Amine substituted N-(1H-benzimidazol-2ylmethyl)-5,6,7,8-tetrahydro-8-quinolinamines as CXCR4 antagonists with potent activity against HIV-1

Article abstract of DOI:10.1016/j.bmcl.2009.07.037

Several novel amine substituted N-(1H-benzimidazol-2ylmethyl)-5,6,7,8-tetrahydro-8-quinolinamines were synthesized which had potent activity against HIV-1. The synthetic approaches adopted allowed for variation of the substitution pattern and resulting ch

Full text of DOI:10.1016/j.bmcl.2009.07.037

Bioorganic & Medicinal Chemistry Letters 19 (2009) 5048–5052
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Amine substituted N-(1H-benzimidazol-2ylmethyl)-5,6,7,8-tetrahydro-8-quino-
linamines as CXCR4 antagonists with potent activity against HIV-1
a
a
a
Kristjan S. Gudmundsson a, , Paul R. Sebahar , Leah D’Aurora Richardson , John F. Miller ,
Elizabeth M. Turner a, John G. Catalano a, Andrew Spaltenstein a, Wendell Lawrence b,
Michael Thomson b, Stephen Jenkinson c
*
a Department of Medicinal Chemistry, Metabolic and Virology Center of Excellence for Drug Discovery, GlaxoSmithKline Research & Development, Five Moore Drive,
Research Triangle Park, NC 27709-3398, USA
b Department of Virology, Metabolic and Virology Center of Excellence for Drug Discovery, GlaxoSmithKline Research & Development, Five Moore Drive,
Research Triangle Park, NC 27709-3398, USA
c Department of Biochemical and Analytical Pharmacology, Metabolic and Virology Center of Excellence for Drug Discovery, GlaxoSmithKline Research & Development,
Five Moore Drive, Research Triangle Park, NC 27709-3398, USA
a r t i c l e i n f o
a b s t r a c t
Article history:
Several novel amine substituted N-(1H-benzimidazol-2ylmethyl)-5,6,7,8-tetrahydro-8-quinolinamines
were synthesized which had potent activity against HIV-1. The synthetic approaches adopted allowed
for variation of the substitution pattern and resulting changes in antiviral activity are highlighted. This
led to the identification of compounds with low and sub-nanomolar anti-HIV-1 activity.
Ó 2009 Elsevier Ltd. All rights reserved.
Received 16 June 2009
Revised 6 July 2009
Accepted 7 July 2009
Available online 10 July 2009
CXCR4 is a 7-transmembrane chemokine receptor.1 Unlike most
of the other receptors within the chemokine family, CXCR4 has
only one known natural ligand, stromal cell-derived factor (SDF-
1). CXCR4, and its interaction with SDF-1, has been shown to play
a role in a number of physiological processes, including the homing
of immune cells to sites of inflammation2 and maintaining the cel-
lular micro-environment of the bone marrow.3 The CXCR4/SDF-1
interaction is involved with metastatic spread and in directly reg-
ulating the growth and/or survival of several types of cancer.4
CXCR4 is a co-receptor for some strains of HIV-1 that are associated
with late stage disease and progression to AIDS.5 The CCR5 (R5)
utilizing HIV-1 strains are generally associated with the initial
infection and asymptomatic phase, however as the disease pro-
gresses towards AIDS, variant forms of the virus emerge that can
utilize both CCR5 and CXCR4 chemokine receptors (dual tropic
viruses) or solely utilize the CXCR4 chemokine receptor (CXCR4
tropic) to gain entry and infect new host cells.6
ALX-40-4C,9 CTCE-9908,10 FC131,11 and POL3026.12 Small mole-
cule CXCR4 antagonists, have been developed by Kureha
(KRH1636)13 and AnorMED (acquired by Genzyme in 2006);
(AMD3100, Plerixafor, Mozobil,14 and AMD07015). AMD3100 was
recently approved by the FDA for stem cell mobilization. We were
interested in further studying AMD070 (1, Fig. 1).
