Exploring the role of the α-carboxyphosphonate moiety in the HIV-RT activity of α-carboxy nucleoside phosphonates

Article abstract of DOI:10.1039/c5ob02507a

As α-carboxy nucleoside phosphonates (α-CNPs) have demonstrated a novel mode of action of HIV-1 reverse transcriptase inhibition, structurally related derivatives were synthesized, namely the malonate 2, the unsaturated and saturated bisphosphonates 3 and 4, respectively and the amide 5. These compounds were evaluated for inhibition of HIV-1 reverse transcriptase in cell-free assays. The importance of the α-carboxy phosphonoacetic acid moiety for achieving reverse transcriptase inhibition, without the need for prior phosphorylation, was confirmed. The malonate derivative 2 was less active by two orders of magnitude than the original α-CNPs, while displaying the same pattern of kinetic behavior; interestingly the activity resides in the "L"-enantiomer of 2, as seen with the earlier series of α-CNPs. A crystal structure with an RT/DNA complex at 2.95 ? resolution revealed the binding of the "L"-enantiomer of 2, at the polymerase active site with a weaker metal ion chelation environment compared to 1a (T-α-CNP) which may explain the lower inhibitory activity of 2.

Full text of DOI:10.1039/c5ob02507a

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1
Exploring the role of the α-carboxyphosphonate
moiety in the HIV-RT activity of α-carboxy
nucleoside phosphonates
†
†
†
║
║
Nicholas D. Mullins, Nuala M. Maguire, Alan Ford, Kalyan Das, Edward Arnold, Jan
‡
†§*
Balzarini and Anita R. Maguire
†
§
Department of Chemistry and School of Pharmacy, Analytical and Biological Chemistry
Research Facility, Synthesis and Solid State Pharmaceutical Centre, University College, Cork,
Ireland
‡
KU Leuven, Rega Institute for Medical Research, Minderbroedersstraat 10, B-3000 Leuven,
Belgium
║
Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical
Biology, Rutgers University, Piscataway, NJ 08854-8020; USA
1

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Table of Contents Graphic and Synopsis
ABSTRACT
As α-carboxy nucleoside phosphonates (α-CNPs) have demonstrated a novel mode of action of
HIV-1 reverse transcriptase inhibition, structurally related derivatives were synthesized, namely
the malonate 2, the unsaturated and saturated bisphosphonates 3 and 4, respectively and the
amide 5. These compounds were evaluated for inhibition of HIV-1 reverse transcriptase in cell-
free assays. The importance of the α-carboxy phosphonoacetic acid moiety for achieving reverse
transcriptase inhibition, without the need for prior phosphorylation, was confirmed. The
malonate derivative 2 was less active by two orders of magnitude than the original α-CNPs,
while displaying the same pattern of kinetic behavior; interestingly the activity resides in the
“
L”-enantiomer of 2, as seen with the earlier series of α-CNPs. A crystal structure with an
RT/DNA complex at 2.95 Å resolution revealed the binding of the “L”-enantiomer of 2, at the
polymerase active site with a weaker metal ion chelation environment compared to 1a (T-α-
CNP) which may explain the lower inhibitory activity of 2.
2

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INTRODUCTION
World Health Organization statistics state that 2.1 million people were infected with the human
immunodeficiency virus (HIV) in 2013, bringing the number of people now living with the virus
1
to approximately 35 million. While a recent study claims that the retrovirus is slowly becoming
2
milder in its virulence due to a number of factors (i.e. mutations, increased drug resistance),
3
other work has predicted increasing rates of disease transmission. Thus, the quest for novel
drugs that possess anti-HIV properties (in terms of mechanism of action, resistance profile,
inhibition potency, side effects profile, etc.) is of utmost importance.
Recently, we disclosed the synthesis and evaluation of a novel class of α-carboxy nucleoside
phosphonates (α-CNPs) 1 which exhibit potent HIV-1 reverse transcriptase (RT) inhibitory
4
,5
properties in cell free assays (Figure 1). Most importantly, these compounds unlike nucleoside-
analog drugs do not require intracellular activation (i.e. phosphorylation) in order to display
activity against the virus-encoded RT. Interestingly, the α-carboxy phosphonate moiety is acting
as a triphosphate mimic as demonstrated by crystallographic analysis. In fact, the carboxylate
2
+
oxygen mimics the interaction of a nucleotide α-phosphate with a Mg ion, while the two
phosphonate oxygens of the α-CNPs mirror the interaction of β- and γ-phosphate oxygens of
2
+
5
nucleotides with the same Mg ion.
CO H
2
O
P
O
B
HO
l
b
= nuc eo ase
B
OH
1
Figure 1. α-carboxynucleoside phosphonate (α-CNP)
3

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Intrigued by this novel mode of action, we decided to investigate the influence of altering the
carboxy phosphonate group on HIV-1 RT inhibition while keeping the remainder of the α-CNP
structure intact. Accordingly, the malonate 2, bisphosphonates 3 and 4 and the amide 5 were
4
chosen as potential targets. In addition, previously synthesized esters 6 and 7 were also included
in the evaluation (Figure 2). The key aspect we wish to investigate is whether the activity of the
α-carboxy phosphonate could be mimicked through the diacid 2 or the bisphosphonates, or
indeed whether the carboxylic acid could be replaced by a primary amide in 5 or an ester in 6
and 7, thereby determining whether the ionizable acid is essential, or whether the metal ion
coordinating ability of a primary amide is sufficient to maintain the inhibitory activity of the α-
CNPs against HIV-1 RT.
O
N
O
N
O
N
O
N
HO C
NH
(HO)
2
OP
NH
(HO) OP
NH
H NOC
NH
2
2
2
HO C
O
O
(HO)
2
OP
O
O
(HO) OP
O
O
(HO) OP
O
O
2
2
2
2
3
4
5
O
O
N
MeO C
NH
MeO C
NH
2
2
HO OP
O
N
O
HO OP
O
O
(
)
2
(
)
2
6
7
Figure 2. Targets selected for HIV-RT inhibition
Compound 2 possesses a diacid moiety which is related to the diketoacid (DKA) structural
6
feature which has been implicated in the activity of HIV-1 integrase (IN) inhibitors, namely
7
,8
9
10
raltegravir 8, elvitegravir 9 and the recently approved dolutegravir 10. The planar geometry
2
+
11,12
of the DKA moiety is believed to facilitate chelation of two Mg ions in the active site.
4

