Cyclic HIV protease inhibitors: Synthesis, conformational analysis, P2/P2' structure-activity relationship, and molecular recognition of cyclic ureas

Article abstract of DOI:10.1021/jm9602571

High-resolution X-ray structures of the complexes of HIV-1 protease (HIV-1PR) with peptidomimetic inhibitors reveal the presence of a structural water molecule which is hydrogen bonded to both the mobile flaps of the enzyme and the two carbonyls flanking

Full text of DOI:10.1021/jm9602571

3514
J . Med. Chem. 1996, 39, 3514-3525
Cyclic HIV P r otea se In h ibitor s: Syn th esis, Con for m a tion a l An a lysis, P 2/P 2′
Str u ctu r e-Activity Rela tion sh ip , a n d Molecu la r Recogn ition of Cyclic Ur ea s
Patrick Y. S. Lam,* Yu Ru, Prabhakar K. J adhav, Paul E. Aldrich, George V. DeLucca, Charles J . Eyermann,
Chong-Hwan Chang, George Emmett, Edward R. Holler, Wayne F. Daneker, Liangzhu Li, Pat N. Confalone,
Robert J . McHugh, Qi Han, Renhua Li, J ay A. Markwalder, Steven P. Seitz, Thomas R. Sharpe,†
Lee T. Bacheler, Marlene M. Rayner, Ronald M. Klabe, Linyee Shum,‡ Dean L. Winslow,§ David M. Kornhauser,
David A. J ackson, Susan Erickson-Viitanen, and C. Nicholas Hodge
The DuPont Merck Pharmaceutical Company, DuPont Merck Experimental Station, P.O. Box 80500,
Wilmington, Delaware 19880-0500
Received April 3, 1996X
High-resolution X-ray structures of the complexes of HIV-1 protease (HIV-1PR) with peptido-
mimetic inhibitors reveal the presence of a structural water molecule which is hydrogen bonded
to both the mobile flaps of the enzyme and the two carbonyls flanking the transition-state
mimic of the inhibitors. Using the structure-activity relationships of C2-symmetric diol
inhibitors, computed-aided drug design tools, and first principles, we designed and synthesized
a novel class of cyclic ureas that incorporates this structural water and preorganizes the side
chain residues into optimum binding conformations. Conformational analysis suggested a
preference for pseudodiaxial benzylic and pseudodiequatorial hydroxyl substituents and an
enantiomeric preference for the RSSR stereochemistry. The X-ray and solution NMR structure
of the complex of HIV-1PR and one such cyclic urea, DMP323, confirmed the displacement of
the structural water. Additionally, the bound and “unbound” (small-molecule X-ray) ligands
have similar conformations. The high degree of preorganization, the complementarity, and
the entropic gain of water displacement are proposed to explain the high affinity of these small
molecules for the enzyme. The small size probably contributes to the observed good oral
bioavailability in animals. Extensive structure-based optimization of the side chains that fill
the S2 and S2′ pockets of the enzyme resulted in DMP323, which was studied in phase I clinical
trials but found to suffer from variable pharmacokinetics in man. This report details the