We were especially interested in investigating whether more
potent analogs of AMD070 could be obtained by moving the basic
side chain to the benzimidazole portion of the molecule. In addi-
tion we wanted to explore the effect of conformationally restrain-
ing the side chain. Herein we describe the synthesis and antiviral
SAR of a series of N-(1H-benzimidazol-2yl-methyl)-5,6,7,8-tetra-
hydro-8-quinolinamine derivatives with basic side chains attached
to the N-1 and C-4 position of the benzimidazole.
For the synthesis of benzimidazole derivatives containing basic
side chains attached to the benzimidazole N-1 nitrogen the first
Therefore, CXCR4 antagonists have potential therapeutic uses
for HIV infection and several other indications, including mobiliza-
tion of hematopoietic stem cells from the bone marrow.7 In addi-
tion, by blocking the homing of inflammatory cells to inflamed
joints, CXCR4 antagonists may be of value in the treatment of rheu-
matoid arthritis.8
N
N
1
NH2
Several CXCR4 antagonists, both peptides and small molecules,
have been described. Peptide-based CXCR4 antagonists include
HN
N
* Corresponding author. Tel.: +44 (0) 1784 482810.
E-mail address: ksgudmundsson@gmail.com (K.S. Gudmundsson).
Figure 1. AMD070 (1).
0960-894X/$ - see front matter Ó 2009 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2009.07.037

K. S. Gudmundsson et al. / Bioorg. Med. Chem. Lett. 19 (2009) 5048–5052
5049
Table 1
step involved coupling of 2-(aminomethyl)benzimidazole 2 and
tetrahydroquinolinone 316 via reductive amination to give 4. Meth-
ylation of 4 with formaldehyde under reductive conditions gave 5.
The basic side chains were subsequently installed using one of two
methods outlined in Scheme 1. Treatment of 5 with bromoalkyl-
nitriles 6a and 6b under basic conditions afforded nitrile interme-
diates that were subjected to Raney Nickel reduction to afford
primary amine derivatives 9 and 11, respectively. Alternatively,
alkylation of 5 with Boc-protected chloroalkylamines 7a and 7b,
Anti-HIV activity for N-1 substituted benzimidazoles
N
N
2
1
3
N
N R
followed by TFA deprotection, gave compounds
respectively.
8 and 10,
Changing the tether length between the benzimidazole N-1 and
the basic nitrogen (Table 1) showed that a 3-carbon propylene
linker (as for 9) was optimal for HIV activity, while the shorter
(2 carbon) or longer (4–5 carbon) linkers gave compounds with
5–10-fold less anti-HIV activity. Alkylation of the primary amino
group of 9 gave the tertiary amine 12, which also showed good
anti-HIV activity. Similar activity was observed for the guanidine
derivative 13. However reducing the basicity of the amine via
trifluoroacetylation gave compound 14, which showed 10-fold
reduction in antiviral activity.
We next investigated the effect of shifting the basic side chain
from the N-1 nitrogen to the C-4 position of the benzimidazole.
For initial exploration of the optimum distance between the benz-
imidazole and the basic amine, several linkers tethering the amine
to the C-4 position of the benzimidazole via an amide were pre-
pared (Scheme 2). Starting from commercially available methyl
2-amino-3-nitrobenzoate (15), hydrogenation gave the phenylene-
diamine 16. Coupling of Cbz-protected glycine and 16, followed by
heating in acetic acid to affect imidazole ring closure, gave the
methyl 4-benzimidazolecarboxylate 17. The tetrahydroquinoline
was attached by reductive amination with 17, to give 18. A second
reductive amination with formaldehyde gave the versatile methyl
4-benzimidazolecarboxylate intermediate 19. Saponification gave
20 and coupling with suitable amines gave desired amides (21–
23), with antiviral activity shown in Table 2.
a
b
Compd
R
IC50
(
lM)
CC50 (lM)
5
8
H
1.35
5.3
>20
NH2
0.197
0.044
0.144
0.228
0.017
9
10
11
12
>20
2.9
NH2
NH2
4.5
NH2
N
16.8
NH
13
14
0.026
>20
N
H
NH2
O
0.243
0.010
10.4
>10
N
H
CF3
1c
AMD070
For these amide-linked analogs, the ethylene diamine derived
amine 21 showed the best activity (Table 2), while amides with
longer tethers (22 and 23) were about 10-fold less potent. This
prompted us to synthesize an additional set of compounds (24–
a
HOS cells (expressing hCXCR4/hCCR5/hCD4/pHIV-LTR-luciferase), HIV-1,
CXCR4 strain (IIIB). Compounds were tested for their ability to block infection of the
HOS cell line. IC50 is the concentration at which 50% efficacy in the antiviral assay is
observed Ref. 18.
b
CC50 is the concentration at which 50% cytotoxicity is observed in the HOS cell
line.
c
AMD070 included for comparison.
N
N
26), with the basic nitrogen incorporated into an imidazole or
piperazine heterocycle, and the distance between the benzimid-
azole and the basic nitrogen approximately the same as for the
ethylene diamine 21. These derivatives (24–26) showed similar
anti-HIV activity as 21.
N
NH2
O
NH
N
3
4
N
H
a
b
HN
2
To preclude any possible metabolic instability associated with
the amide in analogs 21–26, a series of alkyl analogs was synthe-
sized. The versatile 4-benzimidazolecarboxylate 19, was used as
the starting point. First the methyl ester was reduced to the alco-
hol, followed by oxidation to the aldehyde 27 (Scheme 3). Alde-
hyde 27 was used to prepare compounds 28–31 by reductive
aminations, where the basic side chain is linked to the C-4-position
of the benzimidazole via a methylamine linker. While 28 and 29
showed only limited activity, compounds 30 and 31 looked prom-
ising. Notable is the >10-fold difference in activity between 29 and
31, where the more conformationally constrained piperazine
derivative 31 shows much more potent activity. To pursue the
replacement of the amide linker further, propylamine derivatives
were synthesized from the aldehyde 27. Wittig olefination of 27,
followed by LiAlH4 reduction gave alcohol 32 (Scheme 3). Oxida-
tion of 32 to the aldehyde, followed by reductive amination gave
Br
CN
n
6a: n=2
6b: n=4
N
N
N
N
N
5
c or d
N
n NH2
Cl
NHBOC
N
NH
n
8-11
for n = 2-5
7a: n=2
7b: n=4
Scheme 1. Reagents and conditions (a) NaBH4, MeOH, 20 °C, 8 h (87%); (b) H2CO
(37% aqueous), NaBH(OAc)3, AcOH, ClCH2CH2Cl, rt, 18 h, 82%; (c) 6, K2CO3, DMF, 80–
100 °C (50–75%); then H2 (50 psi), Raney Ni, 7 N NH3 in MeOH, rt, 16 h (70–85%);
(d) 7, K2CO3, DMF, 80–100 °C (40–80%); then CF3COOH, CH2Cl2, rt, 8 h (90–100%).

5050
K. S. Gudmundsson et al. / Bioorg. Med. Chem. Lett. 19 (2009) 5048–5052
Table 2
NH2
NH
Anti-HIV activity and cytotoxicity of substituted N-(1H-benzimidazol-2ylmethyl)-
5,6,7,8-tetrahydro-8-quinolinamines
NO2
NH2
NH2
NH2
N
a
b, c
1
N
CO2Me
COOMe
15
COOMe
16
N
2
5
17
N
N
3
4
H
R
N
a
b
N
N
Compd
R
IC50
(lM)
CC50
(lM)
O
3
19
N
N
NH
18
O
O
d
e
21
0.027
0.134
>10
NH2
HN
HN
N
N
H
CO2Me
CO2Me
22
23
24
25
26
28
29
30
31
>20
>20
>10
>20
>10
>20
>20
>20
12
N
H
NH2
N
N
O
O
20
N
N
21
N
N
0.396
0.019
0.046
0.033
1.3
NH2
N
H
f
g
HN
HN
NH2
H
N
HN
CO2H
N
N
H
O
Scheme 2. Reagents and conditions (a) Pd/C (10% w/w), H2 (1 atm), MeOH, 16 h, rt
(99%); (b) BOPCl, carbobenzyloxyglycine (Cbz-glycine), Et(iPr)2N, CH3CN, 16 h, rt;
then AcOH, 70 °C, 150 min (87%); (c) Pd/C (10% w/w), H2 (1 atm), EtOH, 16 h, rt; (d)
3, NaBH(OAc)3, AcOH, ClCH2CH2Cl, rt, 2 h; (e) H2CO (37% aqueous), NaBH(OAc)3,
AcOH, ClCH2CH2Cl, rt, 18 h (68% from 17); (f) LiOH (aq), MeOH, THF, 70 °C, 72 h
(84%); (g) BOPCl, Et(iPr)2N, CH3CN, H2NCH2CH2NHBoc, 16 h, rt; then MP-TsOH, 7 M
NH3 in MeOH (10%).
O
N
NH
O
N
N
C-4 linked propylamine derivatives 33–36, all of which showed
very impressive anti-HIV activity. We subsequently became inter-
ested in studying whether the basic amine could be incorporated
into a heterocycle, such as piperazine, given our previous success
with improving activity of flexible amines by incorporation into
the conformationally constrained piperazine.
The piperazine derivatives were synthesized from 3-chloro-2-
nitroaniline (37) as shown in Scheme 4. Condensation of 37 and
Boc-protected piperazine, followed by catalytic hydrogenation
gave phenylenediamine 38. BOPCl catalyzed coupling of 38 with
N-Cbz-glycine followed by acid catalyzed ring closure gave pro-
tected methylaminobenzimidazole 39. Removal of the Cbz-pro-
tecting group gave amine 40. Compound 41 was obtained by
coupling ketone 3 with amine 40 by reductive amination. Alkyl-
ation of 41 gave 42. Finally, acidic removal of the Boc group gave
piperazine 43 and reductive amination of 43 with formaldehyde
gave the desired methylpiperazine 44. Methylpiperazine derivative
44 showed extremely potent anti-HIV activity at 2 nM, which was
about 10-fold more active than AMD070 or other derivatives we
had prepared.
NH2
NH2
0.54
N
H
HN
N
0.041
0.013
N
H
N
NH
33
34
35
0.024
0.022
0.023
10
The potent anti-HIV activity of the racemate 44 prompted us to
prepare this compound in a chirally pure form as outlined in
Scheme 5. Thus, the known S-4-(methoxyphenylethyl)amine
derivative 45 was used as a chiral starting material.17 Reductive
amination with formaldehyde, followed by deprotection with tri-
fluoroacetic acid gave tetrahydroquinoline methylamine 46. Treat-
ment of 46 with bromobenzylacetate in the presence of base,
followed by removal of the benzyl group with Pd on carbon under
a hydrogen atmosphere gave glycinate 47. Amide 49 was formed
by BOPCl mediated coupling of 47 and 48. Finally the desired S-ste-
NH2
7.5
8.2
N
N

K. S. Gudmundsson et al. / Bioorg. Med. Chem. Lett. 19 (2009) 5048–5052
5051
NCBZ
Table 2 (continued)
NH2
NH2
a
b
Compd
R
IC50
(l
M)
CC50
8.7
(lM)
39
N
NH
N
a
b
NO2
NH2
N
36
0.025
0.271
0.006
Cl
37
N
NBoc
38
NBoc
42
43
>10
>20
N
N
NBoc
NH
NH2
NH
N
41
N
NH
O
3
40
N
c
d
HN
N
N
NBoc
44 (rac)
50 (S)
51(R)
0.002
14
N
N
N
N
N
N
N
NBoc
0.0006
12.5
12.3
N
N
N
N
42
N
N
43 R=H
f
e
g
HN
HN
44 R=Me
0.0069
0.010
N
NBoc
N
N R
1c
AMD070
a
HOS cells (expressing hCXCR4/hCCR5/hCD4/pHIV-LTR-luciferase), HIV-1,
CXCR4 strain (IIIB). Compounds were tested for their ability to block infection of the
HOS cell line. IC50 is the concentration at which 50% efficacy in the antiviral assay is
observed Ref. 18.
Scheme 4. Reagents and conditions (a) t-butyl 1-piperazinecarboxylate, K2CO3,
DMF, 130 °C, 72 h (40%); then Pd/C (10% w/w), H2 (1 atm), EtOH, 3 h, rt (99%); (b)
Cbz-Gly, BOPCl, Et(iPr)2N, MeCN, 14 h; then AcOH, 65 °C, 3 h (69% from 40); (c) Pd/C
(10% w/w), H2 (1 atm), EtOH, 16 h, rt (99%); (d) NaBH(OAc)3, AcOH, ClCH2CH2Cl, rt,
16 h; (e) CH2O (37% aq), AcOH, NaBH(OAc)3, ClCH2CH2Cl, rt, 24 h (35% from 41); (f)
HCl (4 N in 1,4-dioxane), MeOH, rt, 12 h (76%); (g) CH2O (37% aq), AcOH,
NaBH(OAc)3, ClCH2CH2Cl, rt, 24 h (60%).
b
CC50 is the concentration at which 50% cytotoxicity is observed in the HOS cell
line.
c
AMD070 is included for comparison.
a, b
N
c,d
N
N
N
N
OMe
HN
HN
46
N
N
N
N
45
27
28
19
N
N
a
CO2Me
c
b
NH2
H2N
HN
HN
HN
N
N
N
CHO
N
NH2
49
N
48
N
47
e
O
NH
NH2
N
O
OH
N
N
32
N
33
N
N
N
N
d
N
N
50
HN
N
HN
f
HN
OH
NH2
N
N
Scheme 3. Reagents and conditions (a) LiAlH4, THF, 0 °C (96%); then DMSO (COCl)2,
TEA, CH2Cl2 (49%); (b) NH4OAc, MeOH, NaCNBH3, 50 °C, 16 h (99%); (c)
Ph3PCHCO2CH3, toluene, 16 h; then LiAlH4, THF; then Pd/C (10% w/w), H2 (50 psi),
MeOH, 48 h, rt (37% from 29); (d) IBX Resin, CH2Cl2 (99%); then NH4OAc, MeOH,
NaCNBH3, 50 °C, 16 h (13%).
Scheme 5. Reagents and conditions (a) CH2O (37% aq), AcOH, NaBH(OAc)3, ClCH2-
CH2Cl, 12 h, rt; (b) CF3COOH, CH2Cl2, 12 h, rt (91% for a and b); (c) BrCH2COOBn,
Et(iPr)2N, CH2Cl2, 12 h, rt; (d) Pd/C (10% w/w), H2 (1 atm), EtOH, 16 h, rt (80% for c and
d); (e) 48, BOPCl, Et(iPr)2N, MeCN, 14 h, rt; (f) AcOH, 70 °C, 1 h (75% from 47).
reoisomer 50 was formed by treating 49 with acetic acid at
elevated temperature.
The S-enantiomer 50 showed impressive sub-nM anti-HIV
activity, while the R-enantiomer (51) was over 10-fold less active.
Pharmacokinetic studies in rats showed 50 to be orally bioavail-
able. Screening against a panel of enzymes and receptors (PanLabs)
did not show enzyme or receptor inhibition at concentrations close

5052
K. S. Gudmundsson et al. / Bioorg. Med. Chem. Lett. 19 (2009) 5048–5052
10. NCI Cancer Bulletin April 26, 2005, 17, 4.
to those demonstrating anti-HIV activity for 50 (over 500-fold
selectivity for all).
Because of the very good anti-HIV potency and good pharmaco-
kinetic properties, 50 was progressed for further studies and
served as a template for synthesis of additional analogs.
11. Fujii, N.; Oishi, S.; Hiramatsu, K.; Araki, T.; Ueda, S.; Tamamura, H.; Otaka, A.;
Kusano, S.; Terakubo, S.; Nakashima, H.; Broach, J. A.; Trent, J. O.; Wang, Z.;
Peiper, S. C. Angew. Chem. Int. Ed. 2003, 42, 3251.
12. DeMarco, S. J.; Henze, H.; Lederer, A.; Moehle, K.; Maukharejee, R.; Romagnoli,
B. Bioorg. Med. Chem. 2006, 14, 8396.
13. Ichiyama, K.; Yokoyama-Kumakura, S.; Tanaka, Y.; Tanaka, R.; Hirose, K.;
Bannai, K.; Edamatsu, T.; Yanaka, M.; Niitani, Y.; Miyano-Kurosaki, N.;
Takaku, H.; Koyanagi, Y.; Yamamoto, N. Proc. Natl. Acad. Sci. U.S.A. 2003,
100, 4185.