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1
3
Compound 11 exhibits moderate inhibition of wild-type HIV-1 RT polymerase. The
bisphosphonate moiety of 3 and 4 is a key structural motif in compounds such as pamidronic
1
4
acid 12 which is used in the treatment of bone-related diseases. Recently, advocacy for their
1
5
use in the treatment of HIV-related osteoporosis has increased. Inorganic pyrophosphate (PPi)
3 is formed during the catalytic cycle of nucleotide monophosphate incorporation into a
growing nucleotide copolymer and it can induce a conformational change in polymerases from
1
1
6
an open to a closed conformation by binding to the active site. Investigations have centered on
1
7-19
the ability of bioisosteres of PPi to inhibit HIV-1 RT. Foscarnet (phosphonoformic acid)
acts by trapping the pre-translocational state of HIV-1 RT, and while phosphonoacetic acid
14
2
0-22
(PAA) 15 is a potent anti-herpetic agent, it is virtually ineffective against HIV.
2
2,23
Oxophosphonoacetate 16 is an inhibitor of some nucleic acid polymerases.
2
4
Carbonylbisphosphonate (COBP) 17, first isolated by Quimby and further investigated by
2
3,25,26
McKenna, is efficient at inhibiting HIV-1 RT.
Compound 18 is non-inhibitory towards
HIV-1 RT, however, and despite extensive efforts having been devoted to the synthesis of small
molecule substituted derivatives of 15 and 18, these efforts have usually resulted in less effective
2
6
HIV-1 RT inhibitors than foscarnet. The preparation and characterization of AZT 5´-COBP 19
2
7
has been described, but no biological data has been reported. More recently, purine-like
2
8
bisphosphonates 20 and 21 have been shown to inhibit HIV-1 RT-catalyzed synthesis. Finally,
the amide 5 is reminiscent of anti-HIV pronucleosides 22 and 23 documented by Shirokova, with
2
9
2
2 inhibiting virus replication by 90% at significantly lower concentrations than AZT.
5

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O
O
N
F
O
N
Cl
HO
OH
F
N N
O
N
H
H
OMe
N
N
O
O
OH
8
9
O
P
O
O
OH
CO H
2
HO
HO
OH
OH
N
P
O
O
F
F
N
Cl
NH CO H
H
2
HO
N
N
O
H
NH2
11
1
0
12
O
P
O
O
P
O
O
O
O
P
O
O
P
HO
HO
HO
HO
OH
OH
HO
HO
HO
HO
HO
HO
OH
OH
P
OH
P
P
OH
O
OH
O
O
O
1
3
14
15
16
1
7
O
N
N
N
R1
N
N
R1
NH
O
N
N
R2
HO OP
R2
O
(
)
2
O
O
P
HO OP
NH
NH
O
P
O
P
O
(
)
2
HO OP
HO
HO
OH
OH
(
)
2
OH
OH
P
PO OH
( )
2
O
N3
OH
1
8
2
0
21
1
9
O
O
N
NH
NH
O
OEt
OEt
H N
2
O
N
O
O
O
P
H N
P
2
O
O
O
O
O
N3
N3
22
23
In this context, evaluation of the properties of the malonate 2, bisphosphonates 3 and 4 and the
amide 5 was warranted.
6

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RESULTS AND DISCUSSION
a
Scheme 1. Synthesis of malonate derivative 2.
BnO C
2
O
O
a
O
O
b
OH OAc
(
)
( )
BnO C
O
OAc
2
BnO
OBn 64%
BnO
OBn
3
2%
N2
2
6
24
25
27
O
O
O
HO C
NH
c
BnO C
NH
d
( )
2
NH
(
)
2
5
7%
HO C
O
N
O
6
%
BnO C
O
N
O
2
HO C
O
N
O
2
2
2
2
9
2
8
a
Conditions: (a) ABSA, K CO , MeCN, 48 h; (b) 26, Rh (OAc) , C H , 80 °C, 12 h; (c)
2
3
2
4
6
6
thymine, Pd(dba) , dppb, Na CO , aq. MeCN, Microwave (MW) 50 °C; (d) H , Pd/C 1 atm,
2
2
3
2
MeOH, 15 h.
The synthesis of 2 was accomplished in four steps from commercially available dibenzyl
malonate (Scheme 1). Diazo transfer to 24 was achieved in the presence of 4-
acetamidobenzenesulfonyl azide (ABSA) to give the novel dibenzyl 2-diazomalonate 25.
3
0,31
Building upon our previous work with rhodium insertion reactions,
rhodium (II)-catalyzed
3
2-34
OH insertion of 25 with the allylic alcohol 26
furnished 27 in 48% yield. Thymine base
3
5
insertion of 27 in a palladium-catalyzed Tsuji-Trost reaction was carried out under microwave
conditions to afford 28. Finally, simultaneous hydrogenation of the cyclopentyl alkene and
hydrogenolysis of the benzyl esters of 28 was achieved under atmospheric pressure of hydrogen
in the presence of Pd/C to provide the target malonate 2 in racemic form (57% yield). Despite
our initial concerns that 2 may undergo decarboxylation during isolation or upon standing, a
solution of 2 in MeOH-d was found to be stable at room temperature for up to 6 months. We
4
7

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4
have already described the synthesis and characterization of the decarboxylated compound 29
and were unable to detect its presence by NMR in the solution of 2 after 6 months. Furthermore,
storage of malonate 2 in solid state proved easier than anticipated, with little or no evidence of
decarboxylation on storage for several months.
The malonates were also synthesized in both enantiopure forms 2a and 2b. This was achieved
using the same sequence of reactions described for the racemic series starting from the
commercially available enantiomers of the acetoxy alcohol 26a and 26b (Scheme 2). Yields were
consistent with those obtained for the racemic series.
a
Scheme 2. Synthesis of enantiopure forms of 2.
O
O
BnO C
2
c
HO C
NH
BnO C
NH
2
2
( )
63% HO C
OH OAc
BnO C
O
OAc
2
b
O
N
O
BnO C
O
N
O
2
(
)
a
2
(
)
5
6%
11%
2
6a
27a
2a
2
8a
O
O
BnO C
HO C
NH
2
BnO C
NH
c
2
2
( )
82% HO C
OH OAc
BnO C
O
OAc
O
N
O
2
b
BnO C
O
N
O
2
(
)
2
a
(
)
4
%
4
3%
2
6b
27b
2b
2
8b
a
Conditions: (a) 25, Rh (OAc) , C H , 80 °C; (b) thymine, Pd(dba) , dppb, Na CO , aq.
2
4
6
6
2
2
3
MeCN, MW 50 °C; (c) H , Pd/C 1 atm, MeOH.
2
8

