Synthesis and SAR of 2′,3′-bis-O-substituted N6, 5′-bis-ureidoadenosine derivatives: Implications for prodrug delivery and mechanism of action

Article abstract of DOI:10.1016/j.bmcl.2012.08.050

A series of 2′,3′-bis-O-silylated or -acylated derivatives of lead compound 3a (2′,3′-bis-O-tert-butyldimethylsilyl-5′- deoxy-5′-(N-methylcarbamoyl)amino-N⁶-(N-phenylcarbamoyl) adenosine) were prepared and evaluated for antiproliferative activity against a panel of murine and human cancer cell lines (L1210, FM3A, CEM, and HeLa). 2′,3′-O-Silyl groups investigated included triethylsilyl (10a), tert-butyldiphenylsilyl (10b), and triisopropylsilyl (10c). 2′,3′-O- Acyl groups investigated included acetyl (13a), benzoyl (13b), isobutyryl (13c), butanoyl (13d), pivaloyl (13e), hexanoyl (13f), octanoyl (13g), decanoyl (13h), and hexadecanoyl (13i). IC₅₀ values ranged from 3.0 ± 0.3 to >200 μg/mL, with no improvement relative to lead compound 3a. Derivative 10a was approximately equipotent to 3a, while compounds 13e-g were from three to fivefold less potent, and all other compounds were significantly much less active. A desilylated derivative (5′-deoxy-5′-(N-methylcarbamoyl) amino-N⁶-(N-phenylcarbamoyl)adenosine; 5) and several representative derivatives from each subgroup (10a-10c, 13a-13c) were screened for binding affinity for bone morphogenetic protein receptor 1b (BMPR1b). Only compound 5 showed appreciable affinity (K_d = 11.7 ± 0.5 μM), consistent with the inference that 3a may act as a prodrug depot form of the biologically active derivative 5. Docking studies (Surflex Dock, Sybyl X 1.3) for compounds 3a and 5 support this conclusion.

Full text of DOI:10.1016/j.bmcl.2012.08.050

Bioorganic & Medicinal Chemistry Letters 22 (2012) 6067–6071
Contents lists available at SciVerse ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Synthesis and SAR of 20,30-bis-O-substituted N6, 50-bis-ureidoadenosine
derivatives: Implications for prodrug delivery and mechanism of action
Jadd R. Shelton a, Christopher E. Cutler a, Megan S. Browning a, Jan Balzarini b, Matt A. Peterson a,
⇑
a Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602-5700, United States
b Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium
a r t i c l e i n f o
a b s t r a c t
A series of 20,30-bis-O-silylated or -acylated derivatives of lead compound 3a (20,30-bis-O-tert-butyldi-
methylsilyl-50-deoxy-50-(N-methylcarbamoyl)amino-N6-(N-phenylcarbamoyl)adenosine) were prepared
and evaluated for antiproliferative activity against a panel of murine and human cancer cell lines
(L1210, FM3A, CEM, and HeLa). 20,30-O-Silyl groups investigated included triethylsilyl (10a), tert-butyldi-
phenylsilyl (10b), and triisopropylsilyl (10c). 20,30-O-Acyl groups investigated included acetyl (13a), ben-
zoyl (13b), isobutyryl (13c), butanoyl (13d), pivaloyl (13e), hexanoyl (13f), octanoyl (13g), decanoyl
Article history:
Received 5 June 2012
Revised 1 August 2012
Accepted 13 August 2012
Available online 21 August 2012
Keywords:
Purine nucleosides
Bio-active adenosine derivatives
Antiproliferative nucleosides
BMPR1b inhibitors
(13h), and hexadecanoyl (13i). IC50 values ranged from 3.0 0.3 to >200 lg/mL, with no improvement
relative to lead compound 3a. Derivative 10a was approximately equipotent to 3a, while compounds
13e–g were from three to fivefold less potent, and all other compounds were significantly much less
active. A desilylated derivative (50-deoxy-50-(N-methylcarbamoyl)amino-N6-(N-phenylcarbamoyl)adeno-
sine; 5) and several representative derivatives from each subgroup (10a–10c, 13a–13c) were screened for
binding affinity for bone morphogenetic protein receptor 1b (BMPR1b). Only compound 5 showed appre-
ciable affinity (Kd = 11.7 0.5 lM), consistent with the inference that 3a may act as a prodrug depot form
of the biologically active derivative 5. Docking studies (Surflex Dock, Sybyl X 1.3) for compounds 3a and 5
support this conclusion.
