarcodonin ε (1b) shows a positive optical rotation. It is of
note that the synthesized mixtures of 1a:1β-epi-1a and 1b:1r-epi-1b
display negative and positive optical rotations, respectively, thus match-
ing those of the natural samples. It is thus suggested that the correct
absolute configuration of these natural products has been generated
from L-isoleucine, however, this evidence is not conclusive because the
obtained products of the synthesis were mixtures.
ꢁ
the following: (b) Kaizer, J.; Speier, G.; Osz, E.; Giorgi, M.; Reglier, M.
Tetrahedron Lett. 2004, 45, 8011–8013. (c) Aoyagi, Y.; Takahashi, Y.;
Satake, Y.; Fukaya, H.; Takeya, K.; Aiyama, R.; Matsuzaki, T.;
Hashimoto, S.; Shiina, T.; Kurihara, T. Tetrahedron Lett. 2005,
46, 7885–7887. (d) Kuboki, A.; Yamamoto, T.; Taira, M.; Arishige,
T.; Ohira, S. Tetrahedron Lett. 2007, 48, 771–774. (e) Majetich, G.; Zou,
G. Org. Lett. 2008, 10, 81–83. (f) Nicolaou, K. C.; Wang, J.; Tang, Y.
Angew. Chem., Int. Ed. 2008, 47, 1432–1435. (g) Kuboki, A.; Maeda, C.;
Arishige, T.; Kuyama, K.; Hamabata, M.; Ohira, S. Tetrahedron Lett.
2008, 49, 4516–4518.
(11) Sarcodonin natural products that are epimeric at the nitrogen
ring junction are known, see refs 3b and 3d.
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Org. Lett., Vol. 15, No. 9, 2013

whose identity was confirmed by X-ray crystallography.
In the case of pyrazine N-oxide 21, however, the ortho-
quinone instead undergoes reaction with the nitrone CdN
double bond. It is unclear whether the reaction proceeds as
a concerted [4 þ 2] or whether alternative reaction path-
ways (such as an initial [3 þ 2] dipolar cycloaddition,
followed by subsequent rearrangement to the [4 þ 2]
product) are taking place. However, since epimeric side
products are obtained, it is likely that the [4 þ 2] union
occurs in stepwise fashion.
Scheme 3. Formal Hetero-DielsꢀAlder Reaction for the
Synthesis of Phellodonin (1a) and Sarcodonin ε (1b)a
The unusual and seemingly unstable N,N-dioxide-con-
taining benzodioxazine framework has prompted a de-
tailed analysis in structural revision,4 which has sub-
sequently been revisited and reanalyzed by X-ray
crystallography.2 A successful chemical synthesis now
supports the conclusions from the X-ray analysis,2 simul-
taneously confirming the elusive structure12 of the sarco-
donin family, as well as demonstrating the synthetic fea-
sibility and chemical stability of this family of natural
products. In summary, a convergent, biologically inspired
synthesis of phellodonin (1a) and sarcodonin ε (1b) has
been accomplished, involving a key formal hetero-Dielsꢀ
Alder reaction. Combining the strengths of X-ray crystal-
lography and chemical synthesis allows the unambiguous
determination of even highly heterosubstituted com-
pounds and verifies that this unprecedented framework
can be constructed in a laboratory setting.
Acknowledgment. We thank Dr. D.-H. Huang and Dr.
L. Pasternack for NMR spectroscopic assistance, Dr. G.
Siuzdak for assistance with mass spectrometry, and Dr. Y.
Ishihara for assistance in the preparation of this manu-
script (all at The Scripps Research Institute). The National
Science Foundation and Bristol-Myers Squibb funded
graduate fellowships (for D.W.L.). The Uehara Memorial
Foundation (to I.U.) and Daiichi Sankyo(toT.M.) funded
postdoctoral fellowships. Financial support was provided
by the National Institutes of Health (CA134785).
Supporting Information Available. Experimental pro-
cedures, copies of all spectral data, and full characteriza-
tion. This material is available free of charge via the
Internet at http://pubs.acs.org.
a Reagents and conditions: (a) TFA, CH2Cl2, 23 °C, 30 min, then 20,
CDCl3, 23 °C, 1 h, 69% (of which half consists of a mixture of
inseparable epimers 22a:1β-epi-22a and the other half is a mixture of
22b:1r-epi-22b); (b) H2 (1 atm), Pd-BaSO4 (10 mol %), MeOH, 23 °C,
30 min, 82% for 1a:1β-epi-1a, 84% for 1b:1r-epi-1b.
(12) Nicolaou, K. C.; Snyder, S. A. Angew. Chem., Int. Ed. 2005, 44,
1012–1044.
The authors declare no competing financial interest.
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