References and notes
14. De Clercq, E. Nat. Rev. Drug Disc. 2003, 2, 581.
1. Berson, J. F.; Long, D.; Doranz, B. J.; Rucker, J.; Jirik, F. R.; Doms, R. W. J. Virol.
1996, 70, 6288.
2. Buckley, C. D.; Amft, N.; Bradfield, P. F.; Pilling, D.; Ross, E.; Arenzana-Seisdedos,
F.; Amara, A.; Curnow, S. J.; Lord, J. M.; Scheel-Toellner, D.; Salmon, M. J.
Immunol. 2000, 165, 3423.
3. Ma, Q.; Jones, D.; Springer, T. A. Immunity 1999, 10, 463.
4. (a) Zlotnik, A. Int. J. Cancer 2006, 119, 2026; (b) Burger, J. A.; Kipps, T. J. Blood
2006, 107, 1761.
5. Shaheen, F.; Collman, R. G. Curr. Opin. Infect. Dis. 2004, 17, 7.
6. Schuitemaker, H.; Koot, M.; Kootstra, N. A.; Dercksen, M. W.; de Goede, R. E.;
van Steenwijk, R. P.; Lange, J. M.; Schattenkerk, J. K.; Miedema, F.; Tersmette, M.
J. Virol. 1992, 66, 1354.
7. Hendrix, C. W.; Flexner, C.; MacFarland, R. T.; Giandomenico, C.; Fuchs, E. J.;
Redpath,E.;Bridger,G.;Henson,G.W.Antimicrob.AgentsChemother.2000,44,1667.
8. (a) Matthys, P.; Hatse, S.; Vermeire, K.; Wuyts, A.; Bridger, G.; Henson, G. W.; De
Clercq, E.; Billiau, A.; Schols, D. J. Immunol. 2001, 167, 4686; (b) Tamamura, H.;
Fujisawa, M.; Hiramatsu, K.; Mizumoto, M.; Nakashima, H.; Yamamoto, N.;
Otaka, A.; Fujii, N. FEBS Lett. 2004, 569, 99.
15. (a) Bridger, G.; Skerlj, R.; Kaller, A.; Harwig, C.; Bogucki, D.; Wilson, T. R.;
Crawford, J.; McEachern, E. J.; Atsma, B.; Nan, S.; Zhou, Y.; Schols, D.; Smith, C.
D.; DiFluri, R. M. WO Patent 2003/055876.; (b) Crawford, J. B.; Zhu, Y.; Chen, G.;
Baird, I. R.; Skerlj, R. WO Patent 2006/039250.; (c) Crawford, J. B.; Chen, G.;
Gauthier, D.; Wilson, T.; Carpenter, B.; Baird, I. R.; McEachern, E.; Kaller, A.;
Harwig, C.; Atsma, B.; Skerlj, R. T.; Bridger, G. J. Org. Process Res. Dev. 2008, 12,
823; (d) Stone, N.; Dunaway, S. B.; Flexner, C.; Tierney, C.; Calandra, G. B.;
Becker, S.; Cao, Y.-L.; Wiggins, I. P.; Conley, J.; MacFarland, R. T.; Park, J.-G.;
Lalama, C.; Snyder, S.; Kallungal, B.; Klingman, K. L.; Hendrix, C. W. Antimirob.
Agents Chemother. 2007, 51, 2351.
16. (a) Kelly, T. R.; Lebedev, R. L. J. Org. Chem. 2002, 67, 2197; (b)
Tetrahydroquinolone 3 is commercially available.
17. McEachern, E. J.; Bridger, G. J.; Skupinska, K. A.; Skerlj, R. T. WO Patent 2003/
022785.
18. All compounds were also characterized pharmacologically in a cell based
functional assay and shown to be non-competitive antagonists of the CXCR4
receptor.
9. Sumner-Smith, M.; Zheng, Y.; Zhang, Y. P.; Twist, E. M.; Climie, S. C. Drugs Exp.
Clin. Res. 1995, 21, 1.