Discovery of C-(1-aryl-cyclohexyl)-methylamines as selective, orally available inhibitors of dipeptidyl peptidase IV

Article abstract of DOI:10.1016/j.bmcl.2013.12.118

The successful launches of dipeptidyl peptidase IV (DPP IV) inhibitors as oral anti-diabetics warrant and spur the further quest for additional chemical entities in this promising class of therapeutics. Numerous pharmaceutical companies have pursued their proprietary candidates towards the clinic, resulting in a large body of published chemical structures associated with DPP IV. Herein, we report the discovery of a novel chemotype for DPP IV inhibition based on the C-(1-aryl-cyclohexyl)-methylamine scaffold and its optimization to compounds which selectively inhibit DPP IV at low-nM potency and exhibit an excellent oral pharmacokinetic profile in the rat. 2014 Elsevier Ltd. All rights reserved.

Full text of DOI:10.1016/j.bmcl.2013.12.118

Accepted Manuscript
Discovery of C-(1-aryl-cyclohexyl)-methylamines as selective, orally available
inhibitors of dipeptidyl peptidase IV
Kenji Namoto, Finton Sirockin, Nils Ostermann, Francois Gessier, Stefanie
Flohr, Richard Sedrani, Bernd Gerhartz, Jörg Trappe, Ulrich Hassiepen,
Alokesh Duttaroy, Suzie Ferreira, Jon M. Sutton, David E. Clark, Gary Fenton,
Mandy Beswick, Daniel K. Baeschlin
PII:
S0960-894X(13)01502-3
DOI:
http://dx.doi.org/10.1016/j.bmcl.2013.12.118
BMCL 21226
Reference:
Bioorganic & Medicinal Chemistry Letters
To appear in:
Received Date:
Revised Date:
Accepted Date:
4 November 2013
27 December 2013
28 December 2013
Please cite this article as: Namoto, K., Sirockin, F., Ostermann, N., Gessier, F., Flohr, S., Sedrani, R., Gerhartz, B.,
Trappe, J., Hassiepen, U., Duttaroy, A., Ferreira, S., Sutton, J.M., Clark, D.E., Fenton, G., Beswick, M., Baeschlin,
D.K., Discovery of C-(1-aryl-cyclohexyl)-methylamines as selective, orally available inhibitors of dipeptidyl
peptidase IV, Bioorganic & Medicinal Chemistry Letters (2014), doi: http://dx.doi.org/10.1016/j.bmcl.2013.12.118
This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers
we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and
review of the resulting proof before it is published in its final form. Please note that during the production process
errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

Discovery of C-(1-aryl-cyclohexyl)-methylamines as
selective, orally available inhibitors of dipeptidyl
peptidase IV.
Author Names. Kenji Namotoa, Finton Sirockina, Nils Ostermanna, Francois Gessiera,
Stefanie Flohra, Richard Sedrania, Bernd Gerhartza, Jörg Trappea, Ulrich Hassiepena,
Alokesh Duttaroyb, Suzie Ferreirab, Jon M. Suttonc, David E. Clarkc, Gary Fentonc,
Mandy Beswickc, and Daniel K. Baeschlina.
aNovartis Institutes for BioMedical Research, Novartis Campus, Basel, Switzerland
bNovartis Institutes for BioMedical Research, Cambridge, MA, USA
cArgenta Discovery 2009 Ltd., Harlow, CM19 5TR, UK
Corresponding Author. Kenji Namoto (kenji.namoto@novartis.com); phone: +41 61 696
2550; contact address: Fabrikstrasse-16.4.31, Novartis Pharma AG, Postfach, CH-4002,
Basel, Switzerland.
Abstract. The successful launches of dipeptidyl peptidase IV (DPP IV) inhibitors as oral
anti-diabetics warrant and spur the further quest for additional chemical entities in this
promising class of therapeutics. Numerous pharmaceutical companies have pursued
their proprietary candidates towards the clinic, resulting in a large body of published
chemical structures associated with DPP IV. Herein, we report the discovery of a novel
chemotype for DPP IV inhibition based on the C-(1-aryl-cyclohexyl)-methylamine
scaffold and its optimization to compounds which selectively inhibit DPP IV at low-nM
potency and exhibit an excellent oral phamacokinetic profile in the rat.
Keywords. protease inhibition; dipeptidyl peptidase IV; structure-based drug design;
enzyme selectivity; pharmacokinetics; ex vivo plasma DPP IV inhibition
The worldwide morbidity caused by diabetes mellitus is increasing at an alarming rate due to the
aging population in developed countries and the rapid emergence of a middle class in the
developing world.1 Consequently, the pharmaceutical industry has ramped up its R&D efforts to
discover novel oral anti-diabetic therapeutics with enhanced safety and efficacy profiles.2

