Fluoroolefins as amide bond mimics in dipeptidyl peptidase IV inhibitors

Article abstract of DOI:10.1016/j.bmcl.2008.02.050

The synthesis, selectivity, rat pharmacokinetic profile, and drug metabolism profiles of a series of potent fluoroolefin-derived DPP-4 inhibitors (4) are reported. A radiolabeled fluoroolefin 33 was shown to possess a high propensity to form reactive metabolites, thus revealing a potential liability for this class of DPP-4 inhibitors.

Full text of DOI:10.1016/j.bmcl.2008.02.050

Available online at www.sciencedirect.com
Bioorganic & Medicinal Chemistry Letters 18 (2008) 2409–2413
Fluoroolefins as amide bond mimics in dipeptidyl peptidase
IV inhibitors
Scott D. Edmondson,a,* Lan Wei,a Jinyou Xu,a Jackie Shang,b Shiyao Xu,b Jianmei Pang,b
Ashok Chaudhary,c Dennis C. Dean,c Huaibing He,a Barbara Leiting,d
Kathryn A. Lyons,a Reshma A. Patel,d Sangita B. Patel,e Giovanna Scapin,e
Joseph K. Wu,d Maria G. Beconi,f Nancy A. Thornberryd and Ann E. Webera
aDepartment of Medicinal Chemistry, Merck & Co. Inc., PO Box 2000, Rahway, NJ 07065, USA
bPreclinical Drug Metabolism and Pharmacokinetics, Merck & Co. Inc., PO Box 2000, Rahway, NJ 07065, USA
cDMPK Global Technologies, Merck & Co. Inc., PO Box 2000, Rahway, NJ 07065, USA
dDepartment of Metabolic Disorders, Merck & Co. Inc., PO Box 2000, Rahway, NJ 07065, USA
eGlobal Structural Biology, Merck & Co. Inc., PO Box 2000, Rahway, NJ 07065, USA
fDepartment of Drug Metabolism, Abbott Laboratories, 100 Abbott Park Road, Abbot Park, IL 60045, USA
Received 30 January 2008; revised 18 February 2008; accepted 21 February 2008
Available online 26 February 2008
Abstract—The synthesis, selectivity, rat pharmacokinetic profile, and drug metabolism profiles of a series of potent fluoroolefin-
derived DPP-4 inhibitors (4) are reported. A radiolabeled fluoroolefin 33 was shown to possess a high propensity to form reactive
metabolites, thus revealing a potential liability for this class of DPP-4 inhibitors.
Ó 2008 Elsevier Ltd. All rights reserved.
Since the approval of sitagliptin (1, Fig. 1) as a new treat-
ment option for type 2 diabetics, inhibition of dipeptidyl
peptidase IV (DPP-4) has become an established mech-
anism for the treatment of type 2 diabetes.1 DPP-4 is
responsible for the inactivation of glucagon-like peptide
1 (GLP-1) and glucose-dependent insulinotropic poly-
peptide (GIP), both of which enhance the secretion of
insulin in a glucose-dependent manner. Additionally,
GLP-1 has been shown to stimulate insulin biosynthesis,
inhibit glucagon secretion, slow gastric emptying, reduce
appetite, and stimulate the regeneration and differentia-
tion of islet b-cells.2,3 DPP-4 inhibition increases circu-
lating GLP-1 and GIP levels in humans, which leads
to decreased blood glucose levels, hemoglobin A1c levels,
and glucagon levels.3,4 DPP-4 inhibitors offer a number
of advantages over existing diabetes therapies including
a lowered risk of hypoglycemia, the potential for weight
loss, and the potential for the regeneration and differen-
tiation of pancreatic b-cells.5
Previous reports from these laboratories described the
optimization of a b-substituted phenylalanine derived
class of DPP-4 inhibitors which culminated in the dis-
covery of the potent and selective orally active DPP-4
inhibitor 2.6 Further work with b-substituted a-amino
amides afforded a potent and selective oxadiazole class
of DPP-4 inhibitors represented by 3.7 Surprisingly, X-
F
F
Me2N
O
O
F
NH2
O
N
N
N
N
N
N
NH2
N
N
F
F
1
2
CF3
R'
O
F
F
R
N
N
N
MeO2S
O
Keywords: Fluoroolefin; DPP-4; Dipeptidyl peptidase IV; Oxadiazole;
Amide bond mimic; Amide bond mimetic; Amide bond bioisostere;
QPP; DPP-II.
O
NH2
NH2
N
N
F
3
4
*
Figure 1. Potent and selective DPP-4 inhibitors, including sitagliptin
(1), a-amino amides 2 and 3, and fluoroolefins 4.
Corresponding author. Tel.: +1 732 594 0287; fax: +1 732 594
5350; e-mail: scott_edmondson@merck.com
0960-894X/$ - see front matter Ó 2008 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2008.02.050

2410
S. D. Edmondson et al. / Bioorg. Med. Chem. Lett. 18 (2008) 2409–2413
ray crystallographic analysis of compounds from these
structure classes revealed that 2 and 3 interact with dis-
tinct pockets of the DPP-4 binding site.
by thermally induced cyclocondensation to furnish the
desired oxadiazoles.14 Deprotection of the Boc group
then afforded the desired inhibitors 20–28.15
The identification of suitable amide bond bioisosteres is
an active area in medicinal chemistry research.8 Fluoro-
olefins represent one such class of bioisosteres that mi-
Ester 8 was also alkylated with allyl bromide to give a
mixture of syn/anti diastereomeric a-allyl esters 11
(Scheme 2). Ester hydrolysis was followed by oxadiazole
formation as above to afford 12. The terminal olefin of
12 was next converted to an alcohol using the following
three-step sequence: osmylation of the olefin to afford a
diol, oxidative cleavage of the diol to give the acid, and
reduction of the corresponding mixed anhydride to fur-
nish the alcohol. Alternatively, 12 could be chemoselec-
tively cyclopropanated by treatment with diazomethane
under palladium catalysis.16 Separation of the syn/anti
diastereomers (syn was minor, Fig. 2) was followed by
deprotection of the Boc groups to give alcohols 29/30
and cyclopropanes 31/32.
mic
amide
bonds
both
geometrically
and
electronically,9 and the successful incorporation of flu-
oroolefins as amide bond mimetics has been reported
in multiple biologically relevant systems.10 Welch and
co-workers studied a series of fluoroolefin-derived
DPP-4 inhibitors,11 and more recently Van der Veken
et al. also reported structure–activity relationships of a
series of fluoroolefin-derived dipeptidyl peptidase inhib-
itors.12 We sought to incorporate fluoroolefins as amide
bond mimetics into the oxadiazole-derived DPP-4 inhib-
itors 3 in an effort to improve the selectivity and phar-
macokinetic properties of this inhibitor class. This
paper will describe the chiral synthesis and biological
profile of a fluoroolefin class of DPP-4 inhibitors repre-
sented by the general structure 4.
A carbon-14 radiolabeled ethyl sulfone 33 was synthe-
sized by treatment of methyl sulfone 13 with KHMDS
and labeled methyl iodide (Scheme 3). Deprotection of
the Boc group furnished ethyl sulfone 33.
The synthesis of fluoroolefin DPP-4 inhibitors began
with a Horner–Emmons reaction of triethyl 2-fluoro-2-
phosphonoacetate with cyclopentanone (5) to form the
somewhat volatile fluoroenoate, which was quickly re-
duced to afford allylic alcohol 6 (Scheme 1). Oxidation
of 6 with Dess–Martin periodinane afforded the corre-
sponding volatile aldehyde, which was immediately con-
densed with Ellman’s (R) tert-butyl sulfinamide to give
chiral imine 7. Exposure of 7 to the titanium ester eno-
late of methyl acetate generated the desired S-amino ste-
The potency and selectivity profiles of selected oxadiaz-
ole amides and fluoroolefins are reviewed in Table 1.
Compounds were tested for inhibition of DPP-4 and
selectivity over quiescent cell proline peptidase (QPP,
DPP-II), prolyl endopeptidase (PEP), aminopeptidase
P (APP), prolidase, DPP8, and DPP9.17,18 The fluoro-
olefins generally displayed excellent (>1000-fold) selec-
tivity for DPP-4 inhibition over the counterscreens,
reocenter
and
subsequent
protecting
group
MeO2S
F
manipulation produced the Boc protected amine 8.13
Alkylation of the potassium enolate of 9 with methyl io-
dide selectively afforded the syn ester diastereomer 9,7
which was hydrolyzed to give acid 10. Condensation
of 10 with the substituted benzamidoximes was followed
F
a
b, c
R
N
MeO
8
N O
Cl
O
NHBoc
NHBoc
12
11
F
*
Cl
29, syn, R = CH2OH
30, anti, R = CH2OH
d-g
N
MeO2S
31, syn, R =
32, anti, R =
c
c
-Pr
-Pr
O
or h, g
+
N
NH3
TFA-
F
F
H
Scheme 2. Synthesis of DPP-4 inhibitors 29–32. Reagents and condi-
tions: (a) KHMDS, allyl bromide, THF, ꢀ78 °C; (b) LiOH(aq), THF
(60% yield, 2 steps); (c) EDC, 2-Cl-4-(MeSO2)C6H3–C(@NOH)NH2,
CH2Cl2 then tol, dioxane, D (33% yield); (d) OsO4, THF, pyr (73%
yield); (e) NaIO4, KMnO4, THF, H2O; (f) ClCO2i-Pr, THF then
NaBH4, MeOH, separate diastereomers (43% yield, 2 steps; syn/
anti = 1:2 ratio); (g) TFA, CH2Cl2; (h) CH2N2, Pd(OAc)2, Et2O,
separate diastereomers (55% yield, syn/anti = 1:1.5 ratio).
