Evaluation of a 4-aminopiperidine replacement in several series of CCR5 antagonists

Article abstract of DOI:10.1016/j.bmcl.2010.02.004

The bicyclic 5-amino-3-azabicyclo[3.3.0]octanes were shown to be effective replacements for the conformationally restricted 4-aminopiperidine ring found in several series of CCR5 antagonists.

Full text of DOI:10.1016/j.bmcl.2010.02.004

Bioorganic & Medicinal Chemistry Letters 20 (2010) 1830–1833
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Evaluation of a 4-aminopiperidine replacement in several series
of CCR5 antagonists
a,
Rémy C. Lemoine a, , Ann C. Petersen , Lina Setti a, Lijing Chen a, Jutta Wanner a, , Andreas Jekle b,
*
Gabrielle Heilek b, André deRosier b, Changhua Ji b, David M. Rotstein a
a Department of Medicinal Chemistry, Roche Palo Alto, 3431 Hillview Avenue, Palo Alto, CA 94304, USA
b Department of Viral Diseases, Roche Palo Alto, 3431 Hillview Avenue, Palo Alto, CA 94304, USA
a r t i c l e i n f o
a b s t r a c t
Article history:
The bicyclic 5-amino-3-azabicyclo[3.3.0]octanes were shown to be effective replacements for the con-
formationally restricted 4-aminopiperidine ring found in several series of CCR5 antagonists.
Ó 2010 Elsevier Ltd. All rights reserved.
Received 6 January 2010
Revised 28 January 2010
Accepted 1 February 2010
Available online 6 February 2010
Keywords:
5-Amino-3-azabicyclo[3.3.0]octane
4-Aminopiperidine
Replacement
CCR5 antagonists
Chemokine receptor
In addition to its role as a receptor on inflammatory leucocytes,
CCR5 is also the primary co-receptor for macrophage-tropic HIV-1.
Since its discovery, CCR5 has proven to be an extraordinary target
for the pharmaceutical industry, with demonstrated therapeutic
applications in HIV-treatment as well as potential applications in
various chronic or acute inflammatory diseases. Over the last
10 years or so, many CCR5 antagonists chemotypes have been ex-
plored.1 These efforts led to the discovery, optimization and clini-
cal development of several compounds. For example, maraviroc
(SelzentryÒ) was the first CCR5 antagonist approved for the treat-
ment of HIV-1 infection.
We recently described a new template based on the bicyclic
5-amino-3-azabicyclo[3.3.0]octane system (template 1) and
showed it was similar to maraviroc’s 3-amino-8-azabicyclo[3.2.1]-
octane core system.2 Since, the 8-azabicyclo[3.2.1]octane system
can be seen as a conformationally restricted 4-aminopiperidine ring,
we hypothesized that template 1 might also replace the conforma-
tionally restricted 4-aminopiperidine ring found in several CCR5
antagonists including vicriviroc from Schering Plough and ICBN-
9471 from Incyte (Fig. 1). The alternative template could also be
utilized as a replacement in a Roche series, as represented by com-
pound 1.3 Compound 1 contains the four pharmacophore elements
found in most series of CCR5 antagonists: a tertiary amine, two
hydrophobic groups in the western portion of the molecule (hence-
forth referred to as the tail), and one head heteroaryl group in the
eastern portion of the molecule (the head).
Since one of the key interactions between CCR5 and an antago-
nist involves a salt bridge between the tertiary amine of the antag-
onist and a glutamic acid in the CCR5 binding site, we wanted to
evaluate the possibility of a difference in pKa between the basic
amine of the conformationally restricted 4-aminopiperidine in vic-
riviroc, INCB-9471, and compound 1 and that of template 1. The
calculated pKa values of the basic amine of the 4-aminopiperidine
ring in vicriviroc, INCB-9471, and compound 1 were, within the
margin of error, the same as that of the basic amine of the corre-
sponding compounds containing template 1.4 So, we anticipated
that the only difference between the two ring systems would be
structural and conformational.