Among the notable advances in this field in recent years are the successful launches of Galvus
®,3 Januvia ®,4 Nesina ®,5 Onglyza ®,6 and Tradjenta ®,7 all of which belong to a class of drugs
called gliptins, or inhibitors of dipeptidyl peptidase IV (DPP IV). DPP IV is a serine protease
belonging to the S9 family and involved in proteolytic processing of the gut incretin hormone
GLP-1, thereby down-regulating the duration of the hormone’s stimulating effect on insulin
secretion during and after the ingestion of a meal.8 Inhibition of DPP IV has been widely
heralded as the first novel mode of action to control diabetes in the many years since the
introduction of metformin, offering an attractive alternative to treat patients who fail to respond to,
or are contraindicated towards, conventional therapies.9,10 Herein, we describe the discovery of
C-(1-aryl-cyclohexyl)-methylamine as a novel DPP IV inhibitor scaffold with the potential for
development as a once-daily oral therapeutic.
Our quest for a novel, orally efficacious, long-acting DPP IV inhibitor commenced with the HTS
hit syn-7aa (Figure 1, DPP IV IC50 11.9 M). Its cyclohexyl core geminally substituted with an
aminomethyl group and an aromatic ring represents a hitherto unexplored DPP IV inhibitor
scaffold.11 An X-ray co-crystal structure of syn-7aa with recombinant human DPP IV (Figure 2)
revealed that the cyclohexyl core orients the phenyl ring deep into the S1 pocket where it takes
the same orientation as observed for the 2,4,5-trifluorophenyl motif of sitagliptin (pdb:2p8s).12
The basic aminomethyl side chain interacts with the carboxylates of glutamic acids Glu205 and
Glu207.13 The cinnamyl chain is directed further down to the non-prime side of the active site,
albeit with lower electron densities in the X-ray structure, suggesting that there is less specific
binding in this region. As observed in our previous studies on deazaxanthine-based DPP IV
inhibitors,14 the side chain of Tyr547 was flipped upwards compared to its position in the co-
crystal structure of sitagliptin with DPP IV presumably due to the steric bulk of the cyclohexyl
core. With a clear structural proof of binding in hand, we embarked on an initial investigation of
the structure-activity relationships of this new chemical class.

Figure 1. Vildagliptin, sitagliptin, and C-(1-aryl-cyclohexyl)-methylamine HTS hit syn-7aa.

Figure 2. An X-ray structure overlay of HTS hit syn-7aa (ligand shown with ball and stick
representation and grey-white carbon atoms, protein in stick representation with grey-white
carbon atoms) and Januvia (ligand shown with ball and stick representation and magenta carbon
atoms, protein in stick representation with light-pink carbon atoms).