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a
Scheme 3. Synthesis of bisphosphonates 3 and 4.
O
N
O
EtO OP
Et
O) O
P
HO OP
NH
(
)
2
(
NH
(
)
2
O
P
O
P
a
2
c
b
( )
( )
(
)
EtO OP
O
OAc
Et
O) O
P
HO OP
O
N
O
(
)
2
(
O
O
84%
(
)
2
EtO
OEt 87%
4
8
%
2
EtO
OEt
N2
30
31
32
3
d
86%
O
(
)
O
N
EtO OP
NH
(HO) OP
NH
(
)
2
2
e
(
)
EtO OP
(
O
N
O
(HO) OP
O
O
)
2
29%
2
33
4
a
Conditions: (a) 26, Rh (tfacam) , C H , 80 °C; (b) thymine, Pd(dba) , dppb, Na CO , aq.
2
4
6
6
2
2
3
MeCN, 50 °C MW; (c) (i) TMSBr, lutidine, MeCN, MW 50 °C, (ii) MeOH/H O 1 h, (iii)
2
charcoal chromatography; (d) H , Pd/C 1 atm, MeOH, 15 h; (e) (i) TMSBr, MeCN, MW 50 °C,
2
(
ii) MeOH/H O 1 h, (iii) charcoal chromatography.
2
A similar strategy was employed for the preparation of the racemic bisphosphonates 3 and 4
(Scheme 3). It was envisaged that O-H insertion of tetraethyl diazomethylenebisphosphonate
3
6
3
0 with alcohol 26 would require more forcing conditions than the analogous reaction with
diazomalonate 25. Therefore, in this case, the more active rhodium trifluoroacetamide was
employed as catalyst and it was added portionwise over the course of the reaction. Gratifyingly,
under these conditions, the O-H insertion product 31 was obtained in 87% yield after correction
for the recovered starting material 26. Introduction of thymine under Tsuji-Trost conditions
proceeded efficiently in the microwave to afford bisphosphonate 32 in 48% yield. Finally,
cleavage of the phosphonate ethyl esters of 32 was achieved using bromotrimethylsilane
(TMSBr) in the presence of lutidine and the desired unsaturated bisphosphonate 3 was isolated as
its ammonium salt in 84% yield following charcoal chromatography. Interestingly both the O-H
insertion and base insertion steps were effective despite the alteration from the phosphonoacetic
9

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0
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acid moiety to the malonate and bisphosphonate confirming the generality of the synthetic route
developed for the α-CNPs. Palladium mediated hydrogenation of 32 afforded 33 and subsequent
hydrolysis of the phosphonate esters of 33 followed by charcoal chromatography gave 4 as the
ammonium salt.
a
Scheme 4. Synthesis of amide 5.
O
N
O
N
O
N
MeO C
NH
H NOC
H NOC
NH
NH
2
2
2
a
(
)
b
( )
MeO OP
O
O
MeO OP
HO OP
O
O
(
)
2
(
)
2
O
O
(
)
2
3
5%
70%
3
4
35
5
a
Conditions: (a) 7N NH in MeOH, 65 h; (b) (i) TMSBr, MeCN, MW 50 °C, (ii) MeOH/H O
3
2
3
0 min, (iii) charcoal chromatography.
The synthesis of the amide (Scheme 4) derivative 5 commenced with the methyl ester 34, which
4
was also a key intermediate in the synthesis of α-CNPs which we described earlier. Aminolysis
of the carboxy methyl ester was achieved by stirring 34 for 65 h in a 7N solution of ammonia in
methanol to afford 35 in 35% yield. The low yield may be explained by the fact that attack at the
phosphonate ester groups is also possible under the reaction conditions. Following isolation of 35
by chromatography, the phosphonate esters were hydrolyzed and 5 was isolated as the
ammonium salt in 70% yield.
The eight structurally related compounds (malonates 2, 2a, 2b, bisphosphonates 3 and 4, amide 5
and esters 6 and 7) were evaluated for their inhibitory activity using a cell-free HIV-1-RT assay
4
,5
and the results compared with those obtained for the parent α-CNPs (1, 1a, 1b and 36). Poly
3
rA.oligo dT was used as the homopolymeric template/primer, and [ H]dTTP as the radiolabeled
1
0

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1
substrate. The IC (50% inhibitory concentration) was determined as the compound
5
0
concentration required to inhibit RT-catalysed dTTP incorporation into the growing DNA strain.
For the parent α-CNPs, our research has already shown that the “L”-enantiomer 1a is the more
active of the two enantiomeric compounds (Table 1, Entry 2 vs. 3). The effect of unsaturation of
the racemic α-CNPs (i.e. compound 36 compared to 1) is to decrease the activity by ~ 5-fold
4
(Table 1, Entry 4 vs. 1).
Importantly, the presence of a methyl ester in place of the carboxylic acid effectively shuts down
activity as evidenced by results obtained for 6 and 7. This effect is further highlighted by the
amide 5 which shows poor, if any, relevant inhibitory activity against HIV-1 RT (Table 1, Entry
1
2). The lack of significant activity of the amide and esters 6 and 7 confirms that two ionizable
moieties are required to efficiently coordinate the magnesium ions to display efficient RT
inhibition.
The unsaturated bisphosphonate 3 is poorly active (IC : 204 µM) (Table 1, Entry 10), while the
5
0
saturated analog 4 is similarly ineffective to inhibit HIV-1 RT.
The racemic malonate 2 (Table 1, Entry 7) displays an activity approximately 100-fold less than
observed for racemic α-CNP 1 (Table 1, Entry 1). However, the results obtained for the
enantiopure malonates are interesting in terms of mirroring the behavior observed for the α-
CNPs. The malonate 2a (“L”-enantiomer) is 2-fold more active (IC : 20 µM) than the racemic
5
0
mixture 2 (IC : 42 µM) [Table 1, Entry 8 vs. Entry 7], while the “D”-enantiomer lacked any
5
0
relevant inhibitory activity against HIV-1 RT (IC : > 640 µM) [Table 1, Entry 9]. Such a
5
0
selective activity profile (predominant activity by the “L”-enantiomer) has also been observed
for the prototype α-CNPs as mentioned above. Also, it should be noticed that the malonate 2a, as
1
1

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also found for the α-CNPs, does not need metabolic conversion to a higher phosphate metabolite
to exert anti-HIV-1 RT activity.
Table 1. Inhibitory activity of the compounds against HIV-1 RT
a
b
Base = Thymine. Fifty percent inhibitory concentration, or compound concentration required
3
to inhibit HIV-RT-catalyzed incorporation of [ H]dNTP in the homopolymeric template/primer.
Data are the mean ± SD of at least 3 to 4 independent experiments. Synthesis (1, 1a, 1b, 36, 6
and 7) and IC data (1, 1a, 1b, 36) see Ref 4.
c
5
0
1
2

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3
Finally, when the active malonate enantiomer 2a was investigated for its kinetic interaction with
HIV-1 RT, reciprocal velocity versus substrate Lineweaver-Burk plots revealed a competitive
inhibition of the enzyme by 2a with respect to the natural substrate dTTP (Fig. 3). The inhibitory
constant Ki of 2a was 6.6 µM. The Km of dTTP was 5.9 µM. This kinetic behavior was also
5
earlier observed for the prototype α-CNP compound 1.
Figure 3. Lineweaver-Burk plots for the inhibition of HIV-1 RT by compound 2a.
3
7
A crystal structure of 2a was determined in complex with HIV-1 RT/38-mer DNA aptamer; the
3
8-mer DNA template-primer aptamer mimics the binding of a double-stranded (ds) DNA at the
3
7
polymerase active site, and contains a single-stranded (ss) DNA template overhang. The pre-
formed crystals were soaked in a 2mM solution of 2a for the formation of RT/DNA/2a ternary
complex, and the crystal structure revealed the binding of 2a at the polymerase active site (Fig.
4
). The structure contains two copies of RT/DNA, and only the first one has ordered electron
5
density for 2a. The general mode of binding of 2a is similar to that of 1a (T-α-CNP). The
st
thymine base of 2a is base-paired with the adenine base of 1 overhang nucleotide, and the
1
3