Ó 2012 Elsevier Ltd. All rights reserved.
As part of research directed toward the design, synthesis, and
biological evaluation of potential inhibitors of HIV integrase, we
discovered potent antiproliferative activities associated with a
new class of N6,50-bis-ureidoadenosine derivatives exemplified by
compounds 1–3 (Fig. 1).1 IC50 values for 1–3a (R = Ph) ranged from
and have prompted us to investigate the role of the 20,30-O-substi-
tution in this class of compounds. Herein we report the synthesis
and antiproliferative activities for a series of variously substituted
20,30-O-derivatives of the most potent of these compounds (3a),
and draw preliminary conclusions from the mechanistic implica-
tions of this SAR study.
approximately 1–8
lM against a majority of the human cancer cell
lines in the NCI-60. IC50 values for 3b–i ranged from 3–182
l
g/mL
The synthesis begins with 50-azido-50-deoxyadenosine (7) and
gives 20,30-bis-O-silylated or 20,30-bis-O-acylated products in good
to excellent yields (Scheme 1). The synthesis is very straightforward
and is amenable to scale-up. Silylation of 7 with triethylsilylchlo-
ride, tert-butyldiphenylsilylchloride, or triisopropylsilylchloride
gave compounds 8a–c in 42–60% yield. Acylation of compounds
8a–c with phenylisocyanate gave N6-phenylurea derivatives 9a–c
(54–82%). A one-pot, two-step reaction sequence involving reduc-
tion of the 50-azido group of compounds 9a–c followed by acylation
with the relatively safe and innocuous methylisocyanate surrogate,
N-methyl p-nitrophenylcarbamate,2 gave 10a–c in 66–77% yield.
20,30-Bis-O-acylated compounds 13a–c and 13d–i were obtained
via two different routes. Compounds 13a–c were obtained in good
yields via a five-step protocol analogous to the one employed in
preparing 10a–c. However, the more lipophilic 20,30-bis-O-acylated
compounds 13g–i were obtained in very low yields following this
procedure. An alternative route involving one step from compound
5 was investigated. This route was generally much more efficient,
against a panel of tumor cell lines consisting of murine leukemia
(L1210), murine mammary carcinoma (FM3A), human T-lympho-
cyte (CEM), and human cervix carcinoma (HeLa). Preliminary SAR
studies revealed that for optimal cytostatic activities (low
lM),
the N6- and 50-urea moieties are required, and substitution with
at least one 20(30) tert-butyldimethylsilyl (TBS) group is also neces-
sary. Interestingly, compounds 5 and 6 were essentially inactive
against the NCI-60 screen at 10 l
M concentrations. Similarly, 50-
carbamates 4a–i were significantly less active than the analogous
50-ureas (3a–i) against L1210, FM3A, CEM, and HeLa—in spite of
the fact that 4a–i possess nearly identical substitutions as the 50-
ureas.1a
The above observations support the conclusion that the 20,30-O-
TBS groups are necessary, but not sufficient, for biological activity
⇑
Corresponding author.
E-mail address: matt_peterson@byu.edu (M.A. Peterson).
0960-894X/$ - see front matter Ó 2012 Elsevier Ltd. All rights reserved.
http://dx.doi.org/10.1016/j.bmcl.2012.08.050

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J. R. Shelton et al. / Bioorg. Med. Chem. Lett. 22 (2012) 6067–6071
regulate expression of inhibitor of differentiation gene 1 (Id1).3
Overexpression of Id1 has been reported in a number of cancers,
including lung,4 breast,5 colon,6 ovarian,7 pancreas,8 prostate,9
and renal cancers.10 Downregulation, inhibition, and/or inactiva-
tion of Id1 have been shown to induce apoptosis in several of these
cancers.11 Inhibition of BMPR1b by the desilylated analogue of 3a,
compound 5, could constitute a plausible mechanism for the
broad-spectrum antiproliferative activity exhibited by compound
3a.12 In this context, compound 3a would most likely serve as a
prodrug form of the active species, desilylated derivative com-
pound 5.