Compounds syn-7aa–7c were prepared according to Scheme 1. Thus, halophenylacetonitriles
1b–1c underwent double Michael addition to methyl acrylate in the presence of Triton B to yield
the bis-esters 2b–2c, which were cyclized by Dieckmann condensation followed by hydrolytic
decarboxylation to afford cyclohexanones 4b–4c.15 The carbonyl group of cyclohexanones
4a16–4c was reduced with sodium borohydride to give the secondary alcohols syn-5a–5c which
showed a preference for the syn configuration. After chromatographic removal of the minor anti
stereoisomer, the hydroxyl group of syn-5a–5c was deprotonated and alkylated with alkylhalides,
yielding the ethers syn-6aa–6c. Finally, reduction of the nitrile group by borane–THF complex
or lithium aluminum hydride gave the cyclohexyl ether derivatives syn-7aa–7c.
Scheme 1. Synthesis of cyclohexyl ether derivatives syn-7aa – 7c. (a) Methyl acrylate, 40%
Triton B in MeOH, t-BuOH, reflux, 5h (62-72%); (b) t-BuOK, THF, reflux, overnight (40-98%); (c)
10% aq. H2SO4 – AcOH [1:2], 110˚C, overnight (42-75%); (d) NaBH4, THF, -78˚C, 1.5h (45-98%);

(e) Alkyl halide RBr or RI, NaH, THF,0˚C then rt, 3h (19-99%); (f) BH3-THF, THF, reflux, 5h, then
6N aq. HCl, reflux, 2h (7-55%); (g) LiAlH4, THF, 50˚C, 2h (7-24%).

Evaluation of these compounds in a biochemical assay against recombinant human DPP IV
quickly revealed two important structure-activity relationships of this chemotype (Table 1),17
corroborating our observation from the X-ray co-crystal structure. Firstly, truncation of the
cinnamyl chain to a benzyl group could be achieved without loss of potency (syn-7ab),
indicating a potential for further improvement in activity via additional, more specific, interactions
in this region. Further truncation to a methyl group resulted in a six-fold loss of potency but with
an improved ligand efficiency of 0.264 (syn-7ac).18 Secondly, mono-chloro substitution at the
meta position of the S1-binding phenyl ring boosted the potency by 15-fold (syn-7ac vs syn-7b)
while trifluoro substitution, as in sitagliptin, gave only a marginal or low increases in potency
(syn-7ac vs syn-7c).
Table 1. Biochemical IC50 values of syn-7aa – 7c.
hDPP IV
IC50 (M)
Ligand
Efficiency
Compounds
X/Y/Z
R
syn-7aa
syn-7ab
syn-7ac
syn-7b
syn-7c
H/H/H
H/H/H
H/H/H
H/H/Cl
F/F/F
cinnamyl
Bn
Me
Me
Me
11.9
19.9
60.0
4.20
15.7
0.205
0.214
0.264
0.316
0.253
In the light of the opportunities identified in the non-prime S2-S3 region to improve the potency
further, we closely examined the X-ray co-crystal structures of syn-7aa and sitagliptin (Figure 2).
This led us to the formulation of a three-stage optimization strategy. Firstly, it was envisioned
that cyclisation of the flexible cinnamyl ether chain of syn-7aa should give rise to a better
defined overall conformation of the inhibitor, thereby increasing the chance of targeting these
P2-P3 moieties towards a specific area of DPP IV S2-S3 region. In particular, fused bicycles

appeared to potentially provide the ideal rigidity and orientation. Secondly, we hypothesized that
the “up” conformation of Tyr547 in the syn7aa structure would allow a unique opportunity for a
water-mediated interaction, bridging a hydrogen bond between the ligand and the Tyr547 side-
chain hydroxyl group. The distance between the crystallographic water oxygen and the Tyr547
side-chain hydroxyl oxygen is 2.6 Å, showing that this water molecule is clearly hydrogen
bonded with Tyr547. Thirdly, and building further upon the two strategies above, we removed
the second ring of the fused bicycle and appended it under the first ring, based on an overlay of
X-Ray structures of syn-7aa and sitagliptin (cf.Figure 2). This virtual molecule and other putative
ligands were manually built into the syn-7aa X-ray structure and subjected to minimisation with
the OPLS force-field (MacroModel 9.0, Schrödinger, Inc.). Different rings were modelled to
attach to the cyclohexane present in syn-7aa replacing the ether moiety and focusing on
designing a molecule with a substitution allowing for interaction with the water molecule
discussed above. This process eventually resulted in a modified syn-7aa bearing a
pyridazinone ring directly linked to the central cyclohexane.
With this structure-based rationale in mind, we designed and synthesized heterobicyclic
derivatives 12a-c and 13a-c, according to Scheme 2, while pyridazinone derivatives 20a-d were
prepared according to Scheme 3. Thus, the nitrile and keto carbonyl groups of intermediate 4c
were simultaneously reduced and Boc-protected to give rise stereoselectively to the syn-Boc-
aminomethylcyclohxanol 8, which then underwent a two-step Mitsunobu inversion protocol,
providing the anti-Boc-aminomethylcyclohexanol 9. The hydroxyl group was converted to the
mesylate, then to the azide, which was reduced to install an amino group with the opposite
stereochemistry. Acylation of the primary amine 10 with 5-chlorovaleryl chloride followed by
intramolecular cyclisation with sodium hydride furnished the lactam 11. Boc removal gave
compound 12a and subsequent reduction of the lactam carbonyl yielded compound 13a. In
parallel, the ketone of intermediate 4c was protected with 1,3-dioxolane, and the nitrile was
reduced with lithium aluminum hydride to afford the primary amine 14, which was subsequently

protected with a Boc group and treated with pyridine-pTsOH complex in aqueous media to
reveal the ketone 15 chemoselectively. Reductive amination of the ketone carbonyl group with
heterobicycle 16 furnished the intermediate 17, which underwent RuO2-catalyzed benzylic
oxidation and Boc removal to yield compounds 12b-c,19 while direct amine deprotection of 17
gave rise to the corresponding deoxo-derivatives 13b-c. Finally, compounds 20a-d were
prepared in two synthetic steps from the anti cyclohexanol 9 using Mitsunobu chemistry with the
corresponding pyridazinones 18a-d and Boc removal of the desired syn stereoisomers 19a-d
with TFA in DCM (Scheme 3).20

Scheme 2. Synthesis of heterobicyclic derivatives 12a-c and 13a-c. (a) BH3-THF, THF, reflux,
4h, then 2N aq. HCl, r.t. 16h (quant.) (b) Boc2O, TEA, THF, r.t. 16h (87%) (c) Benzoic acid, PPh3,
DIAD, THF, r.t. 20h (63%) (d) NaOMe, MeOH, THF, r.t. 15h (92%); (e) MsCl, TEA, DCM, r.t. 2h
(94%); (f) NaN3, DMF, 100˚C, 5h (97%) (g) PPh3, H2O, toluene, 50˚C, 20h (77%); (h) 5-
Chlorovaleryl chloride, sat. aq. Na2CO3, CHCl3, r.t. 45min (quant.); (i) NaH, DMF, r.t. 16h (77%);
(j) TFA, DCM, r.t. 1h (72-92%); (k) BH3-THF, THF, reflux, 2d, then 1N aq. HCl, MeOH, 90˚C, 7h

(37%); (l) Ethylene glycol, pTSA, toluene, reflux, 18h (89%); (m) LiAlH4, THF, r.t. 1h then 50˚C,
2h (93%); (n) Boc2O, TEA, DCM, r.t. 4h (quant.) (o), PPTS, acetone, H2O, reflux, 2d (50%); (p)
NaBH(OAc)3, heterobicycle 16, AcOH, 1,2-DCE, r.t. 5h (10-50%); (q) RuO2·2H2O, NaIO4, CHCl3,
MeCN, H2O, r.t. 20min (19-76%); (r) TFA, DCM, r.t. 1h (61% for 12b) or 4N HCl in dioxane, r.t.
2.5h (67% for 12c).

Scheme 3. Synthesis of pyrdidazinone derivatives 20a-d. (a) DEAD, polymer-supported PPh3,
pyridazinone 18, THF, r.t. 24h (15-60%); (b) TFA, DCM, r.t. 1h (28-95%).
Evaluation of the compounds thus obtained (Table 2) in the primary assay revealed that all of
them were significantly more potent than the acyclic compounds (cf. Table 1). In addition,
potency enhancements of 5- to 13-fold were observed for the lactam derivatives 12a-c carrying
P2-P3 motifs A, B, and C (X = O) compared with the corresponding de-oxo homologs 13a-c (X =
H,H). We surmised that the lactam group endowed compounds 12a-c with a higher rigidity of the
respective ring systems as well as an additional H-bonding interaction with Tyr547. An X-ray
structure of 12a in complex with human DPP IV revealed that the P1-P2 moieties of the
molecules were perfectly aligned with the initial structure of syn-7aa.21 Furthermore, this
structure unequivocally proved that the designed interaction between the piperidinone carbonyl
and a water molecule bridging a hydrogen bond to Tyr547 side-chain hydroxyl was indeed
present (Figure 3). Gratifyingly, the pyridazinone compounds 20c-d were as potent as the
bicyclic lactam compounds 12b-c, validating the original modelling hypothesis for isosteric
replacement of the heterobicycle with the heterobiaryl moiety. The selectivity window over the
closely related S9 family members DPP8 and 9 improved as the size of the P2-P3 motifs
increased from monocycles (60- to 750-fold, 12a, 13a, 20a-b) to bicycles (750- to 3700-fold,
12b-c, 13b-c) or biaryls (6500- to 8200-fold, 20c-d).22

Table 2. Biochemical IC50 values of 12a-c, 13a-c, 20a-d, and sitagliptin.
hDPP IV
IC50 (M)
Ligand
Efficiency
hDPP8
IC50 (M)
hDPP9
IC50 (M)
Compounds
R
X
Y
-
-
-
0.020
0.007
0.002
0.350
0.281
0.264
10.8
22.4
7.4
9
13
3.5
12a
12b
12c
A
B
C
O
O
O
13a
13b
13c
20a
20b
20c
20d
A
B
C
Da
Db
Dc
Dd
-
H,H
H,H
H,H
-
-
-
-
-
-
-
0.250
0.040
0.009
0.200
0.040
0.003
0.004
0.010
0.314
0.264
0.251
0.305
0.322
0.304
0.300
0.286
14.7
30
>30
NT
28.3
19.4
>30
32.8
14.6
>30
>30
17.6
>30
24.6
>30
61.9
-
H
Me
Phenyl
3-pyridyl
-
sitagliptin

Figure 3. An X-ray structure of compound 12a (ligand shown with ball and stick representation
and orange carbon atoms, protein in stick representation with grey-white carbon atoms).

Three compounds with the best potency and selectivity windows 12b, 12c, and 20d were
chosen for further evaluation in in vitro ADMET assays and pharmacokinetic studies in the rat
(Table 3). There appeared to be an in-vitro / in-vivo disconnect in clearance for 12b, 12c, and
20d which cannot be easily explained. However, oral bioavailability (Foral) followed CaCo-2
permeability well. Compound 12b exhibited relatively low Caco-2 permeability with moderate
clearance in rat microsomes and high in vivo clearance, suggesting some extrahepatic
clearance. Consequently, the overall exposure was low albeit a measurable oral bioavailability
of 17%. Compound 12c, on the other hand, had a moderate microsomal clearance but enjoyed
the lowest in vivo clearance among the three compounds. Helped by higher permeability, it
achieved a very good oral exposure and a high Cmax with an admirable 78% bioavailability.
Finally, compound 20d was found to be highly permeable in the Caco-2 assay, which translated
well into the in vivo setting, with this compound achieving an excellent oral bioavailability of 92%.
However, the overall exposure of 20d was slightly less than that of compound 12c due to its
moderate in vivo clearance. Compared with the other two compounds (12b and 12c), 20d
exhibited improved CYP2D6 profile, indicative of a reduced DDI potential, although the prospect
of hERG-mediated cardiotoxicity still remains a possibility.

Table 3. Selected ADMET and rat PK data for Compounds 12b, 12c, and 20d.
a
Caco-2 AB/BA
(10-6 cm/sec)
Rat CLint
CYP2D6
IC50 (M)
hERGb
IC50 (M)
Compounds
(L/min/mg)
12b
12c
20d
1.6/4.8
4.4/11
8.6/13
21.9
43.4
51.1
4.5
10
>30
0.26
4.4
>10
a rat liver microsome data (RLM). b Dofetilide binding assay.
d
c
c
c
c
Cmax
AUC p.o. (0-8 h)
(nM*h)
Vssd
T1/2
CLd
(mL/min/kg)
Foral
Tmax
(h)
Compounds
(nM)
57.8
1900
921
(L/Kg)
11.7
2.1
(h)
2.7
2.3
2.2
(%)
12be
12cf
20dg
3.3
3.3
1.8
214
7908
4009
69
9.5
29
17
78
3.9
92
c p.o. leg run at 3 mg/kg. d i.v.leg run at 1 mg/kg. e solution in PBS buffer pH 6.88. f solution in sodium acetate buffer pH 4.63. g solution in 10%
PEG300 / 90% PBS.
Compound 20d was further assessed, together with sitagliptin, in our rat PD model using ex vivo
plasma DPP IV inhibition as the pharmacological readout (Figure 4). The compounds were
orally administered at 3mg/kg dose, and the DPP IV activity in plasma was monitored over an
eight-hour period. Sitagliptin reached a peak inhibition level of 82% at around one to two hours
post dose, and then steadily lost its inhibitory activity over the time-course ending in 30% DPP IV
inhibition at eight hours post dose. On the other hand, compound 20d exhibited a superior
profile, achieving both a faster onset of half an hour and a higher peak inhibition of 91%, which
was maintained at nearly 80% at the end of the eight-hour time-course. The overall ex vivo
plasma DPPIV inhibition profile of 20d correlated well with its plasma exposure levels (the
exposure data not shown). The excellent duration of action for 20d clearly demonstrates the
potential for this class of DPP IV inhibitors for development as once-daily oral therapeutics.

Figure 4. Inhibition of plasma DPP IV activity after oral administration of compound 20d and
sitagliptin (both at 3 mg/kg dose) in SD rats.
In conclusion, we have discovered a hitherto unexplored class of DPP IV inhibitors featuring the
C-(1-aryl-cyclohexyl)-methylamine scaffold. Structure-guided medicinal chemistry efforts on the
original screening hit syn-7aa led to successful improvement of target potency in this novel
chemotype, resulting in a number of potent, selective and orally bioavailable DPP IV inhibitors.
The most advanced derivative, 20d, demonstrated significantly enhanced duration of DPP IV
inhibition in the rat compared with the marketed drug sitagliptin, warranting further endeavour in
this arena towards safe and orally efficacious, once-daily antidiabetics.
Acknowledgement
The authors thank Florence Zink for her excellent technical assistance in protein crystallization
and Xia Zhang for running ex vivo plasma DPP IV assay (Novartis Institutes for BioMedical
Research). Numerous contributions to medicinal and synthetic chemistry in this work from the