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cyclopentyl ring is positioned over the aromatic side chain of Tyr115; both interactions of 2a are
analogous to those observed with the binding of 1a (T-α-CNP) to RT. However, metal chelation
at the polymerase active site differs for the two inhibitors. One oxygen from each of the
2
+
carboxyl groups of 2a chelate with a Mg ion (metal B) at the polymerase active site, and the
ion also chelates to the main-chain carbonyl oxygen of V111 and a side-chain oxygen of the
catalytic aspartate Asp185. Interestingly, the catalytic residue Asp110 is switched away from the
2
+
active site, and does not participate in the Mg chelation in the structure of the 2a complex.
Presumably, the chelation of the malonate group of 2a is not compatible with the chelation of all
three catalytic aspartates (Asp110, Asp185, and Asp186), which is observed for the binding of a
5
dNTP and for 1a (T-α-CNP). The binding of 2a involves only 4 observed chelations for the
2
+
Mg ion B in contrast to a complete octahedral coordination environment when T-α-CNP 1a
was bound. We expect that two water molecules might be involved to complete the coordination
2
+
environment for the Mg ion when 2a is bound, however, no clear electron density was
observed for any potentially chelating ordered water molecule in the crystal structure of
RT/DNA/2a complex. In summary, the structure suggests that the significantly perturbed
coordination environment due to the malonate group is a primary contributor to the lower RT
inhibition by 2a compared to the inhibition by 1a (T-α-CNP). Thereby, a potent CNP class of
2
+
nucleoside competing RT inhibitor (NcRTI) should chelate the catalytic Mg ions in a mode
analogous to that observed in the chelation of a dNTP substrate.
1
4

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5
Figure 4. Structure of 2a in complex with HIV-1 RT/DNA. (a) 2.95 Å resolution electron
density map defines the binding of 2a (green) at the polymerase active site of RT. The inhibitor
binding affinity has contributions from the base pairing (gray dotted lines) and base stacking,
hydrophobic stacking of the cyclopentyl ring with the aromatic side chain of Tyr115, and the
2
+
chelation with a Mg ion at the polymerase active site (black dotted lines). The chelation
environment for 2a is significantly different from the octahedral coordination environment
observed for 1a (T-α-CNP) (b).
When evaluated for their anti-HIV activity in cell culture, the compounds were found to be
antivirally inactive at concentrations up to 100 µM. Also, they were devoid of any significant
cytotoxicity. Presumably, the compounds might be too polar to be efficiently taken up by intact
cells. Therefore, a prodrug approach should be considered to deliver the active molecules
directly into the intact virus-infected cells. The design and synthesis of such prodrug derivatives
are currently under investigation.
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CONCLUSION
We designed and synthesized structurally related analogues of α-CNPs and investigated their
ability to inhibit HIV-1 RT in cell-free enzyme assays. The amide derivative 5 was virtually
inactive while the bisphosphonates 3 and 4 also exhibited poor inhibition of HIV-1 RT. The
requirement for two ionizable functional groups to be present in order to exhibit inhibition was
demonstrated through the lack of activity of both esters 6 and 7 and also the amide 5. The
malonate 2 was the most active of the compounds albeit significantly less active that the original
α-CNPs. Enantiopure forms of the malonate behaved in a similar fashion to the parent α-CNP in
that the activity resides in the “L”-enantiomer. The crystal structure together with the RT
inhibition data confirms the significance of the α-carboxy phosphonoacetic acid moiety in
affording efficient RT inhibition without need for any further phosphorylation.
EXPERIMENTAL SECTION
General Information
Solvents were distilled prior to use as follows: dichloromethane was distilled from phosphorus
pentoxide; ethyl acetate was distilled from potassium carbonate. Benzene was dried before use
with activated 4Å molecular sieves. For O-H and base insertion reactions, solvents were
degassed by purging with nitrogen for 5 min. Organic phases were dried using anhydrous
magnesium sulfate. All commercial reagents were used without further purification. Microwave
reactions were carried out using a CEM Discover in conjunction with Synergy software, reaction
1
13
31
temperatures were measured by IR sensor. H, C, and P spectra were recorded at 20 °C on
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6

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7
3
00 or 400 MHz spectrometers. Chemical shifts are given in ppm relative to tetramethylsilane
3
1
(
TMS) as an internal standard. P chemical shifts are referenced to H PO (external standard).
3 4
Coupling constants (J) are given in hertz (Hz). In some cases the signal for the PCH was not
observed in the carbon-13 NMR spectrum. Infrared spectra were recorded neat on a PerkinElmer
Spectrum Two; operating in Universal Attenuated Total Reflectance (UATR) mode. Melting
points were measured using a capillary melting point apparatus and are not corrected. Optical
rotations were measured at 20 °C at 589 nm in a 10 cm cell; concentrations (c) are expressed in
−
1
2
−1
g/100 ml, [α] is expressed in units of 10 deg cm g . Low resolution mass spectra were
recorded in electrospray ionization (ESI) mode, high resolution mass spectra (HRMS) were
recorded on a Time of Flight spectrometer in electrospray ionization (ESI) mode. Column
chromatography was performed using silica gel 60. Thin layer chromatography (TLC) was
carried out on precoated silica gel plates (60 PF254). Visualization was achieved by UV (254
4
4
32-34
36
nm) detection and/or staining with vanillin or permanganate. Compounds 6, 7, 26
and 30
were prepared by literature methods.
Reverse transcription assays
HIV-I RT assays were carried out in the presence of homopolymeric template/primers. Poly(A)
and dT12-18 were from Pharmacia (Uppsala, Sweden). To prepare the template/primers for the
RT experiments, 0.15 mM poly(A) was mixed with an equal volume of 0.0375 mM oligo(dT).
The reaction mixture (50 µl) contained 50 mM Tris.HC1 pH 7.8, 5 mM dithiothreitol, 300 mM
glutathione, 500 µM EDTA, 150 mM KCl, 5 mM MgCl , 1.25 µg of bovine serum albumin, an
2
appropriate concentration of the tritium-labeled substrate [CH3-3H]dTTP (1 µCi/assay; 60
Ci/mmole), a fixed concentration of the template/primer poly(A).oligo(dT) (0.015 mM), 0.06%
Triton X-100, 10 µl of α-CNP inhibitor solution (containing various concentrations of the
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compounds), and 1 µl (being equivalent to 1 pmole (0.13 ng) enzyme or 20 pM final
concentration) of the HIV-1 RT preparation. The reaction mixtures were incubated at 37°C for
3
0 minutes, at which time 100 µl of calf thymus DNA (150 µg/ml), 2 ml of Na P O (0.1 M in 1
4 2 7
M HCl), and 2 ml of trichloroacetic acid (10% v/v) were added. The solutions were kept on ice
for 30 minutes, after which the acid-insoluble material was washed and analyzed for
radioactivity. For the experiments in which the 50% inhibitory concentration (IC ) of the test
5
0
3
compounds was determined, a fixed concentration of 1.25 µM [ H]dTTP was used. For the
experiments in which the kinetic nature of the malonate derivative 2a was determined, different
3
[
H]dTTP concentrations (3, 4, 6, 10, 20 and 40 µM) were used in the presence of different
inhibitor concentrations (75, 30 and 15 µM). The activity values were plotted in a reciprocal
velocity versus substrate Lineweaver-Burk diagram. It should be emphasized that under the
experimental conditions, the RT reaction was linear for up to 30 min, and at the end of the
incubation period, less than 5% of the available dTTP substrate was consumed (incorporated).
X-ray crystallography
The crystals of RT/38-mer DNA aptamer complex were obtained using a previously defined
3
7
protocol. A crystal soaked in a solution containing 2.5mM of 2 and 20mM MgCl for 15
2
minutes diffracted the best up to 2.95Å resolution (Supplementary Information Table-1). X-ray
data were collected at APS 23ID-D beam line. Due to anisotropy diffractions and radiation
sensitivity of the crystal, the collected data is only 84.8% complete with 87.5% in the highest
38
resolution cell. The dataset was processed using Mosflm and the RT/38-mer DNA aptamer
binary complex structure (PDB Id. 5D3G) was used as the starting model for obtaining the
molecular replacement solution. There are two copies of RT/DNA complex in the asymmetric
unit. The difference (|Fo| - |Fc|) electron density map clearly revealed the binding of the
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9
compound 2 at the polymerase active site of one of two RT/DNA copies in the asymmetric unit.
3
9
40
The crystallography software Phenix and Coot were used for structure refinement and model
building, respectively. Final refinement statistics are listed in Supplementary Information Table-
1
5
, and the coordinates and structure factors are deposited in PDB with the accession number
HLF.
Synthesis
Dibenzyl 2-diazomalonate (25)
Potassium carbonate (3.34 g, 0.024 mol) was added to a solution of dibenzyl malonate (3.19 g,
0
.011 mol) and 4-acetamidobenzenesulfonyl azide (2.65 g, 0.011 mol) in MeCN (50 mL). The
resulting suspension was stirred for 24 h at room temperature, filtered and concentrated in vacuo.
The residue was taken up in DCM (50 mL), and the solution was washed with aqueous NaOH
(
50 mL, 1M), water (50 mL) and brine (50 mL), dried (MgSO ) and concentrated in vacuo. The
4
residue was purified by chromatography (SiO , ether) to afford the title compound as a white
2
-1
1
solid (2.21 g, 64%): m.p. = 56-57 °C; νmax/cm : 3407, 2940, 2145, 2129, 1758, 1708, 1690; H
1
3
NMR (300 MHz, CDCl ) δ: 5.27 (s, 2H), 7.29-7.39 (m, 5H); C NMR (75.5 MHz, CDCl ) δ:
3
3
6
7.1, 128.2, 128.4, 128.6, 135.3, 160.8; signal for CN not seen; Anal. calcd for C H N O : C.
2 17 14 2 4
6
5.80; H, 4.55; N, 9.03. Found: C, 65.82; H, 4.62; N, 8.83; HRMS (ES+): calcd for C H N O
4
1
7
15
2
+
+
(
M+H) 311.1032, found 311.1021; MS (ES+) m/z: 311 (M + H) .
(−)-(1S, 4R)-Dibenzyl 2-[(1-acetoxycyclopent-2-en-4-yl)oxy]malonate (27a)
Rhodium(II) acetate (15 mg, 0.033 mmol, 1 mol%) was added to a degassed solution of (1S,4R)-
cis-4-hydroxy-2-cyclopentenyl acetate 26a (0.50 g, 3.52 mmol) and 25 (1.20 g, 3.87 mmol) in
benzene (25 mL). The reaction mixture was stirred while heating under reflux for 24 h under a
nitrogen atmosphere. The mixture was filtered, concentrated and the residue purified by
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chromatography (SiO , 20% ethyl acetate/hexane) to give (−)-(1S, 4R)-27a as a pale yellow oil
2
-1
20
D
1
(
0.82 g, 56%): νmax/cm : 2925, 1730, 1608, 1587, 1235; [α]
- 24.38 (c 0.08, CHCl ); H NMR
3
(
300 MHz, CDCl ) δ: 1.73-1.84 (m, 1H), 1.99 (s, 3H), 2.67-2.81 (m, 1H), 4.62-4.72 (m, 2H),
3
1
3
5
.19 (s, 4H), 5.39-5.47 (m, 1H), 5.94-6.16 (m, 2H), 7.19-7.41 (m, 10H); C NMR (75.5 MHz,
CDCl ) δ: 21.0, 37.1, 67.6, 76.2, 76.8, 82.9, 128.3, 128.53, 128.59, 134.3, 134.8, 135.0, 166.6,
3
+
1
70.6; HRMS (ES+): calcd for C H NaO (M+Na) 447.1420, found 447.1426.
2
4
24
7
(+)-(1R, 4S)-Dibenzyl 2-[(1-acetoxycyclopent-2-en-4-yl)oxy]malonate (27b)
Synthesized following the procedure described for 27a using: rhodium(II) acetate (15 mg, 0.033
mmol, 1 mol%), (1R,4S)-cis-4-hydroxy-2-cyclopentenyl acetate 26b (0.50 g, 3.52 mmol) and 25
(
1.20 g, 3.87 mmol). Purification by chromatography (SiO , 20% ethyl acetate/hexane) afforded
2
2
D
0
(+)-(1R, 4S)-27b as a colorless oil (0.65 g, 43%): [α]
+ 20.00 (c 0.05, CHCl3).
cis-Dibenzyl 2-[(1-acetoxycyclopent-2-en-4-yl)oxy]malonate (27)
Synthesized following the procedure described for 27a using: rhodium(II) acetate (15 mg, 0.033
mmol, 0.8 mol%) , cis-4-hydroxy-2-cyclopentenyl acetate 26 (0.58 g, 4.08 mmol) and 25 (1.40 g,
4
.51 mmol). Purification by chromatography (SiO , 20% ethyl acetate/hexane) gave 27 as a pale
2
yellow oil (0.56 g, 32%, 48% when corrected for recovered alcohol 26).
(−)-(1S, 4R)-Dibenzyl 2-[(1-thymin-1-yl-cyclopent-2-en-4-yl)oxy]malonate (28a)
A microwave vial containing a degassed suspension of thymine (190 mg, 1.51 mmol) and