A commonly used strategy for enhancing membrane permeabil-
ity of nucleosides has been to increase the lipophilicity by protect-
ing hydroxyls as acetyl, benzoyl, or isobutyryl esters that are
cleaved once the compound has crossed the cell membrane.13
TBS-protection has been shown to enhance the activities of a num-
ber of antiproliferative compounds, and activities of several of
these compounds have been positively correlated with the
increased lipophilicity of the biologically active derivative.14
TBS-protected cytidine has been shown to facilitate transport of
guanosine 50-monophosphate through a model membrane (in con-
junction with a lipophilic phosphonium ion co-carrier),15 and sily-
lated nucleosides have been shown to penetrate the blood–brain
barrier where it is presumed they are desilylated to generate the
active species.16 The lipophilic 20,30-bis-O-TBS groups could en-
hance membrane permeability of compound 3a and serve as a pro-
drug depot form of the active derivative compound 5.
Docking studies performed using the Surflex docking program
(Sybyl X 1.3) are supportive of such an interpretation.17 As illus-
trated in Fig. 2, the highest ranked pose for compound 5 is oriented
within the ATP binding cleft of BMPR1b (pdb 3mdy) with the 50-
urea undergoing hydrogen bonding interactions with the highly
conserved catalytic triad18 (Lys 231, Glu 244, Asp 350; Fig. 2).
The N6-phenyl urea moiety in this pose is oriented toward the sol-
vent accessible surface, which is consistent with the relative lack of
sensitivity of the antiproliferative activity of 3a–i to the substitu-
tion pattern in the N6-urea moiety.1a In contrast, the top ranked
pose for compound 3a had nearly the opposite orientation to com-
pound 5, with the N6-phenyl urea moiety undergoing nonpolar
binding interactions with the ‘gatekeeper’ residue (Leu 277; blue
residue; Fig. 2) near the end of the catalytic cleft, in close proximity
to the catalytic triad. In this pose, the very hydrophobic 20,30-bis-O-
TBS groups are exposed to the solvent accessible surface. If such a
pose were biologically relevant, substitution at the N6-urea posi-
tion would be expected to have a much greater effect on the bio-
logical activity than the negligible effect that was observed
experimentally. (The nature of the R group in 3a–i had very little
impact on their antiproliferative activities).1a Furthermore, the
hydrophobic effect resulting from protrusion of the very nonpolar
TBS groups into the aqueous environment would contribute to an
unfavorable entropic term in the overall free energy of binding.
Consistent with these modeling results is the aforementioned
observation that compound 5 binds to BMPR1b with Kd = 11.7
Figure 1.
and yields for 13d–i ranged from 46–63% (the highest yield for 13e
was 26%, even with this more efficient method, presumably due to
the steric bulk of the pivaloyl esters). As a point of comparison, only
trace amounts of 13i were obtained when the five-step sequence—
steps e, f, b, c, and d—was attempted. Finally, compounds 14a–c
were obtained in moderate to good yields (31–66%) by treating
11a–c with the aforementioned one-pot, two-step reduction/acyla-
tion (steps c and d). The antiproliferative activities for compounds
3a, 4a, 10a–c, 13a–i, and 14a–c are shown in Table 1. Interestingly,
the IC50 values for 20,30-bis-O-triethylsilyl derivative 10a were very
similar to those for the 20,30-bis-O-TBS derivative 3a. In contrast,
IC50 values for 20,30-bis-O-tert-butyldiphenylsilyl and/or 20,30-bis-
O-triisopropylsilyl derivatives (10b and 10c, respectively), were
significantly inferior to 3a. Acyl derivatives 13a–i were generally
much less active than 3a, especially the O-benzoyl, O-decanoyl,
and O-hexadecanoyl derivatives (13b, 13h, and 13i, respectively).
The O-pivaloyl, O-hexanoyl, and O-octanoyl derivatives (13e, 13f,
and 13g, respectively) exhibited nearly equivalent antiproliferative
activities, but IC50 values for these compounds were from three to
fivefold higher than those for compound 3a. Compounds 14a–c
(each of which lacks the N6-phenylurea) showed generally lower
antiproliferative activity than their corresponding N6-substituted
analogues (13a–c).