following individuals at Argenta Disovery are greatly acknowledged: Amanda Fillmore, Neil
Harris, Fabien Roussel, Guilaume Brandt, Paul Bury, Rachel Ord and Gwen Hicken.
References
1. Danaei, G.; Finucane, M. M.; Lu, Y.; Singh, G. M.; Cowan, M. J.; Paciorek, C. J.; Lin, J. K.;
Farzadfar, F.; Khang, Y.-H.; Stevens, G. A.; Rao, M.; Ali, M. K.; Riley, L. M.; Robinson, C. A.;
Ezzati, M. Lancet 2011, 378(9785), 31.
2. “The Pharmaceutical Industry And Global Health – Facts And Figures 2012” International
Federation of Pharmaceutical Manufacturers & Associations (2013).
3. Hedge, S.; Schmidt, M. Annu. Rep. Med. Chem. 2008, 43, 494, and references therein.
4. Hedge, S.; Schmidt, M. Annu. Rep. Med. Chem. 2007, 42, 541, and references therein.
5. Bronson, J.; Dhar, M.; Ewing, W.; Lonberg, N. Annu. Rep. Med. Chem. 2011, 46, 446, and
references therein.
6. Hedge, S.; Schmidt, M. Annu. Rep. Med. Chem. 2010, 45, 521, and references therein.
7. Bronson, J.; Dhar, M.; Ewing, W.; Lonberg, N. Annu. Rep. Med. Chem. 2012, 47, 540, and
references therein.
8. Mentlein, R.; Gallwitz, B.; Schmidt, W.E. Eur. J. Biohem. 1993, 214(3), 829.
9. Barnett, A. Int. J. Clin. Pract. 2006, 60(11), 1454.
10. Deacon, C. F.; Holst, J. Expert Opin. Pharmacother. 2013, 14(15), 2047.
11. To the best of our knowledge, the only related compound known in the literature is a
singleton DPP IV inhibitor (human DPP IV IC50 30 µmol) reported in: Nordhoff, S.; Cerezo-
Gálvez, S.; Feurer, A.; Hill, O.; Matassa, V. G.; Metz, G.; Rummey, C.; Thiemann, M.; Edwards,
P. J. Bioorg. Med. Chem. Lett. 2006, 16, 1744.

12. Biftu, T.; Scapin, G.; Singh, S.; Feng, D.; Becker, J.W.; Eiermann, G.; He, H.; Lyons, K.;
Patel, S.; Petrov, A.; Sinha-Roy, R.; Zhang, B.; Wu, J.; Zhang, X.; Doss, G.A.; Thornberry,
N.A.; Weber, A.E. Bioorg. Med. Chem. Lett. 2007, 17, 3384.
13. The structure is deposited in the RCSB Protein Data Bank
(http://www.rcsb.org/pdb/home/home.do). PDB ID: 4N8D.
14. Sutton, J.M.; Clark, D.E.; Dunsdon, S.J.; Fenton G.; Fillmore, A.; Harris, N.V.; Higgs C.;
Hurley, C.A.; Krintel, S.L.; MacKenzie, R.E.; Duttaroy, A.; Gangl, E.; Maniara, W.; Sedrani, R.;
Namoto, K.; Ostermann, N.; Gerhartz, B.; Sirockin, F.; Trappe, J.; Hassiepen, U.; Baeschlin, D.K.
Bioorg. Med. Chem. Lett. 2012, 22, 1464.
15. Uyeo, S; Shirai, H.; Koshiro, A.; Yashiro, T.; Kagei, K.; Chem. Pharm. Bull. 1966, 14 (9),
1033.
16. Cyclohexane 4a was purchased from Acros Organics (Belgium).
17. DPP IV assays were performed as described in: Sutton, J.M.; Clark, D.E.; Dunsdon, S.J.;
Fenton G.; Fillmore, A.; Harris, N.V.; Higgs C.; Hurley, C.A.; Krintel, S.L.; MacKenzie, R.E.;
Duttaroy, A.; Gangl, E.; Maniara, W.; Sedrani, R.; Namoto, K.; Ostermann, N.; Gerhartz, B.;
Sirockin, F.; Trappe, J.; Hassiepen, U.; Baeschlin, D.K. Bioorg. Med. Chem. Lett. 2012, 22, 1464.
18. Hopkins, A. L.; Groom, C. R.; Alex, A. Drug Discovery Today 2004, 9, 430.
19. Tanaka, K.; Yoshifuji, S.; Nitta, Y. Chem. Pharm. Bull. 1988, 36, 3125.
20. Kuroda, S.; Takamura, F.; Tenda, Y.; Itani, H.; Tomishima, Y.; Akahane, A.; Sakane, K.
Chem. Pharm. Bull. 2001, 49, 988.
21. The structure is deposited in the RCSB Protein Data Bank
(http://www.rcsb.org/pdb/home/home.do). PDB ID: 4N8E.

22. DPP8/9 assays were performed as described in: Burkey, B. F.; Hoffmann, P. K.; Hassiepen,
U.; Trappe, J.; Juedes, M.; Foley, J. E. Diabetes, Obesity and Metabolism 2008, 8, 1057.

Table 1. Biochemical IC50 values of syn-7aa – 7c.
hDPP IV
IC50 (M)
Ligand
Efficiency
Compounds
X/Y/Z
R
syn-7aa
syn-7ab
syn-7ac
syn-7b
syn-7c
H/H/H
H/H/H
H/H/H
H/H/Cl
F/F/F
cinnamyl
Bn
Me
Me
Me
11.9
19.9
60.0
4.20
15.7
0.205
0.214
0.264
0.316
0.253

Table 2. Biochemical IC50 values of 12a-c, 13a-c, 20a-d, and sitagliptin.
hDPP IV
IC50 (M)
Ligand
Efficiency
hDPP8
IC50 (M)
hDPP9
IC50 (M)
Compounds
R
X
Y
-
-
-
0.020
0.007
0.002
0.350
0.281
0.264
10.8
22.4
7.4
9
13
3.5
12a
12b
12c
A
B
C
O
O
O
13a
13b
13c
20a
20b
20c
20d
A
B
C
Da
Db
Dc
Dd
-
H,H
H,H
H,H
-
-
-
-
-
-
-
0.250
0.040
0.009
0.200
0.040
0.003
0.004
0.010
0.314
0.264
0.251
0.305
0.322
0.304
0.300
0.286
14.7
30
>30
NT
28.3
19.4
>30
32.8
14.6
>30
>30
17.6
>30
24.6
>30
61.9
-
H
Me
Phenyl
3-pyridyl
-
sitagliptin

Table 3. Selected ADMET and rat PK data for Compounds 12b, 12c, and 20d.
a
Caco-2 AB/BA
(10-6 cm/sec)
Rat CLint
CYP2D6
IC50 (M)
hERGb
IC50 (M)
Compounds
(L/min/mg)
12b
12c
20d
1.6/4.8
4.4/11
8.6/13
21.9
43.4
51.1
4.5
10
>30
0.26
4.4
>10
a rat liver microsome data (RLM). b Dofetilide binding assay.
d
c
c
c
c
Cmax
AUC p.o. (0-8 h)
(nM*h)
Vssd
T1/2
CLd
(mL/min/kg)
Foral
Tmax
(h)
Compounds
(nM)
57.8
1900
921
(L/Kg)
11.7
2.1
(h)
2.7
2.3
2.2
(%)
12be
12cf
20dg
3.3
3.3
1.8
214
7908
4009
69
9.5
29
17
78
3.9
92
c p.o. leg run at 3 mg/kg. d i.v.leg run at 1 mg/kg. e solution in PBS buffer pH 6.88. f solution in sodium acetate buffer pH 4.63. g solution in 10%
PEG300 / 90% PBS.

Figure1

Figure2_Color_Web_and_Print

Figure3_Color_Web_and_Print

Figure4

Scheme1

Scheme2