Flexible cyclic ethers/polyethers as novel P2-ligands for HIV-1 protease inhibitors: Design, synthesis, biological evaluation, and protein-ligand X-ray studies

Article abstract of DOI:10.1021/jm8004543

We report the design, synthesis, and biological evaluation of a series of novel HIV-1 protease inhibitors. The inhibitors incorporate stereochemically defined flexible cyclic ethers/polyethers as high affinity P2-ligands. Inhibitors containing small ring 1,3-dioxacycloalkanes have shown potent enzyme inhibitory and antiviral activity. Inhibitors 3d and 3h are the most active inhibitors. Inhibitor 3d maintains excellent potency against a variety of multi-PI-resistant clinical strains. Our structure-activity studies indicate that the ring size, stereochemistry, and position of oxygens are important for the observed activity. Optically active synthesis of 1,3-dioxepan-5-ol along with the syntheses of various cyclic ether and polyether ligands have been described. A protein-ligand X-ray crystal structure of 3d-bound HIV-1 protease was determined. The structure revealed that the P2-ligand makes extensive interactions including hydrogen bonding with the protease backbone in the S2-site. In addition, the P2-ligand in 3d forms a unique water-mediated interaction with the NH of Gly-48.

Full text of DOI:10.1021/jm8004543

J. Med. Chem. 2008, 51, 6021–6033
6021
Flexible Cyclic Ethers/Polyethers as Novel P2-Ligands for HIV-1 Protease Inhibitors: Design,
Synthesis, Biological Evaluation, and Protein-Ligand X-ray Studies†
Arun K. Ghosh,*,‡ Sandra Gemma,‡ Abigail Baldridge,‡ Yuan-Fang Wang,§ Andrey Yu. Kovalevsky,§ Yashiro Koh,|
Irene T. Weber,§ and Hiroaki Mitsuya|,
Departments of Chemistry and Medicinal Chemistry, Purdue UniVersity, 560 OVal DriVe, West Lafayette, Indiana 47907, Department of
Biology, Molecular Basis of Disease, Georgia State UniVersity, Atlanta, Georgia 30303, Kumamoto UniVersity School of Medicine,
Kumamoto 860-8556, Japan, Department of Hematology and Infectious Diseases, Experimental RetroVirology Section, HIV and AIDS
Malignancy Branch, National Cancer Institute, Bethesda, Maryland 20892
ReceiVed April 21, 2008
We report the design, synthesis, and biological evaluation of a series of novel HIV-1 protease inhibitors.
The inhibitors incorporate stereochemically defined flexible cyclic ethers/polyethers as high affinity P2-
ligands. Inhibitors containing small ring 1,3-dioxacycloalkanes have shown potent enzyme inhibitory and
antiviral activity. Inhibitors 3d and 3h are the most active inhibitors. Inhibitor 3d maintains excellent potency
against a variety of multi-PI-resistant clinical strains. Our structure-activity studies indicate that the ring
size, stereochemistry, and position of oxygens are important for the observed activity. Optically active synthesis
of 1,3-dioxepan-5-ol along with the syntheses of various cyclic ether and polyether ligands have been
described. A protein-ligand X-ray crystal structure of 3d-bound HIV-1 protease was determined. The structure
revealed that the P2-ligand makes extensive interactions including hydrogen bonding with the protease
backbone in the S2-site. In addition, the P2-ligand in 3d forms a unique water-mediated interaction with the
NH of Gly-48.
Introduction
The introduction of protease inhibitors (PIs) into highly active
antiretroviral therapy (HAART), a combination therapy based
on coadministration of PIs with reverse-transcriptase inhibitors,
marked the beginning of a new era in HIV/AIDS chemotherapy.
HAART treatment regimens have led to a significant decline
in the number of deaths due to HIV infection in the developed
world.1 Unfortunately, there are a number of factors that severely
limit current HAART treatment regimens. High frequency of
dosing, heavy pill burden, and issues of tolerability and toxicity
can lead to poor adherence to treatment.2 The need for more
potent, less toxic drug regimens is quite apparent.
It is the rapid emergence of drug resistance, however, that is
proving to be the most formidable problem. Mutations causing
drug resistance are thought to occur spontaneously, through the
recombination of mixed viral populations, and also due to drug
pressure, particularly when administered at substandard doses.3-6
A growing number of patients are developing multidrug-resistant
HIV-1 variants.7,8 There is ample evidence that these viral strains
can be transmitted. Thus, the development of antiretroviral
agents able to maintain potency against resistant HIV strains
has become an urgent priority.
Darunavir (TMC-114, 1, Figure 1) is a new nonpeptidic PI
Figure 1. Structure of inhibitors 1, 2, and 3c,d.
recently approved by the FDA for the treatment of antiretroviral
therapy-experienced patients.9 Inhibitor 1, and its related
analogue 2, are exceedingly active against both wild-type and
multidrug resistant HIV strains. Both PIs demonstrated potent
in vitro activity against viral isolates resistant to currently
licensed PIs.10-12 Our structure-based design strategies for these
PIs are based on the presumption that maximizing active site
interactions with the inhibitor, particularly hydrogen bonding
with the protein backbone, would give rise to potent inhibitors
retaining activity against mutant strains.13,14 Indeed, side chain
amino acid mutations cannot easily disrupt inhibitor-backbone
interactions because the active site backbone conformation of
mutant proteases is only minimally distorted compared to the
wild-type HIV-1 protease.15-17 In this context, the fused bis-
tetrahydrofuran (bis-THF) urethane of compounds 1 and 2 was
demonstrated to be a privileged P2-ligand, being able to engage
†
The PDB accession code for 3d-bound HIV-1 protease X-ray structure
is 3DJK.
* To whom correspondence should be addressed. Phone: (765)-494-5323.
Fax: (765)-496-1612. E-mail: akghosh@purdue.edu.
‡
Departments of Chemistry and Medicinal Chemistry, Purdue University.
Department of Biology, Molecular Basis of Disease, Georgia State
§
University.
|
Kumamoto University School of Medicine.
HIV and AIDS Malignancy Branch, National Cancer Institute.
10.1021/jm8004543 CCC: $40.75
2008 American Chemical Society
Published on Web 09/11/2008

6022 Journal of Medicinal Chemistry, 2008, Vol. 51, No. 19
Table 1. Enzyme Inhibitory and Antiviral Activity of Inhibitors 3a-m
Ghosh et al.
a MT-2 human T-lymphoid cells exposed to HIV-1LAI b nd ) not determined. c SQV ) saquinavir. d APV ) amprenavir.
.
in a number of hydrogen bonding interactions with the backbone
atoms of amino acids at the protease S2-site.
revealed important molecular insight regarding ligand-binding
site interactions.
We are continuing our efforts toward the development of
novel PIs characterized by a high activity against both wild-
type HIV-1 and resistant strains. We further speculated that an
inhibitor interacting strongly with the protein backbone, while
being able to accommodate amino acid side chain variations
by means of repacking with a flexible ring, would maintain
significant affinity against both wild-type and mutant enzymes.
With this goal in mind, we designed a series of PIs based on
the (R)-(hydroxyethylamino)sulfonamide isostere and bearing
flexible cyclic ethers and polyethers as P2-ligands (inhibitors
3a-m, Table 1). Starting from compound 3c, incorporating a
(1R)-3,5-dioxacyclooctan-1-yl urethane, which can be consid-
ered as the flexible counterpart of the bis-THF moiety, we
designed a series of structural variants of this inhibitor. These
inhibitors contain polyether-based P2-ligands ranging from 6-
to 13-membered rings coupled to a p-methoxyphenylsulfona-
mide as the P2′-ligand. Herein we report the structure-based
design, synthesis, and preliminary biological evaluation of
inhibitors 3a-m. Among these inhibitors, 3d (Figure 1) is the
most potent, with an impressive enzyme inhibitory and antiviral
activity (Ki ) 26 pM, IC50 ) 4.9 nM). Furthermore, a
protein-ligand X-ray structure of 3d-bound HIV-1 protease has
Chemistry. The syntheses of seven- and eight-membered 1,3-
dioxacycloalkanes 8a-d for the corresponding inhibitors 3a-d
are shown in Scheme 1. Protected diol 6a was prepared by a
two-step procedure starting from (S)-hydroxyglutaric acid 4,
obtained by following a known protocol.18 The hydroxyl group
of 4 was protected as a tert-butyldiphenylsilylether 5 in
quantitative yield. LiBH4 reduction of both ester groups afforded
6a in good yield.19
Compounds 6a and 6b20 were converted to cyclic derivatives
21
by exposure to paraformaldehyde and BF3 ·OEt2 to afford
cyclic ethers 7a and 7b in 51% and 82% yield, respectively.
Deprotection of compounds 7a to 8a was carried out by using
n-Bu4N+F- in THF. Benzylether of 7b was removed by a
catalytic hydrogenation over 10% Pd-C to furnish 8b. Mit-
sunobu inversion of the secondary hydroxyl groups of 8a,b was
accomplished by using p-nitrobenzoic acid, triphenylphosphine,
and diisopropylazodicarboxylate in benzene at 23 °C. Saponi-
fication of the resulting esters provided 8c and 8d.
For the synthesis of compounds 8e and 8f, which represent
the monoxygenated analogues of 8d, a synthetic strategy based
on a ring-closing metathesis reaction as the key step was planned
(Schemes 2 and 3). Accordingly, secondary alcohol 922 (Scheme

Flexible Cyclic Ethers/Polyethers as P2-Ligands
Journal of Medicinal Chemistry, 2008, Vol. 51, No. 19 6023
Scheme 4. Synthesis of Polyethers 8h-j
Scheme 1. Synthesis of Optically Active 1,3-Dioxacycloalkanes
Scheme 2. Synthesis of Cyclic Ether 8e
following a described procedure starting from acrolein and tert-
butylacetate.23 Alkylation of the primary hydroxyl group of 13
with allyl bromide and n-Bu4N+I- using sodium hydride as the
base furnished the ring closing metathesis precursor 14. The
cyclization reaction was performed by using second generation
Grubbs catalyst (5 mol%) in CH2Cl2 and afforded olefin 15 in
good yield. Subsequent hydrogenation of the double bond and
n-Bu4N+F--mediated removal of TBDMS-ether finally afforded
the target alcohol 8f.
Scheme 3. Synthesis of Cyclic Ether 8f
Alcohols 8h-j required for the preparation of inhibitors 3h-j
were synthesized by starting from the common intermediate
2-benzyloxypropane-1,3-diol 17 as shown in Scheme 4. Com-
pound 17 was prepared by alkylation of commercially available
benzylidene acetal 16 with benzyl chloride in the presence of
sodium hydride and a catalytic amount of n-Bu4N+I- in THF
at 23 °C. The benzylidene group was subsequently removed
by hydrolysis with 6 N HCl in a mixture (1:1) of THF and
water to give 2-benzyloxy-1,3-propanediol 17 in quantitative
yield. Treatment of 17 with paraformaldehyde and BF3 ·OEt2
as described above, followed by hydrogenolysis of the resulting
O-benzylether afforded 8h in 78% overall yield.
Treatment of diol 17 with an excess of sodium hydride in
refluxing THF followed by addition of di(ethyleneglycol)dime-
sylate or tri(ethyleneglycol)dimesylate afforded macrocycles 18
and 19 in 19% and 29% yield, respectively. Dilution of the
reaction mixture to assist the intramolecular cyclization reaction
did not result in a significant improvement of the reaction yields.
Given the poor enzymatic inhibitory activity observed for the
corresponding final compounds 3i and 3j, no further attempts
were made to improve the cyclization yield for the preparation
of these 10- and 13-membered polyether rings. Compounds 18
and 19 were subsequently deprotected by hydrogenolysis to
obtain alcohols 8i and 8j.
We planned to investigate the effect of heteroatom function-
alities in the polyether rings. In this context, we prepared the
compounds 8k, 8l, and 24 from known diols 2024 as shown in
Scheme 5. Thus, exposure of 20 to paraformaldehyde in the
presence of BF3 ·OEt2 furnished the corresponding cyclic
2) was protected as the corresponding methoxyethoxymethyl
(MEM)-ether 10 in 90% yield using an excess of MEM-Cl in
the presence of DIPEA in CH2Cl2.
Subsequent n-Bu4N+F--promoted deprotection of the
TBDMS-group afforded the corresponding primary alcohol,
which was treated with sodium hydride and alkylated with allyl
bromide in the presence of a catalytic amount of n-Bu4N+I- to
afford olefin 11 in 78% yield (2 steps). A 0.01 M solution of
11 in CH2Cl2 was then treated with a catalytic amount (5 mol%)
of second generation Grubbs catalyst and heated to 45 °C to
afford the cyclooxepane 12 in 94% yield. The double bond of
12 was finally reduced by catalytic hydrogenation using 10%
Pd-C as the catalyst, and the MEM-ether was removed by
acidic hydrolysis in a 1:1 THF/H2O mixture to obtain the target
alcohol 8e in good overall yield.
For the synthesis of alcohol 8f (Scheme 3), compound 13
was used as the starting material. It was in turn prepared