sodium carbonate (115 mg, 1.07 mmol) in water (1 mL) and acetonitrile (1 mL) was heated
under microwave conditions (50°C, 200 W) for 30 min. A degassed solution of (−)-(1S, 4R)-27a
(
420 mg, 0.99 mmol) in acetonitrile (1 mL), bis(dibenzylideneacetone)palladium(0) Pd(dba) (30
2
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2
1
mg, 5 mol%) and 1,4-bis(diphenylphosphino)butane (dppb) (40 mg, 9 mol%) was added to the
vial. The resulting solution was irradiated (50°C, 200 W) for 30 min whereupon a second portion
of Pd(dba) (30 mg) and dppb (40 mg) was added followed by irradiation (50°C, 200 W) for a
2
further 30 min. The reaction mixture was cooled to room temperature, gravity filtered and
concentrated under vacuum to give a purple residue which was purified by chromatography
(
SiO , 3% methanol/dichloromethane) to afford compound (−)-(1S, 4R)-28a as an oil (52 mg,
2
-1
1
1
1%): νmax/cm : 3177, 3034, 2924, 1762, 1742, 1686; H NMR (300 MHz, CDCl ) δ: 1.63-1.78
3
(m, 1H), 2.64-2.86 (m, 1H), 4.56-4.67 (m, 1H), 4.71 (s, 1H), 5.06-5.32 (m, 4H), 5.55-5.75 (m,
1
3
1
H), 5.80-5.96 [m, 1H), 6.15-6.29 (m, 1H), 7.21-7.39 (m, 11H), 9.31-9.52 (bs, 1H); C NMR
(
75.5 MHz, CDCl ) δ: 12.3, 37.2, 57.7, 67.8, 77.9, 83.4, 111.6, 128.41, 128.44, 128.63, 128.64,
3
1
28.69, 134.4, 134.65, 134.69, 135.9, 137.1, 151.1, 164.0, 166.1, 166.3; HRMS (ES+): calcd for
+
+
C H N O (M+H) 491.1818, found 491.1829; MS (ES+) m/z: 491 (M + H) .
27
27
2
7
(+)-(1R, 4S)-Dibenzyl 2-[(1-thymin-1-yl-cyclopent-2-en-4-yl)oxy]malonate (28b)
Prepared following the procedure described for 28a using: thymine (190 mg, 1.51 mmol),
sodium carbonate (115 mg, 1.07 mmol), (+)-(1R, 4S)-27b (420 mg, 0.99 mmol), Pd(dba) (30
2
mg, 5 mol%) and dppb (40 mg, 9 mol%). Purification by chromatography (SiO , 3%
2
methanol/dichloromethane) gave (+)-(1R, 4S)-28b as an oil (18 mg, 4%).
cis-Dibenzyl 2-[(1-thymin-1-yl-cyclopent-2-en-4-yl)oxy]malonate (28)
Prepared following the procedure described for 28a using: thymine (160 mg, 1.27 mmol),
sodium carbonate (97 mg, 0.92 mmol), 27 (355 mg, 0.84 mmol), Pd(dba) (25 mg, 5 mol%) and
2
dppb (35 mg, 10 mol%). Purification by chromatography afforded compound 28 as an oil (25
mg, 6%).
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(+)-(1R, 4S)- 2-[(1-thymin-1-yl-cyclopentan-4-yl)oxy]malonic acid (2a)
A mixture of (−)-(1S, 4R)-28a (30 mg, 0.061 mmol) and palladium on carbon (10 mg, 10%) in
methanol (10 mL) was stirred under a balloon of hydrogen at atmospheric pressure for 24 h at
room temperature. The mixture was filtered on Celite and the cake was rinsed with methanol.
2
D
0
The filtrate was concentrated to give (+)-(1R, 4S)-2a (12 mg, 63%): [α]
+ 4.17 (c 0.24,
1
MeOH); H NMR (300 MHz, MeOH-D ) δ: 1.48-2.15 (m, 8H), 2.19-2.36 (m, 1H), 4.02-4.17 (m,
4
1
3
1
H), 4.55 (s, 1H), 5.01-5.18 (m, 1H), 7.88 (s, 1H); C NMR (75.5 MHz, MeOH-d4) δ: 10.8,
2
9.7, 30.7, 37.8, 53.6, 76.5, 80.5, 110.7, 139.2, 151.8, 165.1, 169.0; HRMS (ES+): calcd for
+
+
C H N O (M+H) 313.1036, found 313.1030; MS (ES+) m/z: 313 (M + H) .
13
17
2
7
(−)-(1S, 4R)- 2-((1-thymin-1-yl-cyclopentan-4-yl)oxy)malonic acid (2b)
Synthesized using procedure described for 2a using: (+)-(1R, 4S)-28b (25 mg, 0.051 mmol) and
2
D
0
palladium on carbon (10 mg, 10%) to give (−)-(1S, 4R)-2b (13 mg, 82%): [α]
- 6.67 (c 0.06,
MeOH).
cis-2-[(1-thymin-1-yl-cyclopentan-4-yl)oxy]malonic acid (2)
Synthesized using procedure described for 2a using: 28 (25 mg, 0.051 mmol) and palladium on
carbon (10 mg, 10%) to give 2 (9 mg, 57%).
cis-1-[bis(Diethylphosphono)methoxy]-4-acetoxycyclopent-2-ene (31)
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3
cis-4-Hydroxy-2-cyclopentenyl acetate 26 (0.69 g, 4.7 mmol) and tetraethyl
diazomethylenebisphosphonate 30 (2.95 g, 9.4 mmol) were dissolved in degassed benzene (15
mL). Rhodium (II) trifluoroacetamide (30 mg, 1 mol %) was added and the reaction mixture was
refluxed for 18 h, after which time a second portion (30 mg, 1 mol %) of catalyst was added and
reflux was continued for a further 24 h and then a third portion (30 mg, 1 mol %) was added and
reflux was continued for a further 28 h. After removal of benzene under reduced pressure the
residue was subjected to flash chromatography (EtOAc to 5% MeOH:95% EtOAc) to afford
-1
starting material (0.20 g, 29%) then the title bisphosphonate 31 as an oil (1.25 g, 62%); νmax/cm
1
2
4
984, 1733, 1237, 1013; H NMR (300 MHz, CDCl ) δ: 1.36 (t, J = 7.1, 12H), 1.90 (dt, J = 14.5,
3
.2, 1H), 2.04 (s, 3H), 2.79 (overlapping dt, J = 14.5, 7.4, 1H), 4.11 (t, J = 17.6, 1H), 4.13-4.33
PH
1
3
(
m, 8H), 4.76-4.85 (m, 1H), 5.44-5.53 (m, 1H), 5.99-6.06 (m, 1H), 6.16-6.23 (m, 1H); C NMR
(
75.5 MHz, CDCl ) δ: (75.5 MHz, CDCl ) 16.2-16.5 (m), 21.0, 37.0, 63.2-63.7 (m), 71.8 (t, J
3
3
PC
31
=
157.8), 76.4, 85.6 (t, J = 4.7), 133.6, 135.3, 170.6; P NMR (121.5 MHz, CDCl ) δ: 15.65,
PC 3
+
1
5.80 (q, J = 31.7); HRMS (ES+) Exact mass calculated for C H O P [M+H] 429.1443;
16 31 9 2
found 429.1448.
cis-1-{4-[bis(Diethylphosphono)methoxy]cyclopent-2-en-1-yl}thymine (32)
Thymine (95 mg, 0.75 mmol) and sodium carbonate (80 mg, 0.75 mmol) were suspended in
degassed water (0.8 mL) and degassed acetonitrile (0.8 mL) in a microwave vial and the mixture
was subjected to microwave irradiation at 50 °C for 30 mins. Bisphosphonate 31 (270 mg, 0.63
mmol), Pd(dba) (18 mg, 5 mol %) and dppb (27 mg, 10 mol %) were suspended in degassed
2
acetonitrile (1 mL), transferred to the microwave vial and the resultant mixture was irradiated at
5
0 °C for 30 mins. TLC analysis showed residual starting material, so a second portion of
catalysts was added together with more acetonitrile (1 mL) and the reaction mixture was
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irradiated for a further 30 mins at 50 °C. After cooling, dichloromethane (5 mL) was added and
the mixture was filtered through Celite, washed with dichloromethane (20 mL) and the filtrate
was concentrated under reduced pressure to give a residue which was purified by flash
chromatography (5-10% MeOH in EtOAc) to afford 32 as a foamy solid (148 mg, 48 %);
-1
1
νmax/cm 3169, 2983, 1683, 1251, 1015; H NMR (400 MHz, CDCl ) δ: 1.28-1.45 (m, 12H),
3
1
1
6
3
1
.86 (dt, J = 15.2, 2.8, 1H), 1.92 (s, 3H), 2.81 (overlapping dt, J = 15.6, 7.9, 1H), 4.14 (t, J =
PH
7.8, 1H), 4.17-4.36 (m, 8H), 4.85-4.93 (m, 1H), 5.63-5.73 (m, 1H), 5.87-5.95 (m, 1H), 6.29-
1
3
.38 (m, 1H), 7.23 (s, 1H), 9.79 (s, 1H); C NMR (100.6 MHz, CDCl ) δ: 12.3, 16.0-16.7 (m),
3
6.7, 57.8, 63.1-63.6 (m), 72.0 (t, J = 158.1), 86.1 (t, J = 4.5), 111.2, 134.0, 136.1, 137.2,
PC
PC
31
51.2, 164.1; P NMR (162.0 MHz, CDCl ) δ: 15.72, 15.92 (ABq, J = 31.1); HRMS (ES+)
3
AB
+
Exact mass calculated for C H N O P [M+H] 495.1661; found 495.1660.
1
9
33
2
9 2
cis-1-{4-[(Diphosphono)methoxy]cyclopent-2-en-1-yl}thymine (3)
Bisphosphonate 32 (32 mg, 0.065 mmol) was suspended in acetonitrile (1.5 mL) in a microwave
vial and 2,6-lutidine (75 µL, 0.64 mmol ) then TMSBr (85 µL, 0.64 mmol) were added. The
reaction mixture was irradiated at 50 °C for 30 mins then methanol (1.5 mL) and water (100 µL)
were added and stirring was continued for 1 h. Solvents were removed under reduced pressure
and the residue was subjected to charcoal chromatography, eluting with water then 20% aqueous
1
ammonia, to give the title compound as the ammonium salt (22 mg, 84%); H NMR (400 MHz,
D O) δ: 1.64-1.78 (m, 1H), 1.83 (s, 3H), 2.81-3.02 (m, 1H), 3.67-3.98 (m, 1H), 4.85-4.95 (m,
2
1
3
1
H), 5.36-5.46 (m, 1H), 5.80-5.90 (m, 1H), 6.31-6.42 (m, 1H), 7.49 (s, 1H); C NMR (100.6
MHz, D O) δ: 11.3, 37.2, 59.1, 84.9-85.1 (m), 111.3, 131.9, 137.3, 140.0, 152.4, 166.8, (PCH
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4

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2
5
3
1
not seen); P NMR (162.0 MHz, D O) δ: 13.4; HRMS (ES-) Exact mass calculated for
2
-
C H N O P [M-H] 381.0253; found 381.0240.
11
15
2
9 2
cis-1-{4-[bis(Diethylphosphono)methoxy]cyclopentan-1-yl}thymine (33)
cis-1-{4-[bis(Diethylphosphono)methoxy]cyclopent-2-en-1-yl}thymine (123 mg, 0.25 mmol)
was dissolved in methanol (10 mL), 5% palladium on carbon (40 mg) was added and the mixture
was stirred under hydrogen for 17 h then filtered through Celite. After washing with MeOH ( 2
x 10 mL) then dichloromethane ( 2 x 10 mL) the filtrate was concentrated under reduced
pressure and the residue subjected to flash chromatography (1:9, MeOH:EtOAc) to afford the
-1
1
title product (106 mg, 86%); νmax/cm 3171, 2982, 1667, 1240, 1011; H NMR (400 MHz,
CDCl ) δ: 1.31-1.45 (12H, m), 1.49-1.65 (1H, m), 1.77-1.92 (2H, m), 1.98 (3H, s), 2.10-2.23
3
(
2H, m), 2.33-2.46 (1H, m), 4.04 (t, J = 17.6, 1H), 4.15-4.36 (8H, m), 4.41-4.50 (1H, m), 5.15-
PH
1
3
5
3
1
.28 (1H, m), 7.65 (1H, s), 8.81 (1H, s); C NMR (100.6 MHz, CDCl ) δ: 12.3, 16.3-16.6 (m),
3
0.2, 30.8, 38.3, 53.5, 63.1-63.7 (m), 70.8 (t, J = 158.6), 83.4 (t, J = 4.2), 111.5, 138.0,
PC
PC
31
51.3, 163.7; P NMR (162.0 MHz, CDCl ) δ: 16.25, 16.31 (ABq, J = 31.2); HRMS (ES+)
3
AB
+
Exact mass calculated for C H N O P [M+H] 497.1818; found 497.1821.
1
9
35
2
9 2
cis-1-{4-[(Diphosphono)methoxy]cyclopentan-1-yl}thymine (4)
cis-1-{4-[bis(Diethylphosphono)methoxy]cyclopentan-1-yl}thymine (106 mg, 0.21 mmol) was
suspended in acetonitrile (2 mL) in a microwave vial and TMSBr (420 µL, 0.64 mmol, 15 eq)
was added. The reaction mixture was irradiated at 50 °C for 1 h then methanol (2 mL) and water
(0.5 mL) were added and stirring was continued for 1 h. Solvents were removed under reduced
pressure and the residue was subjected to charcoal chromatography, eluting with water then 20%
aqueous ammonia, to give the ammonium salt of the title compound as a cream solid (24 mg,
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-
1
1
2
2
9%); νmax/cm 2948, 1655, 1272, 1041; H NMR (400 MHz, D O) δ: 1.62-2.11 (m, 8H), 2.31-
2
1
3
.51 (1H, m), 3.72 (t, J = 13, 1H), 4.31-4.51 (1H, m), 4.80-4.95 (1H, m), 7.84 (1H, s); C
PH
NMR (100.6 MHz, D O) δ: 11.5, 29.1, 30.0, 37.3, 54.8, 81.1-81.3 (m), 111.3, 140.6, 152.6,
2
3
1
+
1
)
66.7; P NMR (162.0 MHz, D O) δ: 13.76, 13.96; MS (ES+) m/z: 407 (M + Na) ; HRMS (ES-
2
-
Exact mass calculated for C H N O P [M-H] 383.0409; found 383.0402.
1
1
17
2
9 2
cis-1-{4-[(Aminocarbonyl)dimethylphosphonomethoxy]cyclopentan-1-yl}thymine (35)
cis-1-{4-[(Methoxycarbonyl)dimethylphosphonomethoxy]cyclopentan-1-yl}thymine 34 (155
mg, 0.40 mmol) was dissolved in 7N ammonia in methanol (20 mL, 140 mmol). The flask was
tightly stoppered and the solution stirred at RT for 65 h. After concentration under reduced
pressure, flash chromatography (1:9, MeOH:CH Cl ) afforded 35 as a white solid as an
2
2
-1
essentially equimolar mixture of two diastereomers (52 mg, 35%); νmax/cm 3188, 2958, 1661,
1
1
3
5
0
3
7
1
247, 1026, 727; H NMR (400 MHz, CDCl ) δ: 1.56-2.24 (m, 8H), 2.35-2.50 (m, 1H), 3.80-
3
.93 (m, 6H), 4.18-4.26 (m, 1H), 4.32 (2 overlapping d which appear as a t, J = 18.8), 5.00-
PH
.22 (m, 1H), 6.67-6.78 (br s, 1H), 6.94 (br s, 0.5H), 7.06 (br s, 0.5H), 7.55 (s, 0.5H), 7.57 (s,
1
3
.5H), 9.95 (br s, 1H); C NMR (100.6 MHz, CDCl ) δ: 12.29, 12.33, 29.6, 30.4, 31.6, 37.4,
3
8.5, 53.5, 54.39, 53.8 (d, J = 6.8), 54.0 (d, J = 6.8), 54.2 (d, J = 6.8), 54.3 (d, J = 6.9),
PC
PC
PC
PC
4.1 (d, J = 158.1), 75.3 (d, J = 157.3), 81.8 (d, J = 10.8), 82.7 (d, J = 8.8), 111.4, 111.5,
PC
PC
PC
PC
3
1
37.91, 137.93, 151.49, 151.55, 164.2, 169.07 (d, J = 3.0), 169.35 (d, J = 3.3); P NMR
PC
PC
(162.0 MHz, CDCl ) δ: 18.47, 18.65; HRMS (ES+) Exact mass calculated for C H N O P
3 14 23 3 7
+
[
M+H] 376.1274; found 376.1265.
cis-1-{4-[(Aminocarbonyl)phosphonomethoxy]cyclopentan-1-yl}thymine (5)
2
6

Page 27 of 33
Organic & Biomolecular Chemistry
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DOI: 10.1039/C5OB02507A
2
7
cis-1-{4-[(Aminocarbonyl)dimethylphosphonomethoxy]cyclopentan-1-yl}thymine 35 (66 mg,
.17 mmol) was suspended in acetonitrile (2 mL) in a microwave vial and TMSBr (93 µL, 0.70
0
mmol) was added. The reaction mixture was irradiated at 50 °C for 10 mins then methanol (1.9
mL) and water (100 µL) were added and stirring was continued for 10 minutes. Solvents were
removed under reduced pressure and the residue was subjected to charcoal chromatography,
eluting with water then 10:10:3, H O:MeOH:20% aq NH to afford the ammonium salt of 5 as a
2
3
-1
1
fawn solid (45 mg, 70%); νmax/cm 3186, 2957, 1561, 1270, 1055, 765; H NMR (400 MHz,
D O) δ: 1.52-2.01 (m, 8H), 2.19-2.39 (m, 1H), 3.91 (2 overlapping d which appear as a t, J =
2
PH
1
3
1
7.2), 4.01 (br s, 1H), 4.66-4.85 (m, 1H), 7.61 (s, 0.5H), 7.64 (s, 0.5H); C NMR (100.6 MHz,
D O) δ: 11.46, 11.49, 28.7, 28.9, 29.7, 30.5, 36.5, 37.4, 54.7, 55.0, 77.4 (d, J = 138.3), 78.0 (d,
2
PC
J = 138.7), 80.6 (d, J = 9.2), 81.1 (d, J = 8.8), 111.2, 111.3, 140.1, 140.2, 152.49, 152.51,
PC
PC
PC
31
1
66.49, 166.52, 175.8, 176.0; P NMR (162.0 MHz, D O) δ: 9.7 br; HRMS (ES+) Exact mass
2
+
calculated for C H N O P [M+H] 348.0961; found 348.0953.
1
2
19
3
7
ASSOCIATED CONTENT
1
13
Electronic Supplementary Information (ESI) available: H and C NMR spectra of all
novel compounds. Analytic purity of compounds 2, 2a, 2b, 3, 4, and 5 determined by HPLC.
AUTHOR INFORMATION
Corresponding Author
*
A.R.M.: Fax, +(353)0214274097; Tel, +(353)0214901694; e-mail, a.maguire@ucc.ie
Author Contributions
2
7

Organic & Biomolecular Chemistry
Page 28 of 33
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2
8
DOI: 10.1039/C5OB02507A
All authors contributed equally to this work and have given their approval to the final version of
the manuscript.
ACKNOWLEDGMENTS
This work was supported by Science Foundation Ireland (05/PICA/B802 and SFI
1
4/TIDA/2402). EA acknowledges support from NIH grant R37 MERIT Award AI27690. The
research of JB was supported by the KU Leuven (GOA (GOA 15/19 TBA). We are grateful to
Mrs. Lizette van Berckelaer and Mrs. Ria Van Berwaer for excellent technical assistance,
Matthew T. Miller and Mena Issa for help with crystallization, Argon Photon Source (APS)
beam line 23ID-D for X-ray data collection, and Prof. Pat Guiry, University College Dublin,
Ireland for mass spectrometry.
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