First synthesis of (S)-(+)-hymenoic acid, a DNA polymerase λ inhibitor isolated from Hymenochaetaceae sp

Article abstract of DOI:10.1080/09168451.2017.1406302

Hymenoic acid, isolated from cultures of the fungus, Hymenochaetaceae sp., is a specific inhibitor of DNA polymerase λ. The first synthesis of (S)-(+)-hymenoic acid was achieved by starting from trans-1,4-cyclohexanedimethanol and methyl (R)-(-)-3-hydroxyisobutyrate, and Julia-Kocienski olefination was employed as the key step.

Full text of DOI:10.1080/09168451.2017.1406302

Bioscience, Biotechnology, and Biochemistry
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First synthesis of (S)-(+)-hymenoic acid, a
DNA polymerase λ inhibitor isolated from
Hymenochaetaceae sp
Kensuke Takahashi, Miki Matsui, Masaki Kuse & Hirosato Takikawa
To cite this article: Kensuke Takahashi, Miki Matsui, Masaki Kuse & Hirosato Takikawa
(2018) First synthesis of (S)-(+)-hymenoic acid, a DNA polymerase λ inhibitor isolated from
Hymenochaetaceae sp, Bioscience, Biotechnology, and Biochemistry, 82:1, 42-45, DOI:
10.1080/09168451.2017.1406302
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Bioscience, Biotechnology, and Biochemistry, 2018
Vol. 82, no. 1, 42–45
https://doi.org/10.1080/09168451.2017.1406302
First synthesis of (S)-(+)-hymenoic acid, a DNA polymerase λ inhibitor isolated
from Hymenochaetaceae sp
Kensuke Takahashi, Miki Matsui, Masaki Kuse and Hirosato Takikawa
department of agrobioscience, graduate school of agricultural science, Kobe University, Kobe, Japan
ABSTRACT
ARTICLE HISTORY
received 6 november 2017
accepted 11 november 2017
Hymenoic acid, isolated from cultures of the fungus, Hymenochaetaceae sp., is a specific inhibitor
of DNA polymerase λ. The first synthesis of (S)-(+)-hymenoic acid was achieved by starting from
trans-1,4-cyclohexanedimethanol and methyl (R)-(−)-3-hydroxyisobutyrate, and Julia–Kocienski
olefination was employed as the key step.
KEYWORDS
synthesis; hymenoic
acid; sesquiterpene; dna
polymerase; Julia–Kocienski
olefination
In 2007, Nishida et al. reported the isolation and struc-
ture elucidation of hymenoic acid (1) from a fungus,
Hymenochaetaceae sp [1]. is fungus had been iso-
lated from a coral collected from Hachijo Island, Japan.
Hymenoic acid (1) is a monocyclic sesquiterpene
dicarboxylic acid. Its absolute configuration at C-5′ was
determined to be S, as shown in Figure 1. Although the
well-known sesquiterpene juvabione (2) and its relatives
such as 3 are known to exist [2], only two structurally
analogous marine natural products, namely phorbacins
H and I (4 and 5), have been reported to date [3]. Nishida
et al. also reported that 1 could potently inhibit only the
activity of human and plant DNA polymerase (pol) λ [1].
us, 1 might be useful not only as a specific inhibitor
against pol λ, but also as a lead compound for design of
new antitumor agents.
trans-1,4-cyclohexanedimethanol (C) and methyl (R)-
(−)-3-hydroxyisobutyrate (D), respectively.
Scheme 2 illustrates the synthesis of 1. e starting
material, trans-1,4-cyclohexanedimethanol 6 (= C), was
converted to the known aldehyde 7 (53% in two steps)
[10]. Treatment of 7 with MeMgI afforded 8 (89%). e
alcohol 8 was converted into the corresponding sulfide,
which was immediately oxidized with m-CPBA to give
the key 1-phenyl-1H-tetrazol-5-yl (PT) sulfone 9 (=
A; 56% in two steps). Despite considerable effort, the
corresponding benzothiazole-2-yl (BT) sulfone could
not be prepared in an acceptable yield. By starting from
methyl (R)-(−)-3-hydroxyisobutyrate 10 (=D), the
known aldehyde 12 (= B) was prepared. Although sev-
eral methods of preparation have been reported, [11−13]
we prepared the ester 11 (48% in four steps) according
to Chandrasekhar’s procedure [14] and reduced 11 with
DIBAL to give 12 (quant.).
With the two intermediates (9 and 12) in hand, J–K
olefination was attempted. As stated in review articles,
[8,9] the formation of a trisubstituted olefin via J–K
olefination is difficult as there are only a limited num-
ber of (E)-selective options available for the coupling
between a secondary sulfone and an aldehyde [15−17].
However, because the successful formation of a trisub-
stituted olefin is usually performed using an alkaline
metal hexamethyldisilazide (HMDS) in an ethereal
solvent, the coupling between 9 and 12 with three alka-
line HMDSs in THF is examined. As a result of this
strategy, the desired olefin 13 was obtained (55% yield
based on 11; E:Z = ca. 4:1) only when LiHMDS was
used as a base. e use of NaHMDS and KHMDS gave
Inspired by its interesting biological profiles, we initi-
ated studies toward the synthesis of 1 as a continuation
of our synthetic studies on pol inhibitors [4,5]. Here, we
report the first synthesis of (S)-(+)-1.
Results and discussion
e synthetic plan for 1 is shown in Scheme 1. e basic
skeleton of the target compound 1 would be synthesized
using Julia–Kocienski (J–K) olefination [6−9] between a
sulfone A and an aldehyde B. Although J–K olefination
between A′ and B′ was also possible, this method was
not adopted because early model studies on J–K olefi-
nation showed that the (E)-selectivity in the coupling
between a secondary sulfone and an aldehyde was much
better than that between a ketone and a primary sul-
fone. Intermediates A and B would be preparable from
CONTACT hirosato takikawa
takikawa@kobe-u.ac.jp
© 2017 Japan society for Bioscience, Biotechnology, and agrochemistry

BIOSCIENCE, BIOTECHNOLOGY, AND BIOCHEMISTRY
43
Figure 1. structures of hymenoic acid (1) and the related natural products.
afford (E)-14. Finally, (E)-14 was stepwisely oxidized in
the conventional manner to give (S)-(+)-1 (29%). e
various spectral data of synthetic (S)-(+)-1 were in good
agreement with those of the naturally ocurring 1.
In conclusion, the first synthesis of (S)-(+)-hymenoic
acid (1) was accomplished by employing Juila–Kociensky
olefination as the key step. is synthetic rout is straight-
forward and enables the synthesis of a wide range of
hymenoic acid analogs. To clarify the structure-activity
relationship, the synthesis of hymenoic acid analogs is
an ongoing focus of this research.
Experimental
General procedures
1H-NMR spectra were recorded at 300 MHz with a Jeol
JNM-AL300 spectrometer. TMS or the residual solvent
peak in CDCl3 (at δH = 7.26) or CD3OD (at δH = 3.30),
was used as the internal standard. 13C-NMR spectra were
recorded at 75 MHz with the Jeol JNM-AL300 spectrom-
eter, the peak for CDCl3 (at δC = 77.0) or CD3OD (at
δC = 49.0) being used as the internal standard. Optical
rotations were taken with a HORIBA SEPA-300 polarime-
ter. Mass spectra were measured with a Jeol JMS-SX102A
spectrometer. Anhydrous THF (Cat. No. 41001–84) was
purchased from Kanto Chemical Co., Inc., and other
anhydrous solvents were dried over MS 3A/4A.
Scheme 1. synthetic plan for 1.
no desired adduct. Furthermore, it is important to note
that this base dependency is also observed in early model
studies. Upon treatment with TBAF, two TBS groups of
13 were removed (92%), and the resulting diol 14 was
carefully separated by SiO2 column chromatography to
Scheme 2. synthesis of (S)-(+)-hymenoic acid (1).