c, d
a, b
O
HO
N
t-Bu
S
5
6
7
O
F
Me
F
h
e-g
MeO
RO
i
O
O
NHBoc
NHBoc
9, R = Me
10, R = H
8
Me
F
R
N
N
j, k
Me
F
Cl
+
O
NH3
a, b
N
N
TFA-
MeO2S
20-28
O
NHBoc
13
Scheme 1. Synthesis of DPP-4 inhibitors 20–28. Reagents and condi-
tions: (a) THF, NaH, (EtO)2POCHFCO2Et, rt; (b) DIBAl-H, Et2O,
ꢀ78 °C (79% yield, 2 steps); (c) Dess–Martin periodinane, CH2Cl2
(93% yield); (d) (R)-t-BuSONH2, Ti(OEt)4, THF, D (96% yield); (e)
MeCO2Me, LDA, TiCl(Oi-Pr)3, THF; (f) MeOH, HCl; (g) THF,
NaHCO3 (aq), Boc2O (75% yield, 3 steps); (h) KHMDS, MeI, THF,
Me
F
Cl
N
14CH3CH2SO2
+
O
NH3
N
TFA-
33
ꢀ78 °C (78% yield); (i) LiOH(aq)
,
THF (86% yield); (j) EDC,
Scheme 3. Synthesis of radiolabelled ethyl sulfone 33. Reagents: (a)
KHMDS, 14CH3I, THF; (b) TFA, CH2Cl2.
ArC(@NOH)NH2, CH2Cl2 then tol, dioxane, D; (k) TFA, CH2Cl2.

S. D. Edmondson et al. / Bioorg. Med. Chem. Lett. 18 (2008) 2409–2413
2411
including DPP8 and DPP9.19 They were less selective
over QPP, however, thus only QPP data are presented
for comparison. Although the dichlorophenyl amide
14 was more potent than the fluoroolefin counterpart
20, the phenyl methyl sulfone amides such as 15 and
16 (DPP-4 IC50’s = 122 nM and 17 nM, respectively)
were somewhat less potent than the corresponding flu-
oroolefins 23 and 26 (DPP-4 IC50’s = 90 nM and
7.5 nM, respectively). Similar to previously reported
data in the oxadiazole series,7 the addition of a fluorine
atom to the pyrrolidine ring in the amides resulted in
ꢁ2.4-fold loss of potency at DPP-4 (e.g., 16 vs 17).
Thus, while structurally similar fluoroolefins 29 and 31
were 22-fold and 62-fold more potent at DPP-4 com-
pared to 18 and 19, some of the reduced potency ob-
served with 18 and 19 is likely due to the presence of a
fluorine atom on the pyrrolidine ring in this series of
inhibitors.
Figure 2. X-ray crystal structures of amide 3 (green) and fluoroolefin
31 (yellow) bound to DPP-4.20 Interactions of 3 and 31 with DPP-4 are
shown in blue dotted lines. All water molecules and their hydrogen
bond networks have been omitted for clarity.
Not surprisingly, potency for QPP inhibition also in-
creased substantially in the fluoroolefin series relative
to the amides.12b In contrast to previous reports, how-
ever, many of the fluoroolefins in Table 1 possess excel-
lent potency for DPP-4 inhibition. To better understand
the structural features of these fluoroolefins that afford
potent DPP-4 inhibition, X-ray crystal structures of 3
and 31 bound to DPP-4 were obtained.