0.5
as 30
l
M), while compound 3a did not bind at concentrations as high
l
M (Fig. 3A and 3B, respectively).1a The negative impact of the
Recently, we demonstrated that compound 5 (Fig. 1) binds to
the ATP-binding site of bone morphogenetic protein receptor 1b
20,30-O-substitution on binding was also illustrated for several rep-
resentative members of the presently discussed series of 20,30-O-
derivatives of 3a, none of which showed appreciable binding to
BMPR1b in a competitive inhibition of binding experiment19 at
(BMPR1b) with low
lM affinity (Kd = 11.7 0.5 l
M).1a When
screened against a panel of 441 protein kinases, compound 5
exhibited its greatest activity against BMPR1b, inhibiting binding
of BMPR1b to an ATP-binding site ligand by approx. 50% at
M concentration. Compound 3a, in contrast, did not bind to
BMPR1b at concentrations as high as 30
membrane receptor with serine/threonine protein kinase activity.
The ATP-binding domain lies within the cytoplasm and phosphor-
ylates downstream targets (SMADs 1, 5, and 8), which in turn
10 lM concentrations (Fig. 3C). The relative reactivity of silyl pro-
tecting groups toward hydrolysis (TES > TBS ꢀ TIPS > TBDPS)20 is
in harmony with these results, and is consistent with a mechanism
involving cleavage of the silyl moiety before the nucleoside deriva-
tive can interact with its primary biological receptor.21
10
l
l
M.1a BMPR1b is a trans-
In conclusion, we have developed efficient methods for the
preparation of a variety of 20,30-O-substituted derivatives of our

J. R. Shelton et al. / Bioorg. Med. Chem. Lett. 22 (2012) 6067–6071
6069
Scheme 1. Reagents: (a) R3SiCl, imidazole, DMF; (b) PhN@C@O; (c) H2, Pd–C; (d) p-NO2-C6H4O2CNHCH3; (e) (RC@O)2O; (f) CH3OH,
D.
recently discovered antiproliferative N6,50-bis-ureidoadenosine
compounds. Bis-O-protection of 50-azido-50-deoxyadenosine with
either silyl or acyl protecting groups, followed by sequential acyl-
ation of the N6 and 50-amino groups (with phenylisocyanate or N-
methyl p-nitrophenylcarbamate, respectively) gave 20,30-O-substi-
tuted derivatives of lead compound 3a (10a–c and 13a–c) in good
to excellent yields. An alternative route from the more advanced
intermediate compound 5 gave 13d–i more efficiently than the
route applied for 13a–c. Screening of compounds 10a–c, 13a–i,
and 14a–c against a panel of murine and human cancer cell lines
did not reveal any improved activity relative to lead compound
3a. Several representative 20,30-O-substituted derivatives were
shown to lack binding affinity for BMPR1b at concentrations near
the Kd for desilylated analogue 5. Taken together, these results sug-
gest that the role of the TBS group in compound 3a may be to facil-
itate membrane permeability. Cleavage of the TBS groups within
the cytoplasm could give rise to the active derivative (5) which
previously published screening data1a suggest may target BMPR1b
as its primary biomolecular target. BMPR1b is part of the BMP-sig-
naling pathway that regulates expression of Id1. Overexpression of
Id1 has been reported in numerous cancers.4–10 Inhibition of the
BMP-signaling cascade by desilylated derivative 5 may account
for the broad-spectrum activity of compound 3a.
Table 1
Inhibitory effects of the test compounds on the proliferation of murine leukemia cells
(L1210), murine mammary carcinoma cells (FM3A), human T-lymphocyte cells (CEM)
and human cervix carcinoma cells (HeLa)
a
Compound
IC50
(l
g/ml)
L1210
FM3A
CEM
HeLa
3a
4a
3.8 0.3
160 56
3.8 0.1
>200
>200
97 17
154 30
5.9 1.1
>200
3.0 0.3
>200
8.3 2.9
>200
4.2 0.2
P200
142 81
107
3.2 0.2
P200
3.7 0.4
104 71
P200
>200
>200
73 13
58 25
10a
10b
10c
13a
13b
13c
13d
13e
13f
13g
13h
13i
>200
150 39
8
61
44
18
15
20
32
2
4
1
1
1
1
>200
29
20
4
2
28
29
20
10
12
>100
>100
>200
0
9.7 3.5
9.5 0.3
17
15
16
1
5
9
2
4
11
0
>100
>100
112 31
140 16
>200
>100
>100
>200
14a
14b
14c
>200
16
87
1
1
36
3
19
88 33
8
40
7
107 13
99 14
a
50% Inhibitory concentration or compound concentration required to inhibit
tumor cell proliferation by 50%.

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J. R. Shelton et al. / Bioorg. Med. Chem. Lett. 22 (2012) 6067–6071
2.50E-06
A
R2 = 0.9936
2.00E-06
1.50E-06
1.00E-06
5.00E-07
0.00E+00
0.1
1
10
100
1000
10000 100000
R2 = 0.7227
Concentration (nM)
B
4.00E-06
3.50E-06
3.00E-06
2.50E-06
2.00E-06
1.50E-06
1.00E-06
5.00E-07
0.00E+00
0.1
1
10
100
1000
10000 100000
Concentration (nM)
C
120
100
80
60
40
20
0
100
95
100
100
100
100
100
53
3a
5
10a
10b
10c
13a
13b
13c
Figure 3. Competitive binding inhibition assays.19 Effects of compounds on
equilibrium competition binding of BMPR1b to immobilized ATP-binding site
ligand. (A) Compound 5. (B) Compound 3a. (C) Compounds 3a, 5, 10a–c, and 13a–c
at 10 lM (data expressed as percent of control).
Figure 2. Docking results for 3a and 5 docked into the active site of BMPR1b (pdb
3mdy). Yellow residues: catalytic triad (K231, E244, D350); blue residue: gate-
keeper (L277); magenta tube: G-loop or activation loop (I210, G211, K212, G213,
R214, Y215, G216); magenta ribbon: hinge region (I278, T279, D280, Y281, H282,
E283, N284, G285, S286).18 (A) Space-filling model of highest ranked pose of
compound 5. (B) Tube model of highest ranked pose of compound 5 (G-Loop
omitted for clarity). (C) Space-filling model of highest ranked pose of compound 3a.
Asp 350) and gatekeeper residues (Leu 277), which may lead to en-
hanced binding, as indicated by the docking study, and thus, in-
creased antiproliferative activity.
Acknowledgments
Generous support from the BYU Cancer Research Center and
BYU College of Physical and Mathematical Sciences and the KU
Leuven (GOA 10/14) to J.B. is gratefully acknowledged.
We are currently designing 50-analogues that may more fully
exploit interactions with the catalytic triad (Lys 231, Glu 244,

J. R. Shelton et al. / Bioorg. Med. Chem. Lett. 22 (2012) 6067–6071
6071
Breast Cancer Res. 2010, 124, 623; (e) Mern, D. S.; Hasskarl, J.; Burwinkel, B. Br. J.
Cancer 2010, 103, 1237.
Supplementary data
12. Shelton, J. R.; Burt, S. R.; Peterson, M. A. Bioorg. Med. Chem. Lett. 2011, 21, 1484.
13. (a) Li, F.; Maag, H.; Alfredson, T. J. Pharm. Sci. 2008, 97, 1109; (b) Mackman, R.
L.; Cihlar, T. Ann. Rep. Med. Chem. 2004, 305.
14. (a) Pungitore, C. R.; León, L. G.; García, C.; Martín, V. S.; Tonn, C. E.; Padrón, J. M.
Bioorg. Med. Chem. Lett. 2007, 17, 1332; (b) Donadel, O. J.; Martín, T.; Martín, V.
S.; Villarc, J.; Padrón, J. M. Bioorg. Med. Chem. Lett. 2005, 15, 3536; (c) Szilágyi,
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Supplementary data (experimental procedures and NMR data
for all new for compounds) associated with this article can be
found, in the online version, at http://dx.doi.org/10.1016/j.bmcl.
2012.08.050.
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21. The possibility exists that BMPR1b may not be the primary biomolecular target
for this class of compounds. However, from a panel of 441 protein kinases,
compound 5 bound to BMPR1b with greatest affinity (see Ref. 1a). Thus,
amongst this class of receptors, BMPR1b certainly shows greatest potential.
Optimization of binding to BMPR1b could lead to discovery of more potent
derivatives and/or discovery of additional related inhibitors.