6024 Journal of Medicinal Chemistry, 2008, Vol. 51, No. 19
Scheme 5. Synthesis of Alcohols 8k,l and 24
Ghosh et al.
Scheme 6. Synthesis of Various Active Carbonates
polyether product, which, upon hydrogenolysis, gave alcohol
8k. Bromination of 20 using carbon tetrabromide and triph-
enylphosphine afforded dibromide 21.24 This dibromide was
used for the synthesis of sulfone 8l and protected amine 24.
Thus, compound 21 was reacted with one equivalent of
benzylamine in refluxing MeCN in the presence of sodium
carbonate, as reported by Calverley and Dale,25 to provide 23
in 24% yield. Dimerization is the main side product in this
reaction and one can reduce such dimerization by using an
excess of LiClO4.26 Benzylamine 23 was hydrogenated over
10% Pd-C in the presence of di-t-butyl dicarbonate to provide
N-Boc protected alcohol 24. Sulfone 22 was obtained by
cyclization of 21 with lithium sulfide, followed by oxidation of
the corresponding sulfide with an excess of m-CPBA in CH2Cl2
at 23 °C. Benzyl derivative 22 was converted to 8l by a catalytic
hydrogenation over 10% Pd-C.
Scheme 7. Synthesis of Inhibitors 3a-l
Scheme 6 depicts the conversion of various P2-ligands to
the corresponding active carbonates for urethane formation.
Accordingly, alcohols 8a-h,j-l were reacted with p-nitrophe-
nylchloroformate and N-methylmorpholine in THF at 23 °C to
provide corresponding carbonates 25a-h,j-l in 67-89% yields.
Alcohol 8i was converted to succinimidylcarbamate 25i by
treatment with N,N′-succinimidylcarbonate in the presence of
Et3N in MeCN in 37% isolated yield.
The synthesis of designed inhibitors 3a-l is shown in Scheme
7. Methoxysulfonamide derivative 27 was prepared from
commercially available epoxide 26 as described previously.27
The Boc group in 27 was removed by exposure to a 30%
solution of TFA in CH2Cl2 at 23 °C. The resulting amine 28
was reacted with the suitable mixed activated carbonates 25a-l
in THF at 23 °C for 2-4 days to furnish inhibitors 3a-l in
36-89% yield.
amine was subjected to a reductive amination reaction using
37% aqueous formaldehyde and sodium cyanoborohydride in
1% acetic acid in MeOH to furnish N-methyl derivative 3m in
87% yield.
The synthesis of inhibitor 3m is shown in Scheme 8. Alcohol
24 was converted to active carbonate 29 as described above in
Scheme 6. Reaction of 29 with amine 28 provided urethane 30
in good yield. Removal of Boc group of 30 by exposure to 30%
TFA in CH2Cl2 furnished amine 31. The resulting secondary
Results and Discussion
All inhibitors contain a (R)-hydroxyethylamine sulfonamide
isostere with a p-methoxysulfonamide as the P2′-ligand and
various designed cyclic ethers and polyethers as the P2-ligands.

Flexible Cyclic Ethers/Polyethers as P2-Ligands
Journal of Medicinal Chemistry, 2008, Vol. 51, No. 19 6025
Scheme 8. Synthesis of Inhibitor 3m
position of the oxygen atoms within the polyether structure,
could be important for inhibitory activity. In fact, compound
3k, presenting a 12-membered ring bearing a methylenedioxy
unit instead of the ethylenedioxy of 3j, exhibited 5-fold potency
enhancement compared to inhibitor 3j. It is also more than 2-fold
more potent compared to 3i, which contains a smaller 10-
membered ring. Substitution of a ring oxygen in 3i by a N-Me
group provided inhibitor 3m with no change in inhibitory
activity. However, replacement of ring oxygen with a SO2
moiety provided inhibitor 3l with a 9-fold improvement in
potency. The sulfone oxygens may be involved in specific
interactions with the amino acid residues at the S2 site.
In MT-2 human T-lymphoid cells exposed to HIV-1LAI
,
inhibitors 3d and 3h have shown antiviral IC50 values of 4.9
nM and 3.4 nM, respectively (Table 1). Consistent with its
enzymatic potency, compound 3b showed an antiviral activity
of 30 nM in the same assay system, while compounds 3k-m
did not exhibit appreciable antiviral properties at doses up to 1
µM. We have examined two selected compounds, 3d and 3h,
for their activity against HIV-1 using a human CD4+ T-cell
line (MT-2 cells) and human peripheral blood mononuclear cells
(PBMCs) as target cells. We employed two end points for the
activity against HIV-1: (i) the inhibition of the HIV-1-elicited
cytopathic effect for MT-2 cells and (ii) the inhibition of HIV-1
p24 production for PBMCs.14a As examined in MT-2 cells as
target cells, the two compounds 3d and 3h exerted extremely
These inhibitors were first evaluated in an enzyme inhibitory
assay utilizing a protocol described by Toth and Marshall.28
Compounds that showed potent enzymatic Ki values were then
further evaluated in an antiviral assay. The results are shown
in Table 1. The Ki-values denote the mean values of at least
four determinations.
potent antiviral activity against an X4-HIV-1 isolate (HIV-1LAI
)
As it can be seen, introduction of the 8-membered (S)- or
(R)-1,3-dioxacyclooctan-5-yl urethanes as P2-ligands (inhibitors
3a and 3c) resulted in subnanomolar inhibitors. However, these
inhibitors are significantly less potent than inhibitor 2 that
contains the bis-THF ligand. Interestingly, incorporation of a
(5R)-1,3-dioxacycloheptan-5-yl urethane as the P2-ligand re-
sulted in the most potent inhibitor 3d in this series with a Ki
value of 26 pM. We speculated that the 7-membered 1,3-
dioxepanyl-ligand with R-configuration may bind to residues
in the S2-site similar to bis-THF ligand of inhibitor 2. Inhibitor
3d exhibited more than 6-fold potency increase relative to
epimeric (5S)-1,3-dioxacycloheptan-5-yl urethane 3b, suggesting
an important role for the ring stereochemistry. Inhibitors 3e-g
were prepared to assess the role played by both oxygen atoms
of 3d on the binding mode of this latter compound. As shown
in Table 1, a dramatic drop in enzymatic inhibitory activity was
observed when the cycloheptanol was introduced as the P2-
ligand (3g). Moreover, nearly 30-fold reduction in enzymatic
inhibitory potency of both 3e and 3f with respect to 3d clearly
demonstrated that both oxygen atoms are crucial for the
interaction with the enzyme at the S2-subsite. It appears that
both oxygen atoms engage in strong hydrogen bonding, which
equally contribute to the binding affinity for the enzyme. This
result was further confirmed by the determination of the X-ray
crystal structure of 3d-bound HIV-1 protease.
with IC50 values of 4.9 and 3.4 nM, respectively (Table 1). Such
anti-HIV-1 potency was generally parallel to the potency in
enzymatic inhibition of the compounds. We further examined
the two compounds in PBMCs against a clinical wild-type X4-
HIV-1 isolate (HIV-1ERS104pre) along with various multidrug-
resistant clinical X4- and R5-HIV-1 isolates (Table 2).14 The
activity of 3d and 3h against HIV-1ERS104pre was more potent
or at least comparable as compared to those of currently
available protease inhibitors, APV, IDV, and RTV. It is
interesting to note that the values of 3d were greater than those
with MT-2 cells by factors of about 4. With regard to this
difference, considering that 3d was highly potent as examined
in human T cells (MT-2 cells) but its activity was slightly less
in PBMCs, it is possible that relatively higher concentrations
of 3d are required to suppress HIV-1 production in chroni-
cally infected macrophages.42 Two currently available pro-
tease inhibitors (IDV and RTV) were not capable of
efficiently suppressing the replication of most of the multi-
drug-resistant clinical isolates examined (HIV-1MDR-B, HIV-
1
MDR-G, HIV-1MDR-TM, HIV-1MDR-JSL, and HIV-1MDR-MM) with
IC50 values of >1.0 µM. Although the two selected com-
pounds were also less potent against the multidrug-resistant
clinical isolates examined, their IC50 values were quite low
with 0.22-0.54 µM (Table 2). During testing of the anti-
HIV-1 activity of compounds 3b, 3d, 3h, and 3k-m, we
examined four concentrations (1, 0.1, 0.01, and 0.001 µM)
in the antiretroviral assay, conducted on three independent
occasions (each assay was performed in duplicate). As noted,
no cytotoxicity was observed for any of the compounds
examined. Thus, it was deemed that the CC50 values were
greater than the highest concentration, 1 µM.
Further reduction of the ring size of the P2-ligand resulted
in the design of inhibitor 3h, bearing a 6-membered 1,3-dioxan-
5-yl urethane. This inhibitor also showed an impressive
enzymatic Ki value of 41 pM. This result suggested that the
1,3-dioxane ring could be nicely accommodated by the S2-site.
Furthermore, both oxygens may be involved in specific interac-
tions with the amino acid residues in this region.
Subsequently, we tested compounds 3i-m, presenting larger
polyether rings, but all compounds showed Ki values in the high
nM range (Kis ranging from 6.3 to 33 nM), proving that large
rings could not be easily accommodated at the S2-site.
However, subtle differences in the activity among these
compounds suggested that not only the ring size, but also the
X-ray Crystallography. The mode of binding of the inhibitor
was determined by analyzing the atomic resolution crystal
structure of HIV-1 protease with 3d. The crystal structure was
solved and refined to an R factor of 14.9% at 1.00 Å resolution.
The inhibitor binds with extensive interactions from P2 to P2′
with the protease atoms and, most notably, the favorable polar