X-ray structure confirms the syn stereochemical assign-
ment of potent DPP-4 inhibitor 31. Consistent with
the previously reported X-ray structure of compound
15,7 the phenyl ring of 3 appears to stack against the side
chain of Tyr547. Although the cyclopropyl groups are
oriented into a hydrophobic pocket, they do not reach
far enough into this pocket to interact with Arg358,
which has been shown to be an important DPP-4 bind-
ing residue with other selective inhibitors such as 2.6 Not
surprisingly, the fluoroolefin functionality of 31 forces
the cyclopentane ring into a coplanar orientation with
the double bond. In contrast, the pyrrolidide ring of 3
appears to be bent slightly out of the plane of the amide
pi-system. Consequently, the cyclopentane ring of 31
and the pyrrolidine ring of 3 adopt slightly different ori-
entations in the DPP-4 binding pocket. The fluorine
atom in 31 aligns well with the amide carbonyl oxygen
of 3 and each of these atoms forms two hydrogen bond
interactions with Asn710 and Glu206 in their respective
X-ray crystal structures.
Co-crystallization of 3 (green) and 31 (yellow) with
DPP-4 shows that the major interactions of these inhib-
itors with DPP-4 are similar (Fig. 2).20 Additionally, the
Table 1. Selected oxadiazole-derived DPP-4 inhibitors with amide
bonds and with fluoroolefins
R'
R'
O
F
R
R
N
N
N
N
N
+
+
O
O
NH3
TFA-
3, 14-19
NH3
TFA+
X
20-32
Compound
R
R0
X
IC50 (lM)
DPP-4 QPP
3
2-F, 4-SO2Me
2,4-diCl
4-SO2Me
CH2cPr
Me
Me
F
0.019
0.203
0.122
0.017
0.040
0.070
0.013
1.165
0.525
0.645
0.090
1.490
0.057
18
1.4
Inhibitors that possessed superior potency and selectiv-
ity profiles were evaluated for their rat pharmacokinetic
properties (Table 2). Activity at hERG was also mea-
sured in order to assess potential cardiovascular liabili-
ties.21 Selectivity over hERG was excellent for the
three fluoroolefins evaluated, but the oral bioavailabili-
ties of alcohol 29 (F = 4%) and cyclopropane 31
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29a
30a
31a
32a
H
H
15
6.4
2-Cl, 4-SO2Me
2-Cl, 4-SO2Me
2-Cl, 4-SO2Me
2-Cl, 4-SO2Me
2,4-diCl
Me
Me
H
F
3.5
45
(CH2)2OH
CH2cPr
Me
F
F
17
—
—
—
—
—
—
—
—
—
—
—
—
—
0.25
1.66
0.14
3.91
3.44
0.33
2-Cl, 4-CF3
2-Cl, 4-Br
4-SO2Me
Me
Me
Me
Me
Table 2. Pharmacokinetic properties of selected DPP-4 inhibitors in
the rat (1/2 mg/kg iv/po) and hERG binding
4-SO2CF3
2-Cl, 4-NHSO2Me Me
Compound Clp (mL/min/kg) t1/2 (h) F (%) hERG IC50 (lM)
2-Cl, 4-SO2Me
2-Cl, 4-SO2Et
2-Cl, 4-SO2Me
2-Cl, 4-SO2Me
2-Cl, 4-SO2Me
2-Cl, 4-SO2Me
2-Cl, 4-SO2Me
Me
Me
0.0075 0.33
0.050
0.021
0.42
0.46
16
26
29
31
6
20
51
54
0.86
2.0a
1.6
27
62
4
37
19
47
7.1
H
(CH2)2OH
(CH2)2OH
CH2cPr
CH2cPr
0.0032 1.16
0.093 1.40
0.00021 0.13
0.012 0.21
1.5
1
a Value for mean residence time (MRT) is reported since t1/2 could not
be calculated due to secondary peaks in the plasma concentration
time profile.
a 29 and 31 are syn disastereomers, 30 and 32 are anti diastereomers.

2412
S. D. Edmondson et al. / Bioorg. Med. Chem. Lett. 18 (2008) 2409–2413
Table 3. Rat hepatocyte and rat liver microsomal stability of amide 16
and fluoroolefin 26
the DPP-4 binding pocket. Evaluation of a series of flu-
oroolefins in rat pharmacokinetics studies revealed that
26 shows improved oral bioavailability but higher
intrinsic clearance compared to the structurally related
amide derivative 16. Incubation of the radiolabeled flu-
oroolefin 33 with rat and human liver microsomes
showed that this compound has a high propensity to
form reactive metabolites that can irreversibly bind to
biomolecules. Consequently, the potential liabilities
associated with the high propensity for bioactivation
of these fluoroolefins led to discontinuation of the eval-
uation of this class of potent and selective DPP-4
inhibitors.