synthesis, conformational analysis, structure-activity relationships, and molecular recognition
of this series of C2-symmetry HIV-1PR inhibitors. An initial series of cyclic ureas containing
nonsymmetric P2/P2′ is also discussed.
In tr od u ction
The RNA genome of the human immunodeficiency
virus (HIV), the causative agent of acquired immunede-
ficiency syndrome (AIDS), encodes an essential aspartic
protease (PR)1 that processes the viral gag and gag-pol
polyproteins into structural and functional proteins.
Inhibition of HIVPR in vitro results in the production
of progeny virions which are immature and noninfec-
tious.2 Under clinical settings, three HIVPR inhibitors,
F igu r e 1. (a) Peptidomimetic inhibitor binding at HIV-1PR
active site via a bridging structural water. (b) Preorganized
recently approved by FDA for AIDS therapy in combi-
cyclic urea inhibitor 1 at the active site showing the urea
nation with reverse transcriptase inhibitors, have been
oxygen displacing the structural water.
shown to reduce the viral load and increase the number
of CD4+ lymphocytes in HIV-infected patients.3 In
High-resolution X-ray structures of the complexes of
addition, the large abundance of structural information
on the HIVPR has made the enzyme an attractive target
for computer-aided drug design strategies.4 Conse-
quently, HIVPR has become a prime focus for the
development of HIV therapeutics.5 However, the daunt-
ing ability of the virus to rapidly generate resistant
mutants3e,f,6 suggests that there is an ongoing need for
new HIVPR inhibitors with superior pharmacokinetic
and efficacy profiles.
HIV-1 protease (HIV-1PR) with peptidomimetic inhibi-
tors reveal the presence of a structural water molecule
which is hydrogen bonded to both the mobile flaps of
the enzyme and the two carbonyls flanking the transi-
tion-state mimic of the inhibitors4 (Figure 1a). The
relevance of this structural water to the generation of
HIVPR inhibitors had been previously noted.7 This
water molecule is unique to all retroviral aspartic
proteases but is absent in mammalian aspartic pro-
teases such as renin.8 We recently described the
rational design of a class of novel and highly potent
cyclic urea inhibitors.9 The urea oxygen in the cyclic
urea scaffold was designed to incorporate this structural
water molecule (Figure 1b). Specifically, the design of
these molecules was accomplished using structure-
activity relationship (SAR) data generated from a series
of acyclic C2-symmetric diols,5a,10 computer-aided drug
* To whom correspondence should be addressed. E-mail: lampy@
carbon.dmpc.com.
† Present address: OsteoArthritis Sciences, Inc., Cambridge, MA
02139.
‡ Present address: CoCensys Inc., 213 Technology Dr., Irvine, CA
92718.
§ Present address: Agouron Pharmaceuticals, Inc., 3565 General
Atomics Ct., San Diego, CA 92121.
X Abstract published in Advance ACS Abstracts, August 1, 1996.
S0022-2623(96)00257-9 CCC: $12.00 © 1996 American Chemical Society