6026 Journal of Medicinal Chemistry, 2008, Vol. 51, No. 19
Ghosh et al.
Table 2. Antiviral Activity (IC50) of Inhibitors 3d and 3h against Clinical HIV-1 Isolates in PBMC Cells (nM)
IC50 (nM) valuesa
virus
3d
3h
DRV
RTV
APV
33
IDV
ERS104pre(wild-type)
MDR/TM
MDR/MM
MDR/JSL
MDR/B
20
6
3.5
34
26
220 (11)
250 (13)
500 (25)
340 (17)
210 (11)
360 (18)
20 (1)
64 (10)
110 (5)
330 (55)
230 (38)
160 (27)
300 (50)
13 (2)
4 (1)
17 (5)
26 (7)
26 (7)
7 (2)
7 (2)
3 (1)
>1000 (>29)
>1000 (>29)
>1000 (>29)
>1000 (>29)
>1000 (>29)
>1000 (>29)
>1000 (>29)
290 (9)
300 (9)
430 (13)
320 (10)
230 (7)
340 (10)
100 (3)
>1000 (>38)
>1000 (>38)
>1000 (>38)
>1000 (>38)
>1000 (>38)
290 (11)
MDR/C
MDR/G
MDR/A
>1000 (>38)
a Amino acid substitutions identified in the protease-encoding region compared to the consensus type B sequence cited from the Los Alamos database
include L63P in HIV-1ERS104pre; L10I, K14R, L33I, M36I, M46I, F53I, K55R, I62V, L63P, A71V, G73S, V82A, L90M, and I93L in HIV-1MDR-B; L10I,
V11I, T12E, I15V, L19I, R41K, M46L, L63P, A71T, V82A, and L90 M in HIV-1MDR-G; L10I, K14R, R41K, M46L, I54V, L63P, A71V, V82A, L90M,
I93L in HIV-1MDR-TM; L10I, L24I, I33F, E35D, M36I, N37S, M46L, I54V, R57K, I62V, L63P, A71V, G73S, and V82A in HIV-1MDR-JSL; and L10I, K43T,
M46L, I54V, L63P, A71V, V82A, L90M, and Q92K in HIV-1MDR-MM. HIV-1ERS104pre served as a source of wild-type HIV-1.The IC50 values were determined
by employing PHA-PBMC (phytohemaglutinin-activated peripheral blood mononuclear cells) as target cells and the inhibition of p24Gag protein production
as the end point. All values were determined in triplicate. DRV (Darunavir), SQV (Saquinavir), APV (Amprenavir), IDV (Indinavir).
Figure 2. Stereoview of compound 3d bound to the active site of wild-type HIV-1 protease.
interactions including hydrogen bonds, weaker C-H· · ·O and
C-H· · ·π interactions, as shown in Figure 2. The central
hydroxyl group forms hydrogen bonds to the side chain
carboxylate oxygen atoms of the catalytic Asp25 and Asp25′
residues. The inhibitor hydrogen bonds with protease main chain
atoms of the amides of Asp29 and Asp30, the carbonyl oxygen
of Gly 27, and the water-mediated interactions with the amides
of Ile50 and 50′, which is conserved in the majority of protease
complexes with inhibitors29 and substrate analogues.30 Inhibitor
3d has retained the water-mediated interaction with the π system
of the P2′ aromatic ring, which was observed for darunavir (1)
and GRL-98065.31 The P2′ methoxy group forms a hydrogen
bond with the amide of Asp30′. Interestingly, the P2 group forms
a water-mediated interaction with the amide of Gly48, similar
to the interactions described for several peptide substrate
analogues.30
Conclusions. In summary, a series of novel and highly potent
HIV-1 protease inhibitors were designed, synthesized, and
evaluated. The inhibitors incorporate a variety of flexible cyclic
ethers/polyethers as the P2-ligand. Inhibitors containing small
size 1,3-dioxacycloakanes have shown potent inhibitory proper-
ties. In particular, inhibitors 3d and 3h have shown remarkable
enzyme inhibitory and antiviral potency. Inhibitors incorporating
medium-size cyclic polyethers or polyethers containing a sulfone
or amine functionality were significantly less potent in antiviral
assays. For inhibitor 3d, we have carried out an optically active
synthesis of (R)-1,3-dioxepan-5-ol using (S)-malic acid as the
starting material. Syntheses of various cyclic ethers/polyethers
were developed albeit in moderate yields. Inhibitor 3d has shown
excellent activity against multi-PI-resistant variants compared
to other FDA approved inhibitors. A protein-ligand X-ray
structure of 3d-bound HIV-1 protease was determined at 1.0 Å
resolution. One of the oxygens of the 1,3-dioxepane ligand is
involved in hydrogen bonding with Asp29 and Asp30 NH’s.
The other oxygen is involved in a unique interaction with Gly-
48 NH through a water molecule. One goal of our inhibitor
design strategy is to combat drug-resistant HIV. The design of
inhibitor using the concept of maximizing “backbone binding”
has led to the development of PIs characterized by high potency
against both wild-type and multidrug-resistant HIV-1 strains.
Further design of inhibitors utilizing this molecular insight is
in progress.
Experimental Section
General. All moisture sensitive reactions were carried out under
nitrogen or argon atmosphere. Anhydrous solvents were obtained
as follows: THF, diethyl ether and benzene, distilled from sodium
and benzophenone; dichloromethane, pyridine, triethylamine, and
diisopropylethylamine, distilled from CaH2. All other solvents were
HPLC grade. Column chromatography was performed with What-
man 240-400 mesh silica gel under low pressure of 5-10 psi.
TLC was carried out with E. Merck silica gel 60-F-254 plates. 1H
and 13C NMR spectra were recorded on Varian Mercury 300 and
Bruker Avance 400 and 500 spectrometers. Optical rotations were
measured using a Perkin-Elmer 341 polarimeter.
(S)-2-(tert-Butyldiphenylsilyloxy)pentadioic Acid Dimethyl Ester
(5). A mixture of (2S)-hydroxypentadioic acid dimethyl ester 418
(0.39 g, 2.2 mmol), imidazole (0.45 g, 6.6 mmol), and tert-
butyldiphenylsilyl chloride (1.2 mL, 4.4 mmol) in dry DMF (4 mL)
was stirred at 23 °C for 4 h. Subsequently, the reaction mixture
was poured into water and the aqueous phase was extracted with
Et2O, the organic extracts were washed with 1 N HCl and brine,
dried (Na2SO4), and the solvent was removed. The residue was

Flexible Cyclic Ethers/Polyethers as P2-Ligands
Journal of Medicinal Chemistry, 2008, Vol. 51, No. 19 6027
purified by flash-chromatography (1:10 EtOAc/hex) to furnish
0.89 g (90%) of 5 as a colorless oil: [R]D20 -21.1 (c 9.0, CHCl3).
1H NMR (CDCl3) δ 7.69-7.62 (m, 4H), 7.46-7.33 (m, 6H), 4.31
(t, J ) 5.4 Hz, 1H), 3.64 (s, 3H), 3.45 (s, 3H), 2.57-2.34 (m, 2H),
2.14-2.04 (m, 2H), 1.11 (s, 9H). 13C NMR (CDCl3) δ 173.4, 172.9,
135.9, 135.7, 133.0, 132.9, 129.9, 129.8, 127.7, 127.5, 71.4, 51.6,
51.5, 29.9, 28.9, 26.9, 19.4.
chromatography (1:3 EtOAc/hex). The resulting ester was dissolved
in a 3:2:1 mixture of THF, methanol, and water (4 mL) and
LiOH·H2O (72 mg, 1.7 mmol) was added. The yellow mixture
was stirred at 23 °C overnight and then the solvent was removed
in vacuo, the residue was diluted with water, and the aqueous phase
was extracted with ether. The organic extracts were dried (Na2SO4)
and the solvent evaporated. Purification of the residue by flash-
chromatography (EtOAc) afforded 20 mg (44%) of (R)-8c as a
(S)-2-(tert-Butyldiphenylsilyloxy)pentan-1,5-diol (6a). Com-
pound 5 (0.8 g, 1.8 mmol) was dissolved in dry Et2O (8.5 mL) and
the solution was cooled to 0 °C, afterward lithium borohydride (0.12
g, 5.4 mmol) and dry methanol (0.22 mL, 5.4 mmol) were
sequentially added. The resulting suspension was stirred at 23 °C
for 24 h, then a few drops of 6 N HCl were added and the salts
were filtered off. The filtrate was concentrated under reduced
pressure and the residue was purified by flash-chromatography (1:1
20
1
colorless liquid. [R]D +12.1 (c 1.4, CHCl3). H and 13C NMR
are consistent with those reported for the (S)-enantiomer 8a.
(R)-3,5-Dioxacycloheptan-1-ol (8d). The title compound was
obtained from 8b as described for (S)-8c in 73% yield. Flash-
chromatography was performed using a 1:1 mixture of EtOAc and
CHCl3 as the eluant: [R]D20 -12.6 (c 1.3, CHCl3). 1H and 13C NMR
are consistent with those reported for the (S)-enantiomer 8b.
20
EtOAc/hex) to furnish 0.61 g (93%) of 6a as a colorless oil: [R]D
(R)-1-(tert-Butyldimethylsilyloxy)-2-[(2-methoxyethoxy) me-
thoxy]pent-4-ene (10). To a mixture of 9 (350 mg, 1.6 mmol) and
diisopropylethylamine (1.2 mL, 7.2 mmol) in CH2Cl2 (8 mL),
cooled to 0 °C, MEM-Cl (550 µL, 4.8 mmol) was added and the
resulting mixture was stirred at 23 °C for 56 h. The organic phase
was washed with 0.1 N HCl, brine and dried (Na2SO4). The solvent
was removed and the residue was purified by flash-chromatography
(1:10 EtOAc/hex) to afford 440 mg (90%) of 10 as a colorless oil:
1
-15.6 (c 3.1, CHCl3). H NMR (CDCl3) δ 7.70-7.65 (m, 4H),
7.44-7.32 (m, 6H), 3.82-3.77 (m, 1H), 3.53-3.48 (m, 2H),
3.45-3.41 (m, 2H), 1.65-1.47 (m, 4H), 1.05 (s, 9H). 13C NMR
(CDCl3) δ 135.9, 135.7, 133.8, 133.7, 130.1, 129.8, 127.7, 127.6,
73.6, 65.7, 62.7, 29.7, 28.0, 27.0, 19.3.
(S)-1-(tert-Butyldiphenylsilyloxy)-3,5-dioxacyclooctane (7a).
To a mixture of 6a (0.55 g, 1.5 mmol) and paraformaldehyde (46
mg, 1.5 mmol) in EtOAc (30 mL), boron trifluoride etherate (195
µL, 1.5 mmol) was added and the resulting mixture was stirred at
23 °C for 4 h. The organic phase was washed with a saturated
solution of NaHCO3, dried (Na2SO4), and the solvent was removed.
The residue was purified by flash-chromatography (1:4 EtOAc/hex)
to afford 0.29 g (51%) of 7a as a colorless oil: [R]D20 -8.7 (c 1.9,
20
1
[R]D +12.0 (c 1.1, CHCl3). H NMR (CDCl3) δ 5.88-5.74 (m,
1H), 5.11-5.01 (m, 2H), 4.82 (d, J ) 6.9 Hz, 1H), 4.74 (d, J )
6.9 Hz, 1H), 3.76-3.63 (m, 3H), 3.60-3.51 (m, 4H), 3.37 (s, 3H),
2.38-2.19 (m, 2H), 0.86 (s, 9H), 0.02 (s, 6H). 13C NMR (CDCl3)
δ 134.6, 117.0, 94.8, 77.4, 71.6, 66.7, 65.0, 58.9, 36.0, 25.7, 18.2,
-5.5.
1
CHCl3). H NMR (CDCl3) δ 7.67-7.63 (m, 4H), 7.45-7.34 (m,
(R)-1-Allyloxy-2-[(2-methoxyethoxy)methoxy]pent-4-ene (11). A
mixture of 10 (440 mg, 1.4 mmol) and TBAF (1.0 M solution in
THF, 4.7 mL, 4.7 mmol) in THF (3 mL) was stirred at 23 °C for
3 h, afterward a saturated solution of NaHCO3 was added, the
solvent was removed, and the aqueous phase was extracted with
CHCl3. The organic extracts were dried (Na2SO4), and the solvent
was removed. The residue was purified by flash-chromatography
to afford 237 mg (87%) of (R)-2-[(2-methoxyethoxy)methoxy]pent-
4-en-1-ol as a colorless oil: [R]D20 -55.0 (c 1.3, CHCl3). 1H NMR
(CDCl3) δ 5.85-5.71 (m, 1H), 5.11-5.02 (m, 2H), 4.81 (d, J )
7.5 Hz, 1H), 4.75 (d, J ) 7.5 Hz, 1H), 3.87-3.80 (m, 1H),
3.71-3.61 (m, 3H), 3.59-3.46 (m, 3H), 3.37 (s, 3H), 3.22 (bs,
1H), 2.36-2.19 (m, 2H). 13C NMR (CDCl3) δ 134.1, 117.3, 95.4,
81.0, 71.5, 67.3, 64.8, 58.9, 36.2. To a mixture of the above
compound (240 mg, 1.25 mmol), allyl bromide (225 µL, 1.9 mmol)
and a catalytic amount of TBAI in THF (12 mL), at 0 °C, sodium
hydride (60% dispersion in oil, 102 mg, 2.5 mmol) was added in
small portions. After 30 min, the reaction mixture was allowed to
warm to 23 °C and was stirred at the same temperature for 18 h.
Subsequently, the reaction was quenched with a saturated solution
of NH4Cl, the organic solvent was removed, and the aqueous phase
was extracted with CHCl3. The organic extracts were dried
(Na2SO4), and the solvent was evaporated. The residue was purified
by flash-chromatography (10:1 CHCl3/EtOAc) to afford 229 mg
6H), 4.69 (d, J ) 6.2 Hz, 1H), 4.45 (d, J ) 6.2 Hz, 1H), 4.03-3.95
(m, 1H), 3.70-3.61 (m, 1H), 3.59-3.48 (m, 3H), 1.93-1.80 (m,
1H), 1.77-1.61 (m, 2H), 1.47-1.34 (m, 1H), 1.12 (s, 9H). 13C
NMR (CDCl3) δ 135.7, 134.2, 129.5, 127.5, 95.6, 72.2, 71.9, 69.0,
33.2, 27.0, 26.7, 19.2.
(S)-O-Benzyl-3,5-dioxacycloheptan-1-ol (7b). Compound 6b20
(50 mg, 0.26 mmol) was reacted as described for compound 6a to
afford 44 mg (82%) of 7b after chromatographic purification (1:9
20
EtOAc/hex): [R]D +64.6 (c 1.2, CHCl3). 1H NMR (CDCl3) δ
7.35-7.26 (m, 5H), 4.81-4.77 (m, 2H), 4.58 (s, 2H), 3.95-3.73
(m, 3H), 3.73-3.62 (m, 2H), 1.98-1.91 (m, 2H). 13C NMR
(CDCl3) δ 138.3, 128.3, 127.5, 126.2, 94.9, 75.8, 70.7, 68.8, 62.6,
35.0.
(S)-3,5-Dioxacyclooctan-1-ol (8a). Compound 7a (0.27 g, 0.74
mmol) was dissolved in dry THF (5 mL) and TBAF (1.0 M solution
in THF, 0.81 mL, 0.81 mmol) was added. The resulting mixture
was stirred at 23 °C overnight, afterward a saturated solution of
NaHCO3 was added, the solvent was removed, and the aqueous
phase was extracted with EtOAc. The organic extracts were dried
and evaporated and the residue was purified by flash-chromatog-
raphy (EtOAc) to afford 76 mg (77%) of 8a as a colorless oil:
[R]D20 -12.6 (c 1.6, CHCl3). 1H NMR (CDCl3) δ 4.65 (d, J ) 6.0
Hz, 1H), 4.57 (d, J ) 6.0 Hz, 1H), 4.92-3.81 (m, 2H), 3.75-3.60
(m, 2H), 3.55 (dd, J ) 3.4, 12.1 Hz, 1H), 2.96 (bs, 1H), 1.95-1.69
(m, 3H), 1.65-1.53 (m, 1H). 13C NMR (CDCl3) δ 94.9, 73.7, 69.3,
68.2, 30.2, 24.7.
20
(80%) of 11 as a colorless oil. [R]D -5.2 (c 3.1, CHCl3). 1H
NMR (CDCl3) δ 5.87-5.79 (m, 2H), 5.34 (dd, J ) 1.3, 19.1 Hz,
1H), 5.16-5.03 (m, 3H), 4.81 (d, J ) 7.0 Hz, 1H), 4.77 (d, J )
7.0 Hz, 1H), 3.98-3.97 (m, 2H), 3.84-3.81 (m, 1H), 3.72 (t, J )
5.0 Hz, 2H), 3.54 (t, J ) 5.0 Hz, 2H), 3.46-3.44 (m, 2H), 3.38 (s,
3H), 2.35-2.31 (m, 2H). 13C NMR (CDCl3) δ 134.6, 134.3, 117.3,
116.7, 94.6, 75.3, 72.1, 71.9, 71.6, 66.7, 58.9, 36.3.
(S)-3,5-Dioxacycloheptan-1-ol (8b). To a solution of 7b (38 mg,
0.18 mmol) in EtOAc (3 mL), 10% Pd/C was added and the
resulting suspension was stirred at 23 °C under a hydrogen
atmosphere. After 12 h, the catalyst was filtered off, the filtrate
was evaporated in vacuo, and the residue (19 mg, 91%) was used
20
(R,Z)-3-[(2-Methoxyethoxy)methoxy]-2,3,4,7-tetrahydroox-
epine (12). A mixture of 11 (100 mg, 0.43 mmol) and second
generation Grubbs catalyst (18 mg, 0.02 mmol) in CH2Cl2 (10 mL)
was heated to 45 °C for 1 h. After this time, the solvent was
removed and the residue was purified by flash-chromatography (5:1
CHCl3/EtOAc) to afford 83 mg (94%) of 12 as a colorless oil: 1H
NMR (CDCl3) δ 5.87-5.66 (m, 2H), 4.77-4.18 (m, 2H), 4.18-4.14
(m, 2H), 4.01-3.89 (m, 2H), 3.75-3.68 (m, 3H), 3.56-3.53 (m,
2H), 3.38 (s, 3H), 2.54-2.51 (m, 2H). 13C NMR (CDCl3) δ 130.6,
125.9, 94.3, 75.6, 75.1, 71.6, 70.3, 66.8, 58.9, 31.8.
in the next step without further purification: [R]D +12.9 (c 0.9,
1
CHCl3). H NMR (CDCl3) δ 4.78-4.74 (m 2H), 3.93-3.91 (m,
1H), 3.81-3.75 (m, 4H), 2.51 (bs, 1H), 1.93-1.83 (m, 2H). 13C
NMR (CDCl3) δ 94.4, 69.5, 68.4, 62.3, 37.8.
(R)-3,5-Dioxacyclooctan-1-ol (8c). To a mixture of (S)-8a (46
mg, 0.35 mmol), p-nitrobenzoic acid (86 mg, 0.52 mmol), and
triphenylphosphine (181 mg, 0.69 mmol), diisopropylazodicar-
boxylate (135 µL, 0.69 mmol) was added dropwise and the resulting
mixture was stirred at 23 °C overnight. The solvent was removed
under reduced pressure, and the residue was purified by flash-

6028 Journal of Medicinal Chemistry, 2008, Vol. 51, No. 19
Ghosh et al.
(R)-Oxepan-3-ol (8e). A mixture of 12 (90 mg, 0.44 mmol) and
a catalytic amount of 10% Pd/C in EtOAc (3 mL) was stirred at
23 °C under a hydrogen atmosphere for 3 h. After this time, the
catalyst was filtered off through a pad of celite and the filtrate was
concentrated under reduced pressure to afford (R)-3-[(2-methoxy-
ethoxy)methoxy]oxepane (83 mg, 92%) as a colorless oil. 1H NMR
(CDCl3) δ 4.70 (d, J ) 7.2 Hz, 1H), 4.67 (d, J ) 7.2 Hz, 1H),
3.83-3.58 (m, 7H), 3.50 (t, J ) 4.6 Hz, 2H), 3.34 (s, 3H),
1.72-1.67 (m, 1H), 1.46-1.44 (m, 4H), 1.22-1.19 (m, 1H). 13C
NMR (CDCl3) δ 93.9, 76.5, 73.7, 71.8, 71.6, 66.7, 58.8, 32.6, 30.7,
20.9. A mixture of the above compound (50 mg, 0.24 mmol) and
6 N HCl (0.5 mL) in THF (2 mL) was stirred at 23 °C for 16 h.
The solvent was removed, and the aqueous phase was extracted
with CHCl3. The organic extracts were washed with a saturated
solution of NaHCO3, dried (Na2SO4), and the solvent was removed.
The residue was purified by flash-chromatography (1:4 EtOAc/
were dried and evaporated, and the residue was purified by flash-
column chromatography (2:1 EtOAc/hex) to afford the title
compound as a colorless oil in quantitative yield. Physical and
spectroscopic data are consistent with those reported in the
literature.32
1,3-Dioxan-5-ol (8h). To a mixture of 17 (100 mg, 0.55 mmol)
and paraformaldehyde (17 mg, 0.55 mmol) in EtOAc (10 mL),
boron trifluoride etherate (70 µL, 0.55 mmol) was added and the
reaction mixture was stirred at 23 °C for 4 h. The organic phase
was washed with a saturated solution of NaHCO3, dried, and the
solvent was removed. The residue was purified by flash-chroma-
tography eluting with a 1:4 mixture of EtOAc and hexanes to afford
84 mg (78%) of O-benzyl-1,3-dioxan-5-ol as a colorless oil. The
above compound was dissolved in EtOAc (3 mL), Pd/C was added,
and the resulting suspension was stirred at rt under a hydrogen
atmosphere. After 12 h, the catalyst was filtered off, the filtrate
was evaporated in vacuo, and the residue (39 mg, 100%) was used
20
CHCl3) to afford 8e (24 mg, 84%) as a colorless oil: [R]D -4.2
(c 0.8, CHCl3). 1H NMR (CDCl3) δ 3.87-3.85 (m, 1H), 3.76-3.62
(m, 4H), 2.37 (bs, 1H), 1.78-1.65 (m, 5H), 1.54-1.52 (m, 1H).
13C NMR (CDCl3) δ 73.2, 70.7, 70.4, 36.4, 30.0, 20.2.
1
in the next step without further purification: H NMR (CDCl3) δ
4.93 (d, J ) 6.3 Hz, 1H), 4.76 (d, J ) 6.3 Hz, 1H), 3.94-3.84 (m,
4H), 3.64-3.61 (m, 1H), 2.78 (bs, 1H). 13C NMR (CDCl3) δ 94.0,
71.7, 64.1.
(R)-3-(tert-Butyldimethylsilyloxy)-5-(allyloxy)pent-1-ene (14). A
mixture of 13 (50 mg, 0.23 mmol), allyl bromide (30 µL, 0.35
mmol), and a catalytic amount of TBAI was cooled to 0 °C and
sodium hydride (60% in mineral oil, 11 mg, 0.28 mmol) was added.
The resulting mixture was allowed to warm to 23 °C and stirred
for 18 h. The reaction was quenched by adding a saturated solution
of NH4Cl, the solvent was removed, and the aqueous phase was
extracted with CHCl3. The organic extracts were dried (Na2SO4),
and the solvent was removed. The residue was purified by flash-
chromatography (1:20 EtOAc/hex) to afford 57 mg (97%) of 14 as
a colorless oil. 1H NMR (CDCl3) δ 5.96-5.87 (m, 1H), 5.85-5.78
(m, 1H), 5.29-5.24 (m, 1H), 5.19-5.13 (m, 2H), 5.04-5.00 (m,
1H), 4.31-4.26 (m, 1H), 3.96-3.94 (m, 2H), 3.55-3.42 (m, 2H),
1.84-1.67 (m, 2H), 0.90 (s, 9H), 0.06 (s, 3H), 0.02 (s, 3H). 13C
NMR (CDCl3) δ 141.5, 134.9, 116.6, 113.6, 71.8, 70.6, 66.5, 38.0,
25.8, 18.1, -4.5, -5.1.
(R,Z)-4-(tert-Butyldimethysilyloxy)-2,3,4,7-tetrahydrooxepine (15).
The title compound was obtained from 14 as described for 12 in
80% yield. Flash-chromatography was performed using a 1:10
mixture of EtOAc and hex as the eluant. 1H NMR (CDCl3) δ
5.79-5.75 (m, 1H), 5.63-5.60 (m, 1H), 4.64-4.62 (m, 1H),
4.14-4.12 (m, 2H), 3.91-3.85 (m, 1H), 3.80-3.74 (m, 1H),
2.11-2.05 (m, 1H), 1.96-1.91 (m, 1H), 0.90 (s, 9H), 0.08 (s, 3H),
0.07 (s, 3H). 13C NMR (CDCl3) δ 138.4, 127.8, 69.9, 68.2, 67.4,
38.8, 25.8, 18.3, -4.8.
(S)-Oxepan-4-ol (8f). Hydrogenolysis of 15 was carried out as
described for 8e to afford (S)-4-(tert-butyldimethylsilyloxy)oxepane
in 95% yield as a colorless oil. 1H NMR (CDCl3) δ 4.03-3.96 (m,
1H), 3.79-3.57 (m, 4H), 1.98-1.69 (m, 5H), 1.64-1.51 (m, 1H),
0.88 (s, 9H), 0.044 (s, 3H), 0.038 (s, 3H). 13C NMR (CDCl3) δ
70.2, 69.4, 64.2, 40.1, 34.5, 25.7, 23.7, 18.0, -4.9. Deprotection
of the above compound was performed as described for compound
11 and afforded the title compound in 75% yield as a colorless oil.
1H NMR (CDCl3) δ 4.03-3.98 (m, 1H), 3.82-3.59 (m, 4H),
2.02-1.98 (m, 1H), 1.89-1.80 (m, 4H), 1.66-1.64 (m, 1H). 13C
NMR (CDCl3) δ 70.5, 69.6, 64.7, 38.9, 34.9, 24.3.
2-(Benzyloxy)propane-1,3-diol (17). To a solution of 16 (2.5 g,
13.8 mmol) in dry THF (20 mL), cooled to 0 °C, NaH (60% in
mineral oil, 0.56 g, 14 mmol) was added portionwise. After 30
min, tetra-n-butylammonium iodide (51 mg, 0.14 mmol) and a
solution of benzyl bromide (1.65 mL, 13.9 mmol) in THF (5 mL)
were added. The reaction mixture was stirred at 23 °C for 3 h;
afterward, it was poured into ice. The organic solvent was removed,
and the aqueous phase was extracted with CHCl3. The organic
extracts were dried (Na2SO4), and the solvent was removed. The
crude 5-(benzyloxy)-2-phenyl-1,3-dioxane thus obtained was dis-
solved in a 1:1 mixture of THF and H2O (60 mL), and to the
resulting solution, 6 N HCl was slowly added. After stirring at 23
°C, the reaction mixture was brought to pH 8 by addition of a
saturated solution of NaHCO3, the solvent was removed, and the
aqueous phase was extracted with diethyl ether. The organic extracts
O-Benzyl-3,6,9-trioxacyclodecan-1-ol (18). To a refluxing suspen-
sion of sodium hydride (60% in mineral oil, prewashed with hexane,
84 mg, 2.1 mmol) in dry THF (5 mL), a solution of 17 (182 mg,
1.0 mmol) and di(ethyleneglycol)dimethanesulfonate (260 mg, 1.0
mmol) in dry THF (5 mL) was added dropwise. The resulting
mixture was heated under reflux for 20 h and afterward was cooled
to 23 °C and H2O (2 mL) was added. The solvent was removed,
and the aqueous phase was extracted with CHCl3. The organic
extracts were washed several times with water, dried (Na2SO4),
and evaporated. The residue was purified by flash-chromatography
(2:3 CH2Cl2/EtOAc) to afford 49 mg (19%) of 18 as a colorless
oil. 1H NMR (CDCl3) δ 7.36-7.26 (m, 5H), 4.66 (s, 2H),
3.75-3.57 (m, 13H). MS (ESI) m/z 275 [M + Na]+.
O-Benzyl-3,6,9,12-tetraoxacyclotridecan-1-ol (19). Compound 19
was obtained as described for 18 starting from 17 and tri(ethyl-
1
eneglycol)dimethanesulfonate in 29% yield. H NMR (CDCl3) δ
7.39-7.26 (m, 5H), 4.72 (s, 2H), 3.83-3.58 (m, 17 H). MS (ESI)
m/z 319 [M + Na]+.
3,6,9-Trioxacyclodecan-1-ol (8i). A mixture of 18 (34 mg, 0.13
mmol) and a catalytic amount of 10% Pd/C in methanol (2 mL)
was stirred at 23 °C under a hydrogen atmosphere. After 18 h, the
catalyst was filtered off and the filtrate was evaporated to afford
22 mg (99%) of 8i as a colorless oil. 1H NMR (CDCl3) δ 3.74-3.53
(m, 13H), 2.73 (bs, 1H).
3,6,9,12-Tetraoxacyclotridecan-1-ol (8j). Starting from 19, com-
pound 8j was obtained as described for 8i in quantitative yield: 1H
NMR (CDCl3) δ 3.81-3.60 (m, 17 H), 2.95 (bs, 1H).
3,6,8,11-Tetraoxa-1-cyclododecanol (8k). To a mixture of 2024
(78 mg, 0.29 mmol) and paraformaldehyde (8.7 mg, 0.29 mmol)
in EtOAc (4 mL), boron trifluoride etherate (37 µL, 0.29 mmol)
was added and the resulting mixture was stirred at 23 °C for 2 h.
Subsequently, a saturated solution of NaHCO3 was added and the
aqueous phase was extracted with EtOAc. The combined organic
extracts were dried (Na2SO4), and the solvent was removed in
vacuo. The residue was purified by flash-chromatography to afford
31 mg (37%) of O-benzyl-3,6,8,11-tetraoxacyclododecan-1-ol as
1
a colorless oil. H NMR (CDCl3) δ 7.35-7.27 (m, 5H), 4.67 (s,
2H), 3.88 (s, 2H), 3.86-3.81 (m, 2H), 3.77-3.61 (m, 11H). 13C
NMR (CDCl3) δ 133.6, 128.3, 127.7, 126.2, 94.6, 75.8, 71.5, 69.6,
65.3, 64.6. MS (ESI) m/z 305 [M + Na]+. A mixture of the above
compound and a catalytic amount of 10% Pd/C in EtOAc (2 mL)
was stirred at 23 °C under a hydrogen atmosphere. After 18 h, the
catalyst was filtered off and the filtrate was evaporated to afford
21 mg (99%) of 8k as a colorless oil. 1H NMR (CDCl3) δ 4.67 (s,
2H), 3.85-3.63 (m, 11H), 3.54 (dd, J ) 6.4, 8.2 Hz, 2H), 2.22 (d,
J ) 8.7 Hz, 1H).
O-Benzyl-3,9-dioxa-6-thiacyclodecan-1-ol 6,6-dioxide (22). A
solution of lithium sulfide (11 mg, 0.23 mmol) in water (0.3 mL)
was added dropwise within 30 min to a solution of 2124 (60 mg,
0.15 mmol) in refluxing ethanol (15 mL). The resulting mixture

Flexible Cyclic Ethers/Polyethers as P2-Ligands
Journal of Medicinal Chemistry, 2008, Vol. 51, No. 19 6029
was heated under reflux for 3 h and then was cooled to 23 °C. The
solvent was removed and the aqueous phase was extracted with
CHCl3. The organic extracts were dried (Na2SO4), and the solvent
was removed. Flash-chromatography of the residue (1:4 EtOAc/
hexanes) afforded 16 mg (38%) of O-benzyl-3,9-dioxa-6-thiacy-
(R)-1-(4-Nitrophenoxycarbonyloxy)-3,5-dioxacyclooctane (25c).
The title compound was obtained from (R)-8c as described for 25a
in 87% yield after flash-chromatography (1:4 EtOAc/CHCl3). H
NMR data are consistent with those reported for the (S)-enantiomer
25a.
(R)-1-(4-Nitrophenoxycarbonyloxy)-3,5-dioxacycloheptane (25d).
1
1
clodecan-1-ol as a colorless oil. H NMR (CDCl3) δ 7.36-7.27
The title compound was obtained from (R)-8d as described for 25a
(m, 5H), 4.59 (s, 2H), 3.90-3.85 (m, 2H), 3.82-3.48 (m, 7H),
2.91-2.74 (m, 4H). 13C NMR (CDCl3) δ 133.5, 128.3, 127.7, 126.0,
75.9, 71.9, 71.6, 68.0, 33.4. MS (ESI) m/z 291 [M + Na]+, 286
[M + H + NH3]+, 269 [M + H]+. To a solution of the above
compound (11 mg, 0.040 mmol) in CH2Cl2 (2 mL), cooled to 0
°C, m-chloroperbenzoic acid (77%, 22 mg, 0.09 mmol) was added
in small portions. After 18 h, a 1% solution of sodium bisulfite
was added, the layers were separated, and the organic phase was
washed with a saturated solution of NaHCO3. The organic extracts
were dried (Na2SO4) and evaporated. The residue was purified by
flash-chromatography (1:4 EtOAc/CHCl3) to afford 11 mg (93%)
of 22 as a brown oil. 1H NMR (CDCl3) δ 7.37-7.29 (m, 5H),
4.57 (s, 2H), 4.01-3.96 (m, 4H), 3.77-3.72 (m, 1H), 3.66-3.60
(m, 4H), 3.40-3.38 (m, 2H), 3.34-3.23 (m, 2H). 13C NMR
(CDCl3) δ 133.4, 128.4, 127.9, 127.7, 74.7, 71.8, 66.4, 64.6, 52.4.
3,9-Dioxa-6-thiacyclodecan-1-ol-6,6-dioxide (8l). A mixture of 22
(25 mg, 0.083 mmol) and a catalytic amount of 10% Pd/C in EtOAc
(3 mL) was stirred at 23 °C under a hydrogen atmosphere. After
48 h, the catalyst was filtered off and the filtrate was evaporated to
1
in 70% yield after flash-chromatography (1:5 EtOAc/CHCl3). H
data are consistent with those reported for the (S)-enantiomer 25b.
(R)-3-(4-Nitrophenoxycarbonyloxy)oxepane (25e). The title com-
pound was obtained from 8e as described for 25a in 86% yield.
Flash-chromatography was performed using a 1:20 mixture of
EtOAc and CHCl3 as the eluant. 1H NMR (CDCl3) δ 8.26 (d, J )
9.3 Hz, 2H), 7.38 (d, J ) 9.3 Hz, 2H), 5.02-4.95 (m, 1H),
3.98-3.83 (m, 3H), 3.71-3.63 (m, 1H), 2.15-1.74 (m, 5H),
1.65-1.53 (m, 1H).
(S)-4-(4-Nitrophenoxycarbonyloxy)oxepane (25f). The title com-
pound was obtained from 8f as described for 25a in 77% yield.
Flash-chromatography was performed using a 1:20 mixture of
EtOAc and CHCl3 as the eluant. 1H NMR (CDCl3) δ 8.27 (d, J )
8.8 Hz, 2H), 7.36 (d, J ) 8.8 Hz, 2H), 5.05-5.01 (m, 1H),
3.84-3.62 (m, 4H), 2.18-1.86 (m, 5H), 1.78-1.63 (m, 1H).
1-(4-Nitrophenoxycarbonyloxy)cycloheptane (25g). The title
compound was obtained from commercially available cycloheptanol
as described for 25a in 89% yield. Flash-chromatography was
performed using a 1:10 mixture of EtOAc and CHCl3 as the eluant.
1H NMR (CDCl3) δ 8.26 (d, J ) 8.7 Hz, 2H), 7.37 (d, J ) 8.7 Hz,
2H), 4.96-4.89 (m, 1H), 2.08-2.02 (m, 2H), 1.86-1.78 (m, 2H),
1.71 (m, 2H), 1.59 (m, 4H), 1.40-1.36 (m, 2H).
1
afford 16 mg (92%) of 8l as a colorless oil. H NMR (CDCl3) δ
4.08-3.95 (m, 4H), 3.67 (dd, J ) 4.2, 9.9 Hz, 2H), 3.61-3.59 (m,
1H), 3.51 (dd, J ) 5.7, 9.9 Hz, 2H), 3.38-3.23 (m, 4H). 13C NMR
(CDCl3) δ 69.0, 68.3, 64.5, 52.6.
5-(4-Nitrophenoxycarbonyloxy)-1,3-dioxane (25h). The title com-
pound was obtained from 8h as described for 25a in 72% yield.
Flash-chromatography was performed using a 1:4 mixture of EtOAc
and CHCl3 as the eluant. 1H NMR (CDCl3) δ 8.30 (d, J ) 8.7 Hz,
2H), 7.42 (d, J ) 8.7 Hz, 2H), 5.03 (d, J ) 6.3 Hz, 1H), 4.87 (d,
J ) 6.3 Hz, 1H), 4.71 (t, J ) 2.8 Hz, 1H), 4.19-4.06 (m, 4H).
3,6,9-Trioxa-1-cyclodecanol succinimidylcarbonate (25i). To a
solution of 8i (18 mg, 0.11 mmol) in dry acetonitrile (1 mL), N,N’-
disuccimidyl carbonate (43 mg, 0.17 mmol) and triethylamine (32
µL, 0.23 mmol) were added and the resulting mixture was stirred
at 23 °C. After 8 h, the solvent was removed, the residue was taken
up in a saturated solution of NaHCO3, and the aqueous phase was
extracted with EtOAc. The organic extracts were dried (Na2SO4),
and the solvent was removed in vacuo. Purification of the residue
(10:1 EtOAc/MeOH) afforded 17b (13 mg) in 37% yield. 1H NMR
(CDCl3) δ 5.12-5.03 (m, 1H), 3.96-3.65 (m, 12H), 2.81 (s, 4H).
12-(4-Nitrophenoxycarbonyloxy)-1,4,7,10-tetraoxacyclotride-
cane (25j). The title compound was obtained from 8j as described
for 25a in 70% yield after flash-chromatography (EtOAc). 1H NMR
(CDCl3) δ 8.27 (d, J ) 9.3 Hz, 2H), 7.39 (d, J ) 9.3 Hz, 2H),
5.15-5.08 (m, 1H), 3.92 (dd, J ) 6.3, 10.2 Hz, 2H), 3.82 (dd, J )
4.5, 10.2 Hz, 2H), 3.74-3.60 (m, 12H).
9-(4-Nitrophenoxycarbonyloxy)-1,7-dioxa-4-thiacyclodecane 4,4-
dioxide (25k). The title compound was obtained from 8k as
described for 25a in 73% yield after flash-chromatography (1:4
EtOAc/CHCl3). 1H NMR (CDCl3) δ 8.28 (d, J ) 9.0 Hz, 2H),
7.37 (d, J ) 9.0 Hz, 2H), 5.10-5.03 (m, 1H), 4.13-4.06 (m, 4H),
3.83-3.73 (m, 4H), 3.43-3.22 (m, 4H).
11-(4-Nitrophenoxycarbonyloxy)-1,4,6,9-tetraoxacyclodode-
cane (25l). The title compound was obtained from 8l as described
for 25a in 67% yield after flash-chromatography (EtOAc). 1H NMR
(CDCl3) δ 8.27 (d, J ) 8.7 Hz, 2H), 7.38 (d, J ) 8.7 Hz, 2H),
5.01-4.95 (m, 1H), 4.70 (s, 2H), 3.91-3.76 (m, 12H).
O,6-Dibenzyl-3,9-dioxa-6-azocyclodecan-1-ol (23). A mixture of
2124 (150 mg, 0.37 mmol), benzylamine (41 µL, 0.37 mmol),
lithium perchlorate (340 mg, 3.7 mmol), and sodium carbonate (200
mg, 1.9 mmol) in acetonitrile (7.5 mL) was heated under reflux
for 48 h. After cooling to 23 °C, the solvent was removed, the
residue was suspended in CHCl3, and the organic phase was washed
with water and dried (Na2SO4). Flash-chromatography of the residue
(2:1 EtOAc/CHCl3) afforded 31 mg (24%) of 23 as a colorless oil.
1H NMR (CDCl3) δ 7.36-7.20 (m, 10H), 4.59 (s, 2H), 3.87-3.78
(m, 4H), 3.69 (s, 2H), 3.67-3.49 (m, 5H), 2.91-2.72 (m, 4H).
MS (ESI) m/z 342 [M + 1]+.
N-(tert-Butoxycarbonyl)-3,9-dioxa-6-azocyclodecan-1-ol (24). A
mixture of 23 (40 mg, 0.12 mmol), Boc2O (26 mg, 0.12 mmol),
and a catalytic amount of 10% Pd/C in EtOAc (3 mL) was stirred
at 23 °C under a hydrogen atmosphere. After 18 h, the catalyst
was filtered off and the filtrate was evaporated to afford 26 mg
(95%) of 24 as a colorless oil. 1H NMR (CDCl3) δ 3.83-3.70 (m,
7H), 3.65-3.59 (m, 2H), 3.49-3.29 (m, 4H), 1.75 (bs, 1H), 1.46
(s, 9H). 13C NMR (CDCl3) δ 155.7, 79.8, 71.4, 71.0, 70.3, 69.9,
50.5, 50.2, 28.5.
(S)-1-(4-Nitrophenoxycarbonyloxy)-3,5-dioxacyclooctane (25a).
To a solution of 8a (15 mg, 0.11 mmol) and N-methylmorpholine
(38 µL, 0.34 mmol) in dry THF (3 mL), p-nitrophenylchloroformate
(70 mg, 0.28 mmol) was added and the resulting mixture was stirred
at 23 °C for 1 h. To the reaction mixture was added water, the
solvent was removed under reduced pressure, and the aqueous phase
was extracted with CHCl3. The organic extracts were dried
(Na2SO4), and the solvent was removed. The residue was purified
by flash-chromatography (1:4 EtOAc CHCl3) to afford 28 mg (81%)
of 25a as a pale-yellow solid. 1H NMR (CDCl3) δ 8.27 (d, J ) 9.3
Hz, 2H), 7.38 (d, J ) 9.3 Hz, 2H), 5.09-5.01 (m, 1H), 4.72-4.66
(m, 2H), 3.94-3.82 (m, 3H), 3.64-3.56 (m, 1H), 2.18-2.04 (m,
1H), 2.03-1.93 (m, 2H), 1.90-1.71 (m, 1H).
(1S,2R)-{1-Benzyl-2-hydroxy-3-[isobutyl(4-methoxybenzene-
sulfonyl)amino]propyl}carbamic Acid (1S)-3,5-Dioxacyclooctan-
1-yl ester (3a). A solution of 27 (25 mg, 0.05 mmol) in a mixture
of 30% trifluoracetic acid in CH2Cl2 (5 mL) was stirred at 23 °C
for 40 min and then the solvent was removed under reduced
pressure. Compound 28 thus obtained was dissolved in CH2Cl2 (4
mL) and a solution of 25a (16 mg, 0.05 mmol) in THF (2 mL)
were added followed by diisopropylethylamine. After 48 h, the
organic phase was washed with water, dried (Na2SO4), and
(S)-1-(4-Nitrophenoxycarbonyloxy)-3,5-dioxacycloheptane (25b).
The title compound was obtained from (S)-8b as described for 25a
in 72% yield. Flash-chromatography was performed using a 1:5
1
mixture of EtOAc and CHCl3 as the eluant. H NMR (CDCl3) δ
8.28 (d, J ) 9.3 Hz, 2H), 7.40 (d, J ) 9.3 Hz, 2H), 5.00-4.98 (m,
1H), 4.84 (d, J ) 4.5 Hz, 1H), 4.79 (d, J ) 4.5 Hz, 1H), 4.11 (dd,
J ) 4.7, 13.1 Hz, 1H), 3.99-3.90 (m, 2H), 3.85-3.78 (m, 1H),
2.19-2.04 (m, 2H).

6030 Journal of Medicinal Chemistry, 2008, Vol. 51, No. 19
Ghosh et al.
evaporated. The residue was purified by flash-chromatography
eluting with a 1:4 mixture of EtOAc and hexane to afford 3a in
63% yield after flash-chromatography (1:4 EtOAc/CHCl3) as a
(1S,2R)-{1-Benzyl-2-hydroxy-3-[isobutyl(4-methoxybenzene-
sulfonyl)amino]propyl}carbamic acid (S)-oxepan-4-yl ester (3f).
The title compound was obtained from 27 and 25f as described for
3a in 68% yield after flash-chromatography (1:2 EtOAc/hex) as
an amorphous solid. 1H NMR (CDCl3) δ 7.71 (d, J ) 8.8 Hz, 2H),
7.29-7.21 (m, 5H), 6.98 (d, J ) 8.8 Hz, 2H), 4.78-4.76 (m, 2H),
3.94-3.81 (m, 5H), 3.71-3.60 (m, 3H), 3.56-3.50 (m, 1H), 3.12
(dd, J ) 8.0, 15.2 Hz, 1H), 3.04-2.86 (m, 4H), 2.79 (dd, J ) 6.4,
13.1 Hz, 1H), 1.94-1.64 (m, 7H), 0.91 (d, J ) 6.5 Hz, 3H), 0.86
(d, J ) 6.5 Hz, 3H). HRMS-ESI (m/z): (M + Na)+ calcd for
C28H40N2NaO7S, 571.2454; found, 571.2452.
20
1
foam: [R]D +8.6 (c 1.1, CHCl3). H NMR (CDCl3) δ 7.70 (d, J
) 9.0 Hz, 2H), 7.31-7.21 (m, 5H), 6.97 (d, J ) 9.0 Hz, 2H),
4.83-4.78 (m, 2H), 4.65-4.59 (m, 2H), 3.87 (s, 3H), 3.83-3.81
(m, 3H), 3.68 (dd, J ) 4.9, 12.1 Hz, 1H), 3.55-3.48 (m, 2H),
3.14-2.90 (m, 5H), 2.78 (dd, J ) 6.8, 12.6 Hz, 1H), 1.85-1.80
(m, 5H), 0.90 (d, J ) 6.3 Hz, 3H), 0.85 (d, J ) 6.3 Hz, 3H). 13C
NMR (CDCl3) δ 163.0, 153.4, 137.6, 129.8, 129.6, 129.5, 128.4,
126.5, 114.3, 95.7, 73.9, 72.6, 69.2, 68.6, 58.7, 55.6, 55.0, 53.7,
35.4, 29.2, 27.2, 26.1, 20.1, 29.8. HRMS-ESI (m/z): (M + Na)+
calcd for C28H40N2NaO8S, 587.2403; found, 587.2380.
(1S,2R)-{1-Benzyl-2-hydroxy-3-[isobutyl(4-methoxybenzene-
sulfonyl)amino]propyl}carbamic Acid Cycloheptanyl Ester (3g).
The title compound was obtained from 27 and 25g as described
for 3a in 84% yield after flash-chromatography (1:6 EtOAc/CHCl3)
(1S,2R)-{1-Benzyl-2-hydroxy-3-[isobutyl(4-methoxybenzene-
sulfonyl)amino]propyl}carbamic Acid (1S)-3,5-Dioxacyclohep-
tan-1-yl Ester (3b). The title compound was obtained from 27 and
25b as described for 3a in 69% yield after flash-chromatography
20
as an amorphous solid: [R]D +16.0 (c 0.9, CHCl3). 1H NMR
(CDCl3) δ 7.70 (d, J ) 8.7 Hz, 2H), 7.31-7.22 (m, 5H), 6.97 (d,
J ) 8.7 Hz, 2H), 4.69-4.68 (m, 2H), 3.87 (s, 3H), 3.82-3.78 (m,
2H), 3.05-2.77 (m, 6H), 1.83-1.73 (m, 4H), 1.60-1.45 (m, 8H),
1.22-1.20 (m, 1H), 0.90 (d, J ) 6.3 Hz, 3H), 0.86 (d, J ) 6.3 Hz,
3H). HRMS-ESI (m/z): (M + Na)+ calcd for C29H42N2NaO6S,
569.2661; found, 569.2663.
20
(1:4 EtOAc/CHCl3) as an amorphous solid: [R]D +10.5 (c 1.2,
CHCl3). 1H NMR (CDCl3) δ 7.70 (d, J ) 8.7 Hz, 2H), 7.31-7.19
(m, 5H), 6.97 (d, J ) 8.7 Hz, 2H), 4.93 (d, J ) 8.4 Hz, 1H),
4.77-4.71 (m, 3H), 3.87 (s, 3H), 3.81-3.69 (m, 6H), 3.09-2.90
(m, 5H), 2.77 (dd, J ) 6.9, 13.2 Hz, 1H), 1.98-1.95 (m, 1H),
1.85-1.76 (m, 2H), 0.90 (d, J ) 6.9 Hz, 3H), 0.85 (d, J ) 6.3 Hz,
3H). 13C NMR (CDCl3) δ 162.9, 155.5, 137.5, 129.7, 129.5, 129.4,
128.4, 126.5, 114.3, 94.9, 72.5, 71.9, 68.8, 62.3, 58.9, 55.6, 55.2,
53.7, 35.3, 27.3, 20.2, 19.9. HRMS-ESI (m/z): (M + Na)+ calcd
for C27H38N2NaO8S, 573.2247; found, 573.2260.
(1S,2R)-{1-Benzyl-2-hydroxy-3-[isobutyl(4-methoxybenzene-
sulfonyl)amino]propyl}carbamic Acid 1,3-Dioxan-5-yl Ester
(3h). The title compound was obtained from 25h and 27 as
described for 3a in 67% yield after flash-chromatography (1:6
20
EtOAc/CHCl3): [R]D +7.9 (12.3 mg/mL CH2Cl2). 1H NMR
(CDCl3) δ 7.71 (d, J ) 9.3 Hz, 2H), 7.32-7.22 (m, 5H), 6.98 (d,
J ) 9.3 Hz, 2H), 5.06 (d, J ) 8.4 Hz, 1H), 4.92 (d, J ) 6.2 Hz,
1H), 4.75 (d, J ) 6.2 Hz, 1H), 4.51-4.49 (m, 1H), 3.95-3.74 (m,
9H), 3.14 (dd, J ) 8.1, 15.0 Hz, 1H), 3.06-2.84 (m, 4H), 2.77
(dd, J ) 6.7, 13.3 Hz, 1H), 1.86-1.77 (m, 1H), 0.92 (d, J ) 6.6
Hz, 3H), 0.87 (d, J ) 6.6 Hz, 3H). 13C NMR (CDCl3) δ 162.9,
155.4, 137.3, 129.7, 129.6, 129.5, 128.5, 126.5, 114.3, 93.6, 72.3,
68.7, 66.3, 58.8, 55.6, 55.2, 53.8, 35.7, 27.3, 20.2, 19.9. HRMS-
ESI (m/z): (M + Na)+ calcd for C26H36N2NaO8S, 559.2090; found,
559.2094.
(1S,2R)-{1-Benzyl-2-hydroxy-3-[isobutyl(4-methoxybenzene-
sulfonyl)amino]propyl}carbamic Acid (1R)-3,5-Dioxacyclooctan-
1-yl Ester (3c). The title compound was obtained from 27 and 25c
as described for 3a in 50% yield after flash-chromatography (1:4
EtOAc/CHCl3) as an amorphous solid [R]D20 +9.8 (c 1.1, CHCl3).
1H NMR (CDCl3) δ 7.70 (d, J ) 8.7 Hz, 2H), 7.31-7.21 (m, 5H),
6.97 (d, J ) 8.7 Hz, 2H), 4.80-4.79 (m, 2H), 4.65-4.61 (m, 2H),
3.87 (s, 3H), 3.82-3.80 (m, 2H), 3.71-3.62 (m, 2H), 3.56-3.48
(m, 2H), 3.12-2.85 (m, 5H), 2.77 (dd, J ) 6.3, 13.2 Hz, 1H),
1.83-1.74 (m, 4H), 1.71-1.66 (m, 1H), 0.91 (d, J ) 6.6 Hz, 3H),
0.86 (d, J ) 6.6 Hz, 3H). HRMS-ESI (m/z): (M + Na)+ calcd for
C28H40N2NaO8S, 587.2403; found, 587.2405.
(1S,2R)-(1-Benzyl-2-hydroxy-3-[isobutyl(4-methoxybenzene-
sulfonyl)amino]propyl)carbamic Acid 3,6,9-Trioxacyclodecan-
1-yl Ester (3i). The title compound was obtained from 25i and 27
as described for 3a in 37% yield after flash-chromatography (1:1
20
(1S,2R)-{1-Benzyl-2-hydroxy-3-[isobutyl(4-methoxybenzene-
sulfonyl)amino]propyl}carbamic Acid (1R)-3,5-Dioxacyclohep-
tan-1-yl Ester (3d). The title compound was obtained from 27 and
25d as described for 3a in 59% yield after flash-chromatography
EtOAc/CHCl3) as a white solid: mp 60-62 °C; [R]D + 6.2 (c
0.3, CHCl3). 1H NMR (CDCl3) δ 7.69 (d, J ) 8.7 Hz, 2H),
7.33-7.18 (m, 5H), 6.96 (d, J ) 8.7 Hz, 2H), 5.33 (d, J ) 8.1 Hz,
1H), 4.84-4.82 (m, 1H), 3.86 (s, 3H), 3.79-3.75 (m, 2H),
3.68-3.55 (m, 12H), 3.07-2.78 (m, 6H), 1.84-1.81 (m, 1H), 0.89
(d, J ) 7.2 Hz, 3H), 0.85 (d, J ) 7.2 Hz, 3H). HRMS-ESI (m/z):
(M + Na)+ calcd for C29H42N2NaO9S, 617.2509; found, 617.2501.
(1S,2R)-{1-Benzyl-2-hydroxy-3-[isobutyl(4-methoxybenzene-
sulfonyl)amino]propyl}carbamic Acid 3,6,9,12-Tetraoxacyclo-
tridecan-1-yl Ester (3j). The title compound was obtained from
27 and 25j as described for 3a in 30% yield after flash-
chromatography (EtOAc) as a foam: [R]D20 +17.0 (c 0.9, CHCl3).
1H NMR (CDCl3) δ 7.70 (d, J ) 9.0 Hz, 2H), 7.29-7.19 (m, 5H),
6.97 (d, J ) 9.0 Hz, 2H), 4.96 (d, J ) 8.0 Hz, 1H), 4.85-4.83 (m,
1H), 3.87 (s, 3H), 3.83-3.81 (m, 2H), 3.80-3.60 (m, 15H), 3.52
(dd, J ) 3.5, 9.5 Hz, 1H), 3.13 (dd, J ) 9.0, 15.5 Hz, 1H),
3.02-2.86 (m, 4H), 2.77 (dd, J ) 6.5, 13.5 Hz, 1H), 1.83-1.76
(m, 1H), 0.90 (d, J ) 6.5 Hz, 3H), 0.85 (d, J ) 6.5 Hz, 3H). 13C
NMR (CDCl3) (500 MHz) δ 163.0, 155.4, 137.6, 129.7, 129.6,
129.5, 128.5, 126.5, 114.4, 72.4, 71.7, 70.2, 70.1, 69.9, 67.8, 58.7,
55.6, 55.1, 53.7, 35.5, 27.3, 20.2, 19.9. HRMS-ESI (m/z): (M +
Na)+ calcd for C31H46N2NaO10S, 661.2771; found, 661.2788.
(1S,2R)-{1-Benzyl-2-hydroxy-3-[isobutyl(4-methoxybenzene-
sulfonyl)amino]propyl}carbamic Acid 3,6,8,11-Tetraoxacy-
clododecan-1-yl Ester (3k). The title compound was obtained from
27 and 25k as described for 3a in 47% yield after flash-
20
1
(1:4 EtOAc/CHCl3) as a foam: [R]D +15.9 (c 0.6, CHCl3). H
NMR (CDCl3) δ 7.71 (d, J ) 9.0 Hz, 2H), 7.30-7.18 (m, 5H),
6.98 (d, J ) 9.0 Hz, 2H), 4.88 (d, J ) 8.7 Hz, 1H), 4.77-4.71 (m,
3H), 3.87 (s, 3H), 3.81-3.61 (m, 6H), 3.18-3.07 (m, 2H),
3.04-2.92 (m, 2H), 2.86-2.74 (m, 2H), 1.90-1.77 (m, 3H), 0.92
(d, J ) 6.3 Hz, 3H), 0.86 (d, J ) 6.3 Hz, 3H). 13C NMR (CDCl3)
δ 162.8, 155.5, 137.6, 129.7, 129.5, 129.4, 128.4, 126.4, 114.3,
94.8, 72.6, 71.9, 68.6, 62.3, 58.8, 55.6, 55.1, 53.8, 35.8, 35.2, 27.3,
20.2, 19.9. HRMS-ESI (m/z): (M + Na)+ calcd for C27H38N2NaO8S,
573.2247; found, 573.2254.
(1S,2R)-{1-Benzyl-2-hydroxy-3-[isobutyl(4-methoxybenzene-
sulfonyl)amino]propyl}carbamic Acid (R)-Oxepan-3-yl Ester
(3e). The title compound was obtained from 27 and 25e as described
for 3a in 72% yield after flash-chromatography (1:2 EtOAc/hex)
1
as an amorphous solid. H NMR (CDCl3) δ 7.70 (d, 8.8 Hz, 2H),
7.30-7.19 (m, 5H), 6.97 (d, J ) 8.8 Hz, 2H), 4.81 (d, J ) 8.2 Hz,
1H), 4.77-4.74 (m, 1H), 3.87 (s, 3H), 3.81 (m, 3H), 3.70-3.69
(m, 2H), 3.61-3.57 (m, 1H), 3.12 (dd, J ) 8.2, 14.7 Hz, 1H),
3.05-3.84 (m, 4H), 2.77 (dd, J ) 6.6, 13.2 Hz, 1H), 1.86-1.60
(m, 6H), 1.49-1.41 (m, 1H), 0.91 (d, J ) 6.7 Hz, 3H), 0.86 (d, J
) 6.7 Hz, 3H). 13C NMR (CDCl3) δ 162.9, 155.8, 137.5, 129.6,
129.5, 129.4, 128.4, 126.4, 114.2, 74.5, 73.6, 72.5, 72.4, 58.7, 55.5,
54.8, 53.7, 35.6, 31.9, 30.9, 27.1, 21.0, 20.0, 19.8. HRMS-ESI
(m/z): (M + Na)+ calcd for C28H40N2NaO7S, 571.2454; found,
571.2458.
20
chromatography (EtOAc) as a foam: [R]D +6.5 (c 0.5, CHCl3).
1
H NMR (CDCl3) 7.70 (d, J ) 8.7 Hz, 2H), 7.30-7.18 (m, 5H),
6.97 (d, J ) 8.7 Hz, 2H), 4.92 (d, J ) 8.1 Hz, 1H), 4.81-4.76 (m,
1H), 4.66 (s, 2H), 3.87 (s, 3H), 3.78-344 (m, 14H), 3.13 (dd, J )

Flexible Cyclic Ethers/Polyethers as P2-Ligands
Journal of Medicinal Chemistry, 2008, Vol. 51, No. 19 6031
8.4, 15.3 Hz, 1H), 3.06-2.82 (m, 4H), 2.75 (dd, J ) 6.9, 13.5 Hz,
1H), 1.83-1.74 (m, 1H), 0.90 (d, J ) 6.6 Hz, 3H), 0.85 (d, J )
6.3 Hz, 3H). 13C NMR (CDCl3) δ 163.0, 155.6, 137.5, 129.8, 129.6,
129.5, 128.5, 126.5, 114.4, 94.7, 72.4, 71.5, 69.7, 64.9, 64.5, 58.8,
55.7, 55.1, 53.8, 35.6, 27.3, 20.2, 19.9. HRMS-ESI (m/z): (M +
Na)+ calcd for C30H44N2NaO10S, 647.2615; found, 647.2590.
(1S,2R)-{1-Benzyl-2-hydroxy-3-[isobutyl(4-methoxybenzene-
sulfonyl)amino]propyl}carbamic Acid 3,9-Dioxa-6-thiacyclode-
can-1-yl 6,6-Dioxide Ester (3l). The title compound was obtained
from 27 and 25l as described for 3a in 36% yield after flash-
of CHCl3 and MeOH to afford 8.0 mg (87%) of 3m as an
amorphous solid: [R]D20 +8.1 (c 0.6, CHCl3). 1H NMR (CDCl3) δ
7.70 (d, J ) 8.7 Hz, 2H), 7.3-7.18 (m, 5H), 6.98 (d, J ) 8.7 Hz,
2H), 4.99 (d, J ) 8.1 Hz, 1H), 4.80-4.77 (m, 1H), 3.87 (s, 3H),
3.83-3.74 (m, 4H), 3.70-3.56 (m, 6H) 3.14 (dd, J ) 8.1, 14.7
Hz, 1H), 3.02-2.69 (m, 9H), 2.40 (s, 3H), 1.83-1.74 (m, 1H),
0.90 (d, J ) 6.3 Hz, 3H), 0.85 (d, J ) 6.6 Hz, 3H). 13C NMR
(CDCl3) δ 162.9, 155.5, 137.4, 129.9, 129.4 (×2C), 128.4, 126.4,
114.3, 77.2, 72.3, 69.6, 67.6, 59.0, 55.6, 55.1, 53.6, 44.0, 35.6, 29.7,
27.2, 20.2, 19.9. HRMS-ESI (m/z): (M + Na)+ calcd for
C30H46N3O8S, 608.3006; found, 608.3009.
20
chromatography (1:1 EtOAc/CHCl3) as an amorphous solid: [R]D
1
+5.5 (c 0.7, CHCl3). H NMR (CDCl3) δ 7.70 (d, J ) 9.0 Hz,
Determination of X-ray Structure of 3d-Bound HIV Protease.
The HIV-1 protease construct with the substitutions Q7K, L33I,
L63I, C67A, and C95A to optimize protein stability33 was expressed
and purified as described.34 Crystals were grown by the hanging
drop vapor diffusion method using a 1:15 molar ratio of protease
at 2.0 mg/mL and inhibitor dissolved in dimethylsulfoxide. The
reservoir contained 0.1 M sodium acetate buffer (pH ) 4.2) and
1.2 M NaCl, 10% DMSO. Crystals were transferred into a
cryoprotectant solution containing the reservoir solution and
20-30% (v/v) glycerol, mounted on a nylon loop and flash-frozen
in liquid nitrogen. X-ray diffraction data were collected on the SER-
CAT beamline of the Advanced Photon Source, Argonne National
Laboratory. Diffraction data were processed using HKL2000,35
resulting in an Rmerge value of 8.0% (41.1%) for 110362 unique
reflections between 50 and 1.00 Å resolution with a completeness
of 88.4% (52.6%), where the values in parentheses are for the final
highest resolution shell. Data were reduced in space group P21212
with unit cell dimensions of a ) 57.96 Å, b ) 86.41 Å, c ) 46.03
Å with one dimer in the asymmetric unit. The structure was solved
by molecular replacement using the CPP4i suite of programs,36,37
with the structure of the D30N mutant of HIV protease in complex
with GRL-98065 (2QCI)34 as the starting model. The structure was
refined using SHELX9738 and refitted manually using the molecular
graphics programs O39 and COOT.40 Alternate conformations were
modeled for the protease residues when obvious in the electron
density maps. Anisotropic atomic displacement parameters (B-
factors) were refined for all atoms including solvent molecules.
Hydrogen atoms were added at the final stages of the refinement.
The identity of ions and other solvent molecules from the
crystallization conditions was deduced from the shape and peak
height of the 2Fo - Fc and Fo - Fc electron density, the hydrogen
bond interactions, and interatomic distances. The solvent structure
was refined with two sodium ions, three chloride ions, and 219
water molecules including partial occupancy sites. The final Rwork
was 14.7% and Rfree was 17.5% for all data between 10 and 1.00
Å resolution. The rmsd values from ideal bonds and angle distances
were 0.017 Å and 0.034 Å, respectively. The average B-factor was
11.4 and 16.5 Å2 for protease main chain and side chain atoms,
respectively, 12.9 Å2 for inhibitor atoms, and 22.6 Å2 for solvent
atoms. The X-ray crystal structure of the 3d-bound HIV-1 protease
has been deposited in the Protein Data Bank (PDB)41 with accession
code 3DJK.
2H), 7.31-7.20 (m, 5H), 6.98 (d, J ) 9.0 Hz, 2H), 4.97 (d, J )
8.4 Hz, 1H), 4.85 (t, J ) 4.5 Hz, 1H), 4.01-3.96 (m, 4H), 3.88 (s,
3H), 3.85-3.83 (m, 2H), 3.71-3.69 (m, 1H), 3.61 (dd, J ) 3.9,
9.3 Hz, 1H), 3.54-3.47 (m, 2H), 3.61-3.27 (m, 4H), 3.13 (dd, J
) 8.4, 15.0 Hz, 1H), 3.00-2.82 (m, 4H), 2.75 (dd, J ) 6.6, 13.5
Hz, 1H), 1.83-1.75 (m, 1H), 0.91 (d, J ) 6.6 Hz, 3H), 0.86 (d, J
) 6.3 Hz, 3H). 13C NMR (CDCl3) δ 163.0, 155.1, 137.4, 131.1,
129.6, 129.4, 128.4, 126.5, 114.3, 72.4, 70.2, 66.0, 64.6, 58.8, 55.7,
55.1, 53.7, 52.2, 35.4, 27.3, 20.2, 19.9. HRMS-ESI (m/z): (M +
Na)+ calcd for C29H42N2NaO10S2, 665.2179; found, 665.2191.
N-(tert-Butoxycarbonyl)-9-(4-nitrophenoxycarbonyloxy)-1,7-
dioxa-4-azocyclodecane (29). The title compound was obtained
from 24 as described for 25a in 73% yield after flash-chromatog-
1
raphy (1:4 EtOAc/CHCl3). H NMR (CDCl3) δ 8.27 (d, J ) 9.0
Hz, 2H), 7.37 (d, J ) 9.0 Hz, 2H), 5.02-4.96 (m, 1H), 3.98-3.76
(m, 8H), 4.52-3.23 (m, 4H), 1.47 (s, 9H).
(1S,2R)-{1-Benzyl-2-hydroxy-3-[isobutyl(4-methoxybenzene-
sulfonyl)amino]propyl}carbamic Acid N-(tert-Butoxycarbonyl)-
1,7-dioxa-4-azocyclodecan-9-yl Ester (30). The title compound
was obtained from 27 and 29 as described for 3a in 74% yield
after flash-chromatography (1:1 EtOAc/CHCl3) as a white solid:
mp 71-73 °C; [R]D20 +4.7 (c 1.7, CHCl3). 1H NMR (CDCl3) 7.70
(d, J ) 9.0 Hz, 2H), 7.30-7.20 (m, 5H), 7.0 (d, J ) 9.0 Hz, 2H),
4.92-4.90 (m, 1H), 4.81 (t, J ) 4.0 Hz, 1H), 3.86 (s, 3H),
3.79-3.66 (m, 6H), 3.62-3.57 (m, 2H), 3.49-3.42 (m, 2H),
3.40-3.28 (m, 4H), 3.12 (dd, J ) 7.8, 15.3 Hz, 1H), 3.01-2.82
(m, 4H), 2.75 (dd, J ) 6.3, 13.2 Hz, 1H), 1.83-1.74 (m, 1H), 1.44
(s, 9H), 0.90 (d, J ) 6.6 Hz, 3H), 0.85 (d, J ) 6.6 Hz, 3H). 13C
NMR (CDCl3) 163.0, 155.6, 155.4, 137.4, 129.7, 129.5, 129.4,
128.4, 126.5, 114.3, 79.9, 72.4, 71.9, 71.0, 68.6, 68.1, 58.7, 55.6,
55.0, 53.7, 50.3, 35.6, 28.5, 27.3, 20.2, 19.9.
(1S,2R)-{1-Benzyl-2-hydroxy-3-[isobutyl(4-methoxybenzene-
sulfonyl)amino]propyl}carbamic Acid 1,7-Dioxa-4-azocyclode-
can-9-yl Ester (31). A solution of 30 (13 mg, 0.02 mmol) in a
mixture of 30% trifluoracetic acid in CH2Cl2 (1 mL) was stirred at
23 °C for 30 min and then the solvent was removed under reduced
pressure. The residue was dissolved in CH2Cl2, and the organic
phase was washed with a saturated solution of NaHCO3, dried
(Na2SO4), and evaporated to afford 11 mg (100%) of 31 as a white
20
solid: mp 65-66 °C; [R]D +13.8 (c 0.7, CHCl3). 1H NMR
(CDCl3) δ 7.70 (d, J ) 8.7 Hz, 2H), 7.30-7.18 (m, 5H), 6.97 (d,
J ) 8.7 Hz, 2H), 5.20 (d, J ) 8.4 Hz, 1H), 4.82-4.79 (m, 1H),
3.87 (s, 3H), 3.84-3.80 (m, 2H), 3.75-3.64 (m, 7H), 3.54 (dd, J
) 5.4, 10.2 Hz, 1H), 3.13 (dd, J ) 8.4, 15.3 Hz, 1H), 3.04-2.84
(m, 8H), 2.77 (dd, J ) 6.9, 13.5 Hz, 1H), 2.38 (bs, 1H), 1.85-1.76
(m, 1H), 0.90 (d, J ) 6.3 Hz, 3H), 0.85 (d, J ) 6.6 Hz, 3H). 13C
NMR (CDCl3) δ 162.9, 155.3, 137.5, 129.8, 129.5, 129.4, 128.4,
126.4, 114.3, 72.4, 71.8, 68.6, 58.7, 55.6, 55.1, 53.6, 53.4, 48.2,
35.6, 27.2, 20.2, 19.9.
Acknowledgment. This research was supported by grants
from the National Institutes of Health (GM53386, A.K.G., and
GM62920, I.W.). This work was also supported by the
Intramural Research Program of the Center for Cancer Research,
National Cancer Institute, National Institutes of Health and in
part by a Grant-in-aid for Scientific Research (Priority Areas)
from the Ministry of Education, Culture, Sports, Science, and
Technology of Japan (Monbu Kagakusho), a Grant for Promo-
tion of AIDS Research from the Ministry of Health, Welfare,
and Labor of Japan (Kosei Rohdosho: H15-AIDS-001), and the
Grant to the Cooperative Research Project on Clinical and
Epidemiological Studies of Emerging and Re emerging Infec-
tious Diseases (Renkei Jigyo: no. 78, Kumamoto University)
of Monbu-Kagakusho. The work was also supported in part by
the Georgia State University Molecular Basis of Disease
(1S,2R)-{1-Benzyl-2-hydroxy-3-[isobutyl(4-methoxybenzene-
sulfonyl)amino]propyl}carbamic Acid N-Methyl-1,7-dioxa-4-
azocyclodecan-9-yl Ester (3m). To a solution of 31 (9.0 mg, 0.015
mmol) in a mixture of 1% acetic acid in methanol (0.5 mL),
formaldehyde (37% solution in H2O, 12 µL, 0.15 mmol), and
sodium cyanoborohydride (2.0 mg, 0.03 mmol) were added. After
18 h, a saturated solution of NaHCO3 was added, the solvent was
removed and the aqueous phase was extracted with CH2Cl2. The
organic extracts were dried (Na2SO4), evaporated, and the residue
was purified by flash-chromatography eluting with a 10:1 mixture

6032 Journal of Medicinal Chemistry, 2008, Vol. 51, No. 19
Ghosh et al.
Chemother 2003, 47, 3123–3129. (b) Ghosh, A. K.; Pretzer, E.; Cho,
H.; Hussain, K. A.; Duzgunes, N. Antiviral activity of UIC-PI, a novel
inhibitor of the human immunodeficiency virus type 1 protease.
AntiViral Res. 2002, 54, 29–36.
Program, the Georgia Research Alliance, the Georgia Cancer
Coalition. We thank the staff at the SER-CAT beamline at the
Advanced Photon Source, Argonne National Laboratory, for
assistance during X-ray data collection. Use of the Advanced
Photon Source was supported by the U.S. Department of Energy,
Office of Science, Office of Basic Energy Sciences, under
contract no. DE-AC02-06CH11357. We also thank Sofiya
Leshchenko-Yashchuk for her assistance in HIV-1 protease
inhibitory assay.
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Supporting Information Available: HPLC and HRMS data of
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