Conformational analysis showed a good overlap (Fig. 2) of the
lowest energy conformations of a representative example of the
key structural features in vicriviroc and INCB-9471 (structure 1)
and the corresponding example containing template 1 (structure
2). In particular, both structures presented the basic amine in the
same position, with the lone pair in an axial orientation. With
the basic nitrogen atoms in perfect alignment, the only difference
between the two structures was seen in the distance between
atoms 2(20) and 4(40). In the case of structure 2, containing tem-
plate 1, the distance was longer than in the structure containing
the 4-aminopiperidine, structure 1 (6.34 Å and 5.3 Å, respectively).
* Corresponding author. Tel.: +1 650 855 5774; fax: +1 650 855 5237.
E-mail address: remy.lemoine@roche.com (R.C. Lemoine).
Present address: Discovery Chemistry, Hoffmann-La Roche, 340 Kingsland Street,
Nutley, NJ 07110 USA.
0960-894X/$ - see front matter Ó 2010 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2010.02.004

R. C. Lemoine et al. / Bioorg. Med. Chem. Lett. 20 (2010) 1830–1833
1831
O
Vicriviroc
INCB-9471
tail
compound 1
O
O
N
N
N
O
N
N
N
N
O
O
O
O
F
F
F
N
N
F
F
N
F
N
N
N
N
N
head
O
template 1
template 1
O
template 1
H
R
H
H
N
X
N
N
N
N
N
O
O
O
F
O
N
O
N
N
F
F
H
H
F
R
R
H
F
F
R
series A
series B
series C
X = H, CH3
Figure 1. Proposed replacement of the conformationally restricted 4-aminopiperidine in vicriviroc, INCB-9471 and compound 1 with template 1.
These analogs were tested in a RANTES binding inhibition assay,
RANTES being one of the natural chemokine ligands of CCR5, and in
a HIV-1 antiviral assay (Table 1).9 Compounds 4–6 in series A were
devoid of binding inhibition and antiviral activity at the highest
concentrations tested in the assays, which suggested that the con-
formationally restricted 4-aminopiperidine ring of this particular
series could not be replaced by template 1.
Compound 7 in series B was active in the binding inhibition as-
say but inactive in the antiviral assay. Interestingly, compound 8
had the same binding inhibition as compound 7, but was active
in the antiviral assay. This discrepancy could be explained by the
accepted mechanism of action of antiviral CCR5 antagonists in
which the antagonist binds to the receptor causing a change in
conformation which itself prevents interaction of the CCR5 with
the HIV-1 gp120 envelop protein. In other words, two CCR5 antag-
onists could have the same binding inhibition, but different antivi-
ral activities if one causes a better change of receptor conformation
than the other. Mechanistically, it is still not clear to us why one
antagonist would induce a conformational change leading to a bet-
ter antiviral activity than another antagonist. Due to the discrep-
ancy between the RANTES binding inhibition assay and the
functional antiviral assay, we used the binding inhibition assay
as a first line assay, while we only compared compounds with each
other based on their functional antiviral activity. Introduction of
more potent head groups10 such as the pyridine and the cyanopyr-
idine increased antiviral activity (e.g., 8 and 9). This indicated to us
that the decrease of potency observed by the introduction of tem-
plate 1 in INCB-9471 could be compensated for, in this series, by
fine-tuning of the head substituent. These results proved that
while the introduction of the bicyclic template could lead to diver-
gent SARs from the parent series, further optimization could lead
to active compounds.
Figure 2. Overlaps of the lowest energy conformations of structure 1 (orange) and
structure 2 (blue). (a) Overlaps were performed in MOE5 using atoms 1, 2, 3, and 4
as anchoring points and were not manually modified. (b) Conformations were
generated in Maestro6 (OPLS-2005 force field, CHCl3 as solvent and distance-
dependent dielectric constant of 2 to mimic the hydrophobic nature of the CCR5
binding site) and processed using MOE.
This indicated to us that the head substituent in compounds of ser-
ies A and B might not be able to overlap optimally with that of the
corresponding compounds containing the 4-aminopiperidine tem-
plate. However, with these encouraging conformational results and
keeping in mind the flexibility of the CCR5 receptor, we decided to
prepared representative compounds in series A, B, and C. We did
not perform a conformational comparison of compounds from ser-
ies C with compound 1, but hypothesized that the result would be
similar to that we observed in the case of series A and B.
Compounds in series A and B were prepared according to
Scheme 1. Intermediate 2a was prepared according to literature
procedures.7 Intermediate 2b was prepared according to a slight
modification of literature procedures.8 After hydrolysis of the boc
group, the piperazines were coupled with ketone 3.2 In both in-
stances, the endo/exo ratio of the products could not be deter-
mined due to the complexity of the 1H NMR spectra of the
products created by the presence of several amide rotational iso-
mers. However, the prior observation of the quasi stereospecific
behavior of ketone 3 toward reductive N-alkylation suggested that
the endo isomer could have been formed predominantly.2 It is
noteworthy to point out as well that during our conformational
analysis, we observed that every conformations of structure 2
within 5 kcal/mol of the energy minimum showed the endo con-
formation. Hydrolysis of the pyrrolidine protecting group and reac-
tion with several carboxylic acids using standard amide coupling
procedures provided compounds 4–9.
With these encouraging results, we finally explored the replace-
ment of the conformationally restricted 4-aminopiperidine of com-
pound 1 with template 1. Compounds 13–20 were prepared
according to Scheme 2.
Intermediate 10 was prepared according to literature proce-
dures.11 After hydrolysis of the protecting group, the piperidine
was reacted with ketone 3 to give compound 11. Introduction of
the ipso methyl group in compound 12 was performed in two steps
by treating 10 with ketone 3 in the presence of titanium tetraiso-
propoxide, diethylzinc cyanide, and treatment of the intermediate
with methylmagnesium bromide. Here as well, the ratio of endo
and exo isomers could not be determined but was assumed to be
mostly in favor of the endo isomer. The tail substituents were
introduced by alkylation with the appropriate bromide or tosy-
lates. The head substituents were finally introduced after the

1832
R. C. Lemoine et al. / Bioorg. Med. Chem. Lett. 20 (2010) 1830–1833
H
3
O
2
N
Boc
R1
R1
(a)
R1
H
H
N
N
N
N
N
N
NH
Boc
(b)
N
N
Boc
H
O
O
(a) (c)
R1 =
a
b
F
F
F
R1
F
F
H
F
N
O
x
y
z
R2 =
H
4-9
N
N
R2
N
N
N
Scheme 1. Reagents and conditions. Reagents and conditions: (a) HCl 4 M in dioxane, CH2Cl2, rt, 2 h; (b) ketone 3, NaBH(OAc)3, CH2Cl2, rt (69%, 83% over two steps for R1 = a,
R1 = b, respectively); (c) R2–COOH, EDCI, HOBt, DIPEA, CH2Cl2, rt.
methyl 4-ethoxybenzoate as starting material. As far as R1 = d
was concerned, direct alkylation of methyl 4-hydroxybenzoate
with cyclopropylbromide did not provide any cyclopropoxybenzo-
ate, so the cyclopropyl was introduced via a Simmons–Smith reac-
tion of the vinylic ether.
Table 1
RANTES binding inhibition and antiviral activity of compounds 4–9
Compounds
Bindinga (nM)c
Antiviralb (nM)c
R1
R2
4
5
6
7
8
9
a
a
a
b
b
b
x
y
z
x
y
z
>500
>500
>500
92
98
45
>625
>625
>625
>625
357
Compounds 13–20 were tested in the RANTES binding inhibi-
tion and antiviral assays (Table 2).9
As it was observed earlier, introduction of template 1 in this ser-
ies led to a decrease in antiviral activity (e.g., compound 13 com-
pared to compound 1). Interestingly the benefit of having the
ipso methyl observed in the SAR optimization that led to the iden-
tification of compound 13 did not translate in this particular series,
with compound 15 being virtually inactive in the antiviral assay. In
this series as well, the decrease in potency could be compensated
by the introduction of a more potent head (compounds 14 and
16), by the introduction of a different tail (compound 17), or by
the combination of both (compound 18). Compound 18 was the
most active of the series in the antiviral assay, with an IC50 of
4 nM. It is noteworthy to point out the outstanding boost of po-
tency observed by the introduction of the cyanopyridine head. In-
deed, while compound 15 was virtually inactive in the antiviral
assay (IC50 P 625 nM), compound 17 had an antiviral IC50 of
19 nM. Unfortunately, we observed that the introduction of the
cyanopyridine head led to a decrease in metabolic stability (data
not shown), so we decided to focus on increasing potency by
changing the tail substituent while keeping the pyrimidines head,
our most metabolically stable substitutent.5 Switching the tail sub-
stituent from a tetrahydropyranyl (compound 13) to a 4-eth-
oxycyclohexyl (compound 18) increased potency about 14-fold.
59
a
b
c
Binding inhibition (IC50) of [128I]-RANTES to CCR5-expressing CHO cells.
Replication inhibition (IC50) of R5 HIVNLBal in JC53-BL cells.
Values are means of at least two experiments.
hydrolysis of the pyrrolidine protecting group and reaction with
the appropriate carboxylic acids using standard amidation reaction
conditions.
The bromide R1–Br in which R1 = a was prepared according to
literature procedures.10 The tosylate R1–OTs in which R1 = c was
prepared from the commercially available methyl 4-isopro-
poxybenzoate (Scheme 3). The phenyl ring was hydrogenolyzed
using rhodium to give a 9/1 mixture of cis and trans 4-alkoxy
cyclohexyl methyl carboxylates which were equilibrated under ba-
sic condition to give a 1/1 mixture of isomers. The ester was re-
duced using lithium aluminium hydride and the primary alcohol
was treated with tosyl chloride. At this stage, the cis and trans iso-
mers could be separated using silica gel chromatography. The tos-
ylate R1–OTs in which R1 = b was prepared the same way using
(a) (b)
(e)
R1
HN
O
HN
O
N
X
X
H
O
H
N
or (a) (c) (d)
N
N
O
O
O
Boc
O
O
N
N
Boc
Boc
10
11, X = H
H
H
X= H, CH3
12, X = CH3
(a) (f)
O
O
O
O
13-20
O
R1
N
X
H
N
N
N
N
N
N
O
O
R2
H
R1 =
a
b
c
d
R2 =
x
y
z
X= H, CH3
N
Scheme 2. Synthesis of compounds in series C. Reagents and conditions: (a) HCl 4 M in dioxane, CH2Cl2, rt, 2 h; (b) ketone 3, NaBH(OAc)3, CH2Cl2, rt (69% over two steps); (c)
ketone 3, Ti(OiPr)4, Et2AlCN, CH2Cl2, rt; (d) MeMgBr, THF, rt (37% over two steps); (e), R1–Br or R1–OTs, NaH, DMF, rt; (f) R2–COOH, EDCI, HOBt, DIPEA, CH2Cl2, rt.

R. C. Lemoine et al. / Bioorg. Med. Chem. Lett. 20 (2010) 1830–1833
1833
O
O
O
O
O
O
(a)
(e)
(b)
(c)
(g)
(d)
O
O
O
O
OH
OTs
O
O
O
Cl
HO
O
O
O
(b), (c), (d)
(f)
O
O
O
OTs
O
O
O
O
Scheme 3. Synthesis of tosylates R1–OTs. Reagents and conditions: (a) Rhodium 5% on alumina, MeOH, H2, 55 psi, rt, 70%; (b) MeONa/MeOH, 50 °C, 65%; (c) LiAlH4, THF, 0 °C,
>95%; (d) TsCl, Et3N, DCM, 0 °C, rt, 41% cis, 48% trans; (e) 2-chloroethyl p-toluenesulfonate, K2CO3, DMF, 60 °C, 95%; (f) t-BuOK, THF, ꢀ15 °C, 16% (also isolated 14% of the t-
butyl ester and 50% of a mixture of t-butyl and methyl esters); (g) CH2I2, Et2Zn, CCl3CO2H, DCE, ꢀ15 °C to rt, 62% .
Table 2
be an acceptable replacement for the conformationally restricted
4-aminopiperidine system found in several series of CCR5 antago-
nists. After the introduction of the bicyclic replacement, further
SAR optimization led to the identification of active new series of
CCR5 antagonists.
RANTES binding inhibition and antiviral activity of compounds 13–20
Compounds
Bindinga (nM)c
Antiviralb (nM)c
R1
R2
X
1
13
14
15
16
17
18
19
20
—
a
a
a
a
b
b
c
—
x
z
x
z
x
y
x
x
—
H
H
CH3
CH3
H
H
H
4
14
15
25
61
44
34
23
27
6
262
9
P625
18
19
4
12
12
References and notes
1. Lemoine, R.; Wanner, J. Curr. Topics Med. Chem., in press.
2. Lemoine, R. C.; Petersen, A. C.; Setti, L.; Baldinger, T.; Wanner, J.; Jekle, A.;
Heilek, G.; deRosier, A.; Ji, C.; Rotstein, D. M. Bioorg. Med. Chem. Lett., in press.
3. Rotstein, D. M.; Gabriel, S. D.; Makra, F.; Filonova, L.; Gleason, S.; Brotherton-
Pleiss, C.; Setti, L. Q.; Trejo-Martin, A.; Lee, E. K.; Sankuratri, S.; Ji, C.; de Rosier,
A.; Dioszegi, M.; Heilek, G.; Jekle, A.; Berry, P.; Weller, P.; Mau, C.-I. Bioorg. Med.
Chem. Lett. 2009, 1918, 5401.
4. pKa values were calculated using Moka Linux version 20090616 T.
5. MOE software version 2006.08 available from the Chemical Computing Group
Inc., 1010 Sherbrooke Street West, Montreal, Québec, Canada [www.chem
comp.com].
d
H
a
b
c
Binding inhibition (IC50) of [128I]-RANTES to CCR5-expressing CHO cells.
Replication inhibition (IC50) of R5 HIVNLBal in JC53-BL cells.
Values are means of at least two experiments.
6. Maestro software version 8.5 available from Schrodinger Software Inc., 101 SW
Main Street, Suite 1300, Portland, OR 97204, USA [www.schrodinger.com].
7. Ramanathan, R.; Ghosal, A.; Miller, M. W.; Chowdhury, S. K.; Alton, K. B. U.S.
Pat. Appl. Publ. US20060105964.
8. Xue, C.-B.; Cao, G.; Huang, T.; Chen, L.; Zhang, K.; Wang, A.; Meloni, D.; Anand,
R.; Glenn, J.; Metcalf, B. W. U.S. Pat. Appl. Publ. US2005261310. In the key
reaction, (R)-1-Boc-3-methyl-piperazine was used instead of the fully
functionalized intermediate.
Further exploration of the ether alkyl substituent did not signifi-
cantly improve potency (compounds 19 and 20 compared to com-
pound 18). This indicated to us that we had reached the maximum
optimization potential of this series. Compound 17 was about two-
fold more potent than compounds 19 and 20 in the binding inhibi-
tion assay, but was 27-fold less potent in the antiviral assay. This
discrepancy showed that slight modifications in the tail substitu-
tion pattern could have a dramatic effects on antiviral activity in
the absence of significant change in the ability to bind to the
receptor.
9. For details on these assays, please see Melville, C. R.; Rotstein, D. M. PCT Int.
Appl. WO2008119663.
10. Rotstein, D. M.; Melville, C. R.; Padilla, F.; Cournoyer, D.; Lee, E. K.; Lemoine, R.;
Petersen, A. Setti, L. Q.; Wanner, J.; Chen, L.; Filonova, L.; Loughhead, D.; Manka,
J.; Lin, X.-F.; Gleason, S.; Sankuratri, S.; Ji, C.; deRosier, A.; Dioszegi, M.; Heilek,
G.; Jekle, A.; Berry, P.; Mau, C.-I.; Weller, P. Bioorg. Med. Chem. Lett., in
preparation.
In conclusion, as far as functional activity is concerned, the
5-amino-3-azabicyclo[3.3.0]octane bicyclic system was shown to
11. Gabriel, S. D.; Rotstein, D. M. U.S. Pat. Appl. Publ. US2005176703.