Compound
% Parent remaining at 60 min
RLMa + NADPH
Rat hepatocytes
16
26
56%
<LOQb
88%
3%
a RLM, rat liver microsomes.
b LOQ, limits of quantitation.
(F = 1%) were too low to merit further profiling. In con-
trast, methyl analog 26 displayed improved oral bio-
availability (F = 62%) relative to 29 and 31 and the
corresponding amide derivative 16 (F = 27%). On the
other hand, 26 also exhibited increased clearance rela-
tive to amide 16.
Acknowledgments
The authors thank I. Capodanno, M. Donnelly, J.E. Fe-
nyk-Melody, J. Hausamann, C. Nunes, X. Shen, J.
Strauss, K. Vakerich, Z. Yao for dosing the animals
used in pharmacokinetic experiments.
In order to better understand the difference in rat intrin-
sic clearance between 16 and 26, each compound was
incubated with rat hepatocytes and rat liver microsomes
and the percentage parent remaining was measured at
60 min (Table 3). Fluoroolefin 26 was significantly less
stable than amide 16 in rat liver microsome and hepato-
cyte incubations, and the metabolism of 26 in liver
microsomes was NADPH-dependent. Mass spectromet-
ric analyses of the rat liver microsome and hepatocyte
incubations of 16 revealed a predominance of oxidative
metabolites formed on the pyrrolidine ring.22 In con-
trast, major metabolites identified from fluoroolefin 26
were oxidized at the cyclopentanyl fluoroolefin moiety.
Moreover, multiple glutathione adducts were detected
in the incubations with fluoroolefin 26, indicating a po-
tential propensity for this compound to form reactive
metabolites.
Supplementary data
Supplementary data associated with this article can be
found, in the online version, at doi:10.1016/
j.bmcl.2008.02.050.
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17. IC50 determinations for DPP-4 and QPP were carried out
as described in: Leiting, B.; Pryor, K. D.; Wu, J. K.;
Marsilio, F.; Patel, R. A.; Craik, C. S.; Ellman, J. A.;
Cummings, R. T.; Thornberry, N. A. Biochem. J. 2003,
371, 525.
18. All DPP-4 IC50’s are an average of n P 2, with standard
deviations less than 75% of the average.
19. For a discussion of the relevance of selectivity over DPP8
and DPP9, see: Lankas, G. R.; Leiting, B.; Sinha Roy, R.;
Eiermann, G. J.; Beconi, M. G.; Biftu, T.; Chan, C.-C.;
Edmondson, S.; Feeney, W. P.; He, H.; Ippolito, D. E.;
Kim, D.; Lyons, K. A.; Ok, H. O.; Patel, R. A.; Petrov, A.
N.; Pryor, K. A.; Qian, X.; Reigle, L.; Woods, A.; Wu, J.
K.; Zaller, D.; Zhang, X.; Zhu, L.; Weber, A. E.;
Thornberry, N. A. Diabetes 2005, 54, 2988.
20. The atomic coordinates for the X-ray structures of DPP-4
in complex with 3 and 31 have been deposited into the
RCSB protein data bank under RCSB ID codes
rcsb046315 and rscb046317, and under PDB ID codes
3C43 and 3C45, respectively.
21. IC50 determinations for hERG was carried out as
described in: Friesen, R. W.; Ducharme, Y.; Ball, R. G.;
Blouin, M.; Boulet, L.; Cote, B.; Frenette, R.; Girard, M.;
Guay, D.; Huang, Z.; Jones, T. R.; Laliberte, F.; Lynch, J.
J.; Mancini, J.; Martins, E.; Masson, P.; Muise, E.; Pon,
D. J.; Siegel, P. K. S.; Styhler, A.; Tsou, N. N.; Turner, M.
J.; Young, R. N.; Girard, Y. J. Med. Chem. 2003, 46,
2017.
22. For related work done to identify metabolites on fluoro-
pyrrolidine-derived DPP-4 inhibitors, see: Xu, S.; Zhu, B.;
Teffera, Y.; Pan, D. E.; Caldwell, C. G.; Doss, G.; Stearns,
R. A.; Evans, D. C.; Beconi, M. G. Drug Metab. Dispos.
2005, 33, 121.
23. Evans, D. C.; Watt, A. P.; Nicoll-Griffith, D. A.; Baillie,
T. A. Chem. Res. Toxicol. 2004, 17, 3.
24. Uetrecht, J. P. Chem. Res. Toxicol. 1999, 12, 387.
13. Tang, T. P.; Ellman, J. A. J. Org. Chem. 2002, 67, 7819.