Novel trifluoroacetophenone derivatives as malonyl-CoA decarboxylase inhibitors

Article abstract of DOI:10.1016/j.bmcl.2006.09.023

A series of trifluoroacetophenone derivatives were prepared and evaluated as malonyl-CoA decarboxylase (MCD) inhibitors. Some of the 'reverse amide' analogs were found to be potent inhibitors of MCD enzyme activity. The trifluoroacetyl group may interact with the MCD active site as the hydrate in a similar fashion to the hexafluoroisopropanol analogs reported previously. Adding electron-withdrawing groups to the phenyl ring stabilizes the hydrated species and enhances this interaction.

Full text of DOI:10.1016/j.bmcl.2006.09.023

Bioorganic & Medicinal Chemistry Letters 17 (2007) 1127–1130
Novel trifluoroacetophenone derivatives as malonyl-CoA
decarboxylase inhibitors
David M. Wallace,*, Masayuki Haramura,à Jie-Fei Cheng,§ Thomas Arrhenius and
Alex M. Nadzan
Department of Chemistry, Chugai Pharma USA, LLC., 6275 Nancy Ridge Dr., San Diego, CA 92121, USA
Received 28 July 2006; revised 7 September 2006; accepted 8 September 2006
Available online 17 January 2007
Abstract—A series of trifluoroacetophenone derivatives were prepared and evaluated as malonyl-CoA decarboxylase (MCD) inhib-
itors. Some of the ‘reverse amide’ analogs were found to be potent inhibitors of MCD enzyme activity. The trifluoroacetyl group
may interact with the MCD active site as the hydrate in a similar fashion to the hexafluoroisopropanol analogs reported previously.
Adding electron-withdrawing groups to the phenyl ring stabilizes the hydrated species and enhances this interaction.
Ó 2006 Elsevier Ltd. All rights reserved.
The enzyme malonyl-CoA decarboxylase (MCD, EC
4.1.1.9; CoA, coenzyme A) catalyzes the conversion of
malonyl-CoA to acetyl-CoA, thereby regulating malo-
nyl-CoA levels in the cells. Malonyl-CoA is a key inter-
mediate for fatty acid synthesis and a key regulator for
fatty acid oxidation through carnitine palmitoyltransfer-
ase I (CPT-I). CPT-I is required for the transport of
long-chain acyl-CoA molecules from the cytosol to the
mitochondria where they are oxidized.1 Different iso-
form distributions of CPT-1 have the potential to medi-
ate its responsiveness to malonyl-CoA, in particular
during pathophysiological changes.2 As a metabolic fuel
sensor, malonyl-CoA also regulates nutrition partition-
ing,3 insulin secretion and sensitivity4,5, and food in-
take.6 MCD was first purified from uropygial glands
of goose and subsequently from a number of mammali-
ans, plants, and bacteria.7 Identification of patients with
MCD deficiency led to the cloning of a human MCD
gene that is highly homologous to the goose and rat
genes.8 The highest MCD mRNA expression levels in
rats are found in muscle and heart tissues, followed by
liver, kidney, and pancreas, with detectable amounts
found in many other tissues including brain.9 Recent
studies indicate that MCD exists in cytosolic, mitochon-
drial, and peroxisomal compartments.8b,10 Targeting
malonyl-CoA regulation through MCD inhibition is
an attractive approach to certain diseases involving dis-
orders of fatty acid metabolism such as diabetes, obesi-
ty, and myocardial ischemia.
We have recently described the first generation of small
molecule MCD inhibitors containing a hexafluoroiso-
propanol moiety.11 As expected, those MCD inhibitors
significantly increased malonyl-CoA levels and de-
creased the fatty acid oxidation rates in ex vivo experi-
ments with isolated working rat hearts. As a result, the
glucose oxidation rates were accelerated in these work-
ing rat hearts, consistent with ‘glucose-fatty acid cycle’
or ‘Randle cycle’ hypothesis.12 Previous SAR studies
on HTS hit 1 led to the identification of several potent
MCD inhibitors (2–4, Fig. 1).11a,b,c In the process of
investigating the SAR of the hexafluoroisopropanol
pharmacophore, we discovered that the trifluoroacetyl
function could serve as a potential bioisostere. Herein
we described the design, synthesis, and SAR of a series
of trifluoroacetophenone MCD inhibitors 5.
Keywords: Trifluoroacetyl; Trifluoroacetophenone; Malonyl-CoA;
Acetyl-CoA; Malonyl-CoA decarboxylase; MCD; Fatty acid oxida-
tion; Glucose oxidation.
*
Corresponding author. Tel.: +1 858 204 5412; fax: +1 858 450
9834; e-mail: davidmw@san.rr.com
Present address: Allylix, Inc. 9710 Scranton Road, Suite 170, San
Diego, CA 92121, USA.
à
Present address: Fuji Gotemba Research Laboratories, Chugai
Pharmaceutical Co., Ltd, 1-135, Komakado, Gotemba, Shizuoka
412-8513, Japan.
§
Synthesis of aniline-based trifluoroacetophenone MCD
inhibitors is illustrated in Scheme 1. According to the
Present address: Tanabe Research Laboratories USA, Inc. 4540
Towne Centre Court, San Diego, CA 92121, USA.
0960-894X/$ - see front matter Ó 2006 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2006.09.023

1128
D. M. Wallace et al. / Bioorg. Med. Chem. Lett. 17 (2007) 1127–1130
Figure 1. Representative MCD inhibitors.
Scheme 1. Reagents and conditions: (a) i—CF3TMS, DCM, cat. TBAF, À78 °C to rt, ii—aq HCl, acetone, 92%; (b) Fe/HOAc, EtOH, reflux, 79%;
(c) R2COCl, DCM, Et3N, rt, 81–96%; (d) MeI, NaH, THF; (e) i—NaBH4, MeOH, ii—R1X, NaH, THF, rt, 45–65%; (f) Dess–Martin periodinane in
DCM, 83%; (g) MeMgBr, THF, À30 °C, 67%.
literature procedure,13 methyl 4-nitrobenzoate 6 was
treated with (trifluoromethyl)-trimethylsilane in the
presence of catalytic TBAF to afford the hydrated form
of 2,2,2-trifluoro-1-(4-nitrophenyl)ethanone 7. Reduc-
tion of the nitro group with iron provided the desired
aniline compound 8. Reaction of 8 with acyl chlorides
gave the amide derivatives 9. Attempts to alkylate the
amide nitrogen at this step produced primarily the cor-
responding methyl ester 10. This transformation is
potentially due to methylation of the hydrate, followed
by the elimination of the CF3 function. Therefore, ke-
tone 9 was reduced with NaBH4 in MeOH, followed by
alkylation of the amide with an alkyl bromide in the
presence of NaH to give predominately the desired tri-
substituted amide 11. O-Alkylated products also were
obtained in 10–30% yield, depending on the alkyl ha-
lide used. Amide 11 was then oxidized using Dess–
Martin periodinane to afford the trifluoroacetyl deriva-
tive 12. As part of our SAR study of the hexafluoroiso-
propanol compound series, ketones 12 were treated
with MeMgBr at À30 °C to produce trifluoroisopropa-
nols 13.
The synthesis of benzoic acid-based trifluoroacetyl
MCD inhibitors 15 is illustrated in Scheme 2. To distin-
guish these amides from the ones mentioned above, we
designated these analogs as ‘reverse amides’. The reverse
amides were prepared efficiently by conventional peptide
coupling methods in a 96-well plate format from com-
mercially available 4-(trifluoroacetyl)benzoic acid 14.
MCD inhibitors synthesized above were evaluated for
their ability to inhibit the soluble form of recombinant
Scheme 2. Reagents and conditions: (a) R1R2NH, EDC, DMAP,
DCM.