44
K. TAKAHASHI ET AL.
1-[trans-4′-(t-Butyldimethylsilyloxymethyl)-
cyclohexyl]ethanol (8)
(5′S)-trans-1-(t-Butyldimethylsilyloxymethyl)-4-(6′-
t-butyldimethylsilyloxy-1′,5′-dimethyl-1′-hexenyl)-
cyclohexane (13)
To an ice-cooled solution of MeMgI (ca. 1.0 M in Et2O;
35 mL, 35 mmol), a solution of 7 (1.84 g, 7.19 mmol) in
dry Et2O (15 mL) was added dropwise. Afer removal
of an ice-bath, the stirring was continued for 1.5 h. e
reaction mixture was quenched with sat. NH4Cl aq. and
extracted with EtOAc. e organic layer was washed with
water and brine, dried (MgSO4), and concentrated under
reduced pressure. e residue was chromatographed
on SiO2 to give 8 (1.74 g, 89%). NMR δH (CDCl3): 0.03
(6H, s, Si-Me), 0.89 (9H, s, t-Bu), 0.88–1.60 (6H, m),
1.17 (3H, d, J = 6.3 Hz, CH-Me), 1.65–1.94 (4H, m),
3.40 (2H, d, J = 6.3 Hz, O-CH2), 3.56 (1H, m, O-CH).
NMR δC (CDCl3): −5.4, 18.4, 20.5, 26.0, 27.7, 28.1, 29.2,
29.3, 40.5, 45.3, 68.7, 72.2. HREIMS m/z [M]+: calcd. for
C15H32O2Si, 272.2172; found, 272.2198.
To a solution of 9 (140 mg, 0.301 mmol) in dry THF
(2 mL), LiHMDS (1.09 M in THF; 0.45 mL, 0.49 mmol)
was added dropwise at −78 °C under Ar. Afer stirring
for 30 min, a solution of 12 (88 mg) in THF (1 mL) was
added, and the mixture was stirred overnight with grad-
ual warming to room temperature. It was then quenched
with sat. NH4Cl aq. and extracted with Et2O. e organic
layer was washed with water and brine, dried (MgSO4),
and concentrated under reduced pressure. e residue
was chromatographed on SiO2 to give a mixture of
(E)- and (Z)-13 (77 mg, 55% based on 11 in two steps,
E:Z = ca. 4:1). [α]D21 = −0.58 (c 1.04, CHCl3). NMR δH
(CDCl3): 0.03, 0.04 (12H, each s, Si-Me), 0.84–0.90
(12H, m), 0.90–2.40 (15H, m), 1.56 (3H, br s, 1′-Me),
3.32–3.48 (4H, m, O-CH2), 5.05 (1/5H, t, J = 6.9 Hz,
Z-2′-H), 5.11 (4/5H, t, J = 6.9 Hz, E-2′-H). NMR δC
(CDCl3): −5.34, −5.32, 14.3, 16.71, 16.73, 18.36, 18.40,
19.6, 24.7, 25.3, 25.97, 26.00, 29.7, 29.8, 30.4, 31.3, 33.4,
33.8, 35.4, 35.5, 39.8, 40.3, 40.4, 47.4, 68.3, 68.4, 68.87,
68.90, 122.9, 124.7, 139.7, 139.9. HREIMS m/z [M]+:
calcd. for C27H56O2Si2, 468.3819; found, 468.3818.
5-{1-[trans-4′-(t-Butyldimethylsilyloxymethyl)-
cyclohexyl]ethanesulfonyl}-1-phenyl-1H-tetrazole
(9)
To an ice-cooled solution of 8 (270 mg, 0.993 mmol)
in dry THF (10 mL), 5-mercapto-1-phenyl-1H-tetra-
zole (0.53 g, 3.0 mmol), Ph3P (0.79 g, 3.0 mmol) and
DEAD (2.2 M in toluene; 1.4 ml, 3.1 mmol) were added
successively under Ar. Afer stirring overnight at room
temperature, the reaction mixture was diluted with
water and extracted with EtOAc. e organic layer was
washed with brine, dried (MgSO4), and concentrated
under reduced pressure to give the residue (0.36 g). To
a solution of this residue in CH2Cl2 (10 mL), m-CPBA
(75%, 0.58 g, 2.5 mmol) was added at 0 °C. Afer stirring
overnight at room temperature, the reaction mixture
was diluted with sat. NaHCO3 aq. and extracted with
CH2Cl2. e organic layer was washed with 10% Na2S2O3
aq., sat. NaHCO3 aq., and brine, dried (MgSO4), and
concentrated under reduced pressure. e residue was
chromatographed on SiO2 to give 9 (257 mg, 56% in
two steps). NMR δH (CDCl3): 0.03 (6H, s, Si-Me), 0.89
(9H, s, t-Bu), 0.88–1.60 (6H, m), 1.45 (3H, d, J = 7.2 Hz,
CH-Me), 1.65–1.98 (4H, m), 2.27 (1H, m), 3.38 (2H, d,
J = 6.3 Hz, O-CH2), 3.98 (1H, dq, J = 2.4, 7.2 Hz, SO2-
CH), 7.53–7.69 (5H, m, Ph). NMR δC (CDCl3): −5.4, 9.5,
18.4, 25.9, 26.9, 28.8, 29.5, 30.8, 36.4, 39.9, 65.2, 68.3,
125.4, 129.6, 131.4, 133.3, 153.3. HREIMS m/z [M]+:
calcd. for C22H36N4O3SSi, 464.2277; found, 464.2273.
(2S,5E)-6-[trans-4-(Hydroxymethyl)cyclohexyl]-2-
methylhept-5-en-1-ol (14)
To a solution of 13 (93 mg, 0.20 mmol) in THF (3 mL),
TBAF (1.0 M in THF; 0.6 mL, 0.6 mmol) was added.
Afer stirring for 2 h at room temperature, the reaction
mixture was diluted with sat. NH4Cl aq. and extracted
with EtOAc. e organic layer was washed with brine,
dried (MgSO4), and concentrated under reduced pres-
sure. e residue was chromatographed on SiO2 to give
a mixture of (E)- and (Z)-14 (44 mg, 92%). Further chro-
matographic purification of this mixture was carefully
23
performed to give the pure (E)-14 (24 mg, 55%). [α]D
= −5.8 (c 0.33, CHCl3). NMR δH (CDCl3): 0.93 (3H, d,
J = 6.6 Hz, 2-Me), 0.96–1.06 (2H, m), 1.10–1.30 (2H,
m), 1.39–1.58 (2H, m), 1.60 (3H, s, 6-Me), 1.75–2.15
(8H, m), 3.43 (1H, dd, J = 10.2, 6.3 Hz), 3.46 (2H, d,
J = 6.0 Hz), 3.51 (1H, dd, J = 10.2, 5.8 Hz), 5.12 (1H,
t, J = 6.9 Hz, 5-H). NMR δC (CDCl3): 14.4, 16.5, 25.1,
29.6, 31.1, 33.2, 35.4, 40.3, 47.2, 68.3, 68.7, 122.6, 140.0.
HREIMS m/z [M]+: calcd. for C15H28O2, 240.2089;
found, 240. 2097.
(S)-5-(t-Butyldimethylsilyloxy)-4-methylpentanal
(12)
(S)-(+)-Hymenoic acid (1)
To a solution of 14 (12.3 mg, 51.2 μmol) in DMSO
(0.2 mL), IBX (57.8 mg, 0.206 mmol) in DMSO (0.7 mL)
was added. Afer stirring at room temperature for
4 h, the reaction mixture was diluted with water and
extracted with EtOAc. e organic layer was washed
with brine, dried (MgSO4), and concentrated under
reduced pressure to give the crude products, which was
immediately dissolved into t-BuOH (0.2 ml) and water
(0.2 mL). To this solution were added 2-methyl-2-butene
To a solution of 11 (78 mg, 30 mmol) in toluene (2 mL),
DIBAL (1.0 M in toluene; 0.33 mL, 33 mmol) was slowly
added at −78 °C under Ar. Afer stirring for 2 h at
−78 °C, the reaction mixture was quenched with MeOH
and then diluted with hexane. e resulting mixture was
filtered through Celite, and the filtrate was concentrated
under reduced pressure to give 12 (88 mg, quant.). is
was used for the next step immediately.

BIOSCIENCE, BIOTECHNOLOGY, AND BIOCHEMISTRY
45
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(0.55 mL, 5.1 mmol), NaH2PO4 (30.5 mg, 0.196 mmol),
NaOCl2 (26.4 mg, 0.292 mmol). Afer stirring for 3.5 h
at room temperature, the reaction mixture was diluted
with sat. NH4Cl aq. and extracted with CH2Cl2. e
organic layer was washed brine, dried (MgSO4), and
concentrated under reduced pressure. e residue was
chromatographed on SiO2 to give (S)-(+)-1 (4.0 mg,
25
29% in two steps). [α]D = + 7.9 (c 0.080, CH3OH).
It should be noted that the absolute value of specific
rotation of the synthesized 1 has fluctuated considerably
due to unknown reason. NMR δH (CD3OD): 1.13 (3H,
d, J = 6.9 Hz), 1.21–1.34 (2H, m), 1.37–1.49 (3H, m),
1.58 (3H, s), 1.62–1.77 (3H, m), 1.84 (1H, tt, J = 11.7,
3.0 Hz), 1.99–2.06 (4H, m), 2.21 (1H, tt, J = 12.0, 3.6 Hz),
2.33–2.42 (1H, m), 5.15 (1H, t, J = 6.9 Hz). NMR δC
(CD3OD): 14.4, 17.7, 26.5, 30.5, 32.1, 35.0, 40.3, 44.4,
47.9, 123.3, 141.5, 180.1, 180.8. HREIMS m/z [M]+:
calcd. for C15H24O4, 268.1675; found, 268.1682.
Author contribution
H.T. designed the synthetic route and wrote the manu-
script. K.T. and M.M. conducted the synthetic experi-
ments with the aid of M.K. M.K. specially contributed
to analytical works.
[10] Fotsop DF, Roussi F, Leverrier A, et al. Biomimetic total
synthesis of meiogynin A, an inhibitor of Bcl-xL and
Bak interaction. J Org Chem. 2010;75:7412–7415.
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relationship of α hormones, the mating factors of
phytopathogen Phytophthora. Bioorg Med Chem.
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Acknowledgments
We thank Prof. Koji Kuramochi (Tokyo University of
Science) for his helpful discussion. We also thank Mr. Kazuto
Imaizumi (Kobe University) for his contribution in the early
phase of this work.
[13] Williams BD, Smith AB III. Total synthesis of
( )-18-epi-latrunculol A. Org Lett. 2013;15:4584–4587.
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of epothilone A: asymmetric synthesis of C(1)-C(6)
and C(7)-C(15) fragments. Tetrahedron: Asymmetry.
2002;13:261–268.
Disclosure statement
No potential conflict of interest was reported by the authors.
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