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P. Jones et al. / Bioorg. Med. Chem. Lett. 18 (2008) 3456–3461
lation with IC50 = 12 lM, whereas only 40% inhibition
of histone H3 deacetylation was seen at 50 lM, thereby
demonstrating that these compounds are selective class
II HDACis in cells.
Replacement with a weaker zinc binding group, carbox-
ylic acid 7i abolished activity on all HDAC isoforms. In
a similar manner, no inhibition of any of the HDAC iso-
forms was seen with the methyl ketone 10d. To explore the
importance of the trifluoromethyl group, the correspond-
ing difluoromethyl 15h and pentafluoroethyl 11f deriva-
tives were synthesized. The former by lithiation of the
thiophene 13h with LDA, followed by quenching with
ethyl difluoroacetate, whereas the latter was obtained by
addition of the lithium pentafluoroethyl onto the Weinreb
amide 9f. Both compounds showed substantial losses of
activity on all HDAC isoforms. In particular, difluoroke-
tone 15h while potently inhibiting HDAC4GOF lost
more than 10-fold activity on HDAC4WT and therefore
was not pursued further. Finally, the boronic acid 16h,
methyl sulfone 17h, and phosphonic acid 14h derivatives
were all inactive.
Having shown that potent class II HDACis could be
developed, a more in depth understanding of the deter-
minants of activity was undertaken, focusing on three
regions of the inhibitors: the trifluoromethyl ketone zinc
binding group, the central thiophene ring and the amide
moiety.
The zinc binding group was explored as outlined in
Scheme 1 and Table 1. Reduction of the trifluoromethyl
ketone to alcohol 4c with NaBH4 resulted in a complete
loss of activity. As did protection of the ketone as ketal
5h, the formation of which required cyclization with chlo-
roethanol under basic conditions to form the dioxolane.
In contrast, the corresponding hydroxamic acid 8d, read-
ily prepared from thiophene-2,5-dicarboxylic acid (6)
proved to be a potent but unselective HDACi, showing
nanomolar activity against both class I and II HDACs.
To enable SAR studies to look for alternatives to the 5-
carboxamide group, chemistry had to be established to
introduce the trifluoroacetyl group onto the thiophene
as the ultimate synthetic step. Therefore simple func-
tional group transformations were conducted on the
5-position of the thiophene and then the 2-position
was deprotonated with LDA at ꢀ78 °C and the lithio
derivative quenched with 2,2,2-trifluoro-N-methoxy-N-
methylacetamide (Scheme 2). In this manner amines
19c + d, ether 21f and sulfonamides 25c + g were inves-
tigated. The 4-position of the thiophene was also
explored by sulfonylation with chlorosulfonic acid and
PCl5, followed by preparation of the sulfonamide 23c.
These alternative capping groups were all tolerated to
some extent on the class II HDACs (Table 2), although
a loss in HDAC4 activity was seen with all derivatives
compared to the 5-carboxamides. For instance the ether
21f resulted in a more than 30-fold loss in activity on
HDAC4, although maintained HDAC6 activity. While
whereas tertiary amine 19c lost 2- to 6-fold activity on
HDAC4, the secondary amines 19d lost more than 20-
fold activity. The isomeric sulfonamides 23c and 25c
demonstrated the importance of the substitution pattern
on the thiophene, as whilst the 5-substituted isomer 25c
remained a hundred nanomolar HDAC4 inhibitor, the
region isomer 23c lost almost all deacetylase activity.
F
Me
N
F
F
NaBH4
3c
1
S
OH
O
O
4c
F
F
F
1) K2CO3
ClCH2CH2OH
N
S
O
O
2) LiOH
3) EDC, HOBT
RR'NH
5h
1) MeOH, HBTU
2) NH2OH, NaOMe
R
N
R
N
H
HO
HO
N
HO
R'
R'
R'
S
7
S
8
O
O
O
O
O
1) SOCl2
2) Morpholine, Et3N
HBTU,
RNH2
3) MeMgBr, 0 oC to RT
R
N
OH
Me
F3CF2C
F
S
S
O
O
O
O
O
6
10
1) HBTU, RNH2
2) HBTU, NH(Me)OMe
CF3CF2I
MeLi.LiBr
-78 to 0 o
R
N
Me
N
NHR
C
MeO
R'
S
S
Having established that the trifluoroacetyl group could
be introduced as the ultimate synthetic step, this meth-
odology was applied in the investigation of thiophene
replacement (Scheme 3). In this manner, the 3-trifluoro-
acetylthiophene derivative 27c was prepared from the
3-bromothiophene-5-carboxylic acid (26) by Br–Li
exchange and quenching as previously. Similar chemis-
try, but using Mg–Br exchange, was used for the pyri-
dine analogue 37. The corresponding thiazoles 29c + g
could be prepared by direct lithiation of the thiazole
with n-BuLi and quenching. Preparation of the corre-
sponding pyrrole derivative 31h necessitated sequential
Br–Li exchanges on N-Boc 2,5-dibromopyrrole (30),
firstly to allow introduction of the carboxylate group,
and secondly the trifluoroacetyl group. In contrast, the
analogous phenyl derivatives 34g and 35g were more
straightforward, being readily prepared readily from
carboxylic acids 32 and 33.
O
O
9
11
OH
1) LDA, -78 o
C
S
O
2) CF2HCO2Et
12
-78 o
C
N
HATU
F
RR'NH
S
O
O
O
15h
1) LDA, -78 o
C
N
2) B(OMe)3, -78 o
3) H3O+
C
OH
B
S
N
N
O
HO
13h
S
1) LDA, -78 o
2) ClPO(OEt)2
-78 oC to RT
3) TMSBr
C
O
1) LDA, -78 o
2) ClSO2Me,
C
16h
-78oC to RT
HO
HO
N
S
S
P
S
14h
O
O
O
O
O
17h
Scheme 1. SAR exploration of the zinc-binding group.