D. M. Wallace et al. / Bioorg. Med. Chem. Lett. 17 (2007) 1127–1130
1129
MBP fusion protein (MBP-hMCD) as described previ-
ously.11b,14 The IC50 values for some selected com-
pounds are tabulated in Tables 1 and 2.
propanol series. Both compounds were found to be
significantly less active than the corresponding hexaflu-
oroisopropanol compound
1 against MBP-hMCD
(IC50: 1: 0.93 lM vs. 11: 32.4 lM; 13: 19.8 lM). The
weak activity of mono trifluoromethyl substituted
compounds 11 or 13 indicates how sensitive the
MCD active site is to the acidity of the hydroxyl
group.11a,11b,11c The trifluoroacetophenone analogs 12
were found to be the most active of the modifications
made to the hexafluoroisopropanol moiety, but they
were still weaker than the corresponding hexafluoroiso-
propanol analogs (IC50: 1: 0.93 lM vs. 12d: 4.51 lM).
The fact that trifluoromethyl ketone compounds showed
higher activity than the corresponding alcohol com-
pound may be due to the presence of the hydrated form
(ketal), which mimics the acidic hydroxyl moiety of the
hexafluoroisopropanol group. It is therefore reasonable
to hypothesize that improving the stability of the
hydrate could increase the activity of the trifluoroace-
tophenone derivatives.
Compounds 11 and 13 (R1 = Me; R2 = –CH2OPh) were
evaluated as part of a SAR study on the hexafluoroiso-
Table 1. Amide MCD inhibitors
a
Compound
R1
R2
IC50 (lM)
12a
12b
12c
12d
12e
12f
H
i-Pr
4-CNPh
5.45
4.9
H
H
–CH2OPh
–CH2OPh
1-Morpholinyl
–N(i-Bu)2
1.5
4.5
Me
H
17.2
2.8
Accordingly, the 4-(trifluoroacetyl)benzamide analogs
or reverse amide analogs were found to have increased
potency against MBP-hMCD (Table 2) when compared
to the ‘normal amide’ analogs. 1H NMR of these reverse
n-Pr
a Data are reported as means of n P 3 determinations. SD was gen-
erally 20% of the average.
Table 2. Reverse amide MCD inhibitors
R1
R2
a
IC50 (nM)
Compound
15a
15b
15c
15d
15e
15f
i-Pr
n-Pr
Ph
n-Pr
1731
153
n-Pr
i-Bu
Cyclopropylmethyl
3-NitrophenylCO2CH2CH2–
i-Bu
68
80
i-Bu
H
73
i-Bu
i-Pr
1531
3361
2034
679
15g
15h
15i
H
H
2-Furanylmethyl
n-Hexyl
H
15j
H
–CH(CH3)(CH2)4CH3
–CH(CH3)CH2CH(CH3)2
–CH2CH2C(CH3)3
2-Methylcyclohexyl
Cyclohexylmethyl
2-MeOphenyl
3-CF3benzyl
115
242
15k
15l
H
H
2753
304
15m
15n
15o
15p
15q
15r
15s
15t
H
H
2298
5011
507
H
H
H
3,5-(CF3)2benzyl
–CH2(CH2)2CH2Ph
–CH2CH2CH2Ph
–CH2CH2Ph
–CH2CH2Ph
–CH2CH2CN
–CH2CH2CN
–CH2C(CH3)2OH
–CH2CH2OMe
Et
654
H
1739
1351
566
H
H
Me
15u
15v
15w
15x
15y
15z
15aa
953
155
Ph
Et
214
399
Et
Et
1105
1619
3280
Et
–CH2CH2CH2CH2–
a Data are reported as means of n P 3 determinations. SD was generally 20% of the average.

1130
D. M. Wallace et al. / Bioorg. Med. Chem. Lett. 17 (2007) 1127–1130
Chohnan, S.; Lane, M. D. Proc. Natl. Acad. Sci. U.S.A.
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amide compounds showed the hydrated form is the pri-
mary form in a CDCl3 solution, while the normal amide
showed very little of the hydrated species. This improved
activity is most likely due to the electron-withdrawing
effects of the reverse amide affecting the formation of
the hydrate. Two of the three most active compounds
15c–e were found to be substituted on the nitrogen with
two aliphatic substituents, one of which is a branched
aliphatic chain. The third active compound 15d also
possesses a branched aliphatic chain along with an ali-
phatic alcohol as its 3-nitrophenylcarboxylic ester. Sim-
ilar activity trends were observed in the reverse amide
hexafluoroisopropanol series (data not shown).11b In
fact, when 15e or 15u is compared with its correspond-
ing hexafluoroisopropanol analog, the trifluoroacetoph-
enone analogs are of similar or enhanced potency (IC50:
15e: 73 nM vs. 70 nM; 15u: 953 nM vs. 1990 nM). A
notable exception was those compounds substituted
with a single aliphatic chain containing an a-methyl
(e.g., 15j, IC50: 115 nM).
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In summary, a series of trifluoroacetophenone MCD
inhibitors were designed to replace the hexafluoroiso-
propanol moiety found in the original HTS hit. Some
of the reverse amide analogs were found to be potent
inhibitors of MCD enzyme activity in the in vitro
MCD enzyme assay. The trifluoroacetyl group may
interact with the MCD active site as the hydrate in a
similar fashion to the hexafluoroisopropanol analogs
reported previously. Adding electron-withdrawing
groups to the phenyl ring, thereby stabilizing the hydrat-
ed species, can enhance this interaction.
Acknowledgments
We thank Dr. Peter Simms, Ms. Cynthia Jeffries, and
Aixia Sun for providing analytical data (HPLC and
MS).
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