Cyclic HIV Protease Inhibitors
J ournal of Medicinal Chemistry, 1996, Vol. 39, No. 18 3515
Sch em e 1. Synthesis of Symmetric Cyclic Ureasa
a
(a) DMSO, COCl2, TEA, CH2Cl2, -78 °C; (b) VCl3‚(THF)3, Zn, rt, THF; (c) SEMCl or MEMCl, Hunig’s base, DMF; (d) H2, Pd/C,
EtOAc, MeOH; (e) CDI, CH2Cl2; (f) NaH, p-NCC6H4CH2Br, DMF; (g) DIBAL-H, THF, -78 °C; (h) NaBH4, EtOH; (i) 4 M HCl in dioxane,
MeOh; (j) NaH, m-NO2C6H4CH2Br, DMF; (k) 4 M HCl in dioxane; (l) H2, Pd/C; (m) CH3SO3H.
design tools, and first principles.9c,11 The displacement
of the unique structural water molecule by incorporation
into the inhibitor structure is expected to increase
retroviral protease specificity and gain in entropy of
binding. The entropic gain of liberating a tightly bound
water molecule in proteins to the bulk solvent has been
estimated as high as 2 kcal/mol.12 The cyclic urea
scaffold also takes advantage of the principle of preor-
ganization13 which states that “the more highly hosts
and guests are organized for binding and low solvation
prior to their complexation, the more stable will be their
complexes”. In our case, the preorganized inhibitor is
anticipated to have higher affinity for HIVPR than its
F igu r e 2. Conformational analysis of designed cyclic ureas
flexible counterpart since no conformational entropic
predicting that 2 is preferred when the nitrogens are not
substituted, whereas conformation 3 is preferred when the
penalty need be paid during binding, the penality
having been prepaid during the synthesis of the preor-
ganized structure. As a result of the increased potency
of the cyclic ureas due to water displacement and
preorganization, fewer subsites of the HIVPR active site
need to be occupied to achieve a given level of inhibitory
potency. An important consequence of reducing molec-
ular weight is a higher probability of improved oral
bioavailability.14 We describe here the conformational
prediction, synthesis, P2/P2′ structure-activity rela-
tionship, and molecular recognition of these cyclic urea
HIV-1PR inhibitors.
nitrogens are substituted due to A1,2 strain.
groups, the converse is true even for a substituent as
small as a methyl group. The partial double bond
character of the urea C-N bond introduces severe allylic
1,2-strain16 between the benzylic groups and the nitro-
gen substituents. This allylic 1,2-strain overcomes the
1,3-diaxial strain, and conformer 3 with pseudodiaxial
benzyl groups and pseudodiequatorial hydroxyl groups
is preferred. This conformational prediction by first
principles was subsequently confirmed by small-mol-
ecule X-ray crystallography (vide infra).
Resu lts a n d Discu ssion
With an idea of the preferred conformation in hand,
we proceeded to determine the stereochemistry neces-
sary for active site complementarity by interactive
graphics. The preferred stereochemistry was predicted
to be 4R,5S,6S,7R. It is with this stereochemistry that
the P1/P1′/P2/P2′ side chains can project optimally into
the S1/S1′/S2/S2′ pockets, respectively. The preferred
RSSR stereochemistry is derived from unnatural D-
phenylalanine. This contrasted with the SAR of acyclic
C2-symmetric diols where the unnatural D-phenylala-
nine at P1/P1′ is highly disfavored.17 The stereochem-
ical predictions were subsequently confirmed by bio-
logical activity and X-ray structures (vide infra).
Syn th esis. The synthesis of cyclic ureas is shown
in Scheme 1 as exemplified by 56, DMP323. Oxidation
Con for m a tion a l P r ed iction . One of the critical
features of our design strategy is the qualitative predic-
tion of the conformation of seven-membered ring cyclic
ureas. It is only with the correct prediction that the
preferred stereochemistry complementary to the active
site can be successfully evaluated using interactive
graphics. The conformational analysis is shown in
Figure 2.
Seven-membered ring cyclic ureas can exist in two
pseudochair conformations. When the nitrogens are
unsubstituted, 1,3-diaxial strain15 dominates and con-
former 2 with pseudodiequatorial benzyl groups and
pseudodiaxial hydroxyl groups is preferred. In contrast,
when the two nitrogens are substituted with P2/P2′

3516 J ournal of Medicinal Chemistry, 1996, Vol. 39, No. 18
Ta ble 1. Physical Data for HIVPR Inhibitors
Lam et al.
ethoxy]methyl chloride (SEMCl) and N,N-diisopropyl-
ethylamine in dry DMF at 50 °C in 91% yield, and the
benzyloxycarbonyl (Cbz) protecting groups were re-
moved by hydrogenolysis with 10% Pd/C in ethyl
acetate/methanol. The crude diamine was cyclized with
carbonyl diimidazole (CDI) and pyridine in methylene
chloride to give cyclic urea 6 in 52% yield (two steps).
Alternatively, (2-methoxyethoxy)methyl chloride (MEM-
Cl) could be used as the protecting group to give 7 in
62% overall yield from 5.
Alkylation of 7 with p-cyanobenzyl bromide and NaH
in anhydrous DMF gave the corresponding nitrile in
40% yield. Diisobutylaluminum hydride (DIBAL) re-
duction of the nitrile gave the corresponding aldehyde
in 43% yield. The aldehyde was further reduced to
benzyl alcohol with sodium borohydride in ethanol
followed by deprotection with HCl in methanol to give
the desired cyclic urea 56 in 64% yield (two steps).
Cyclic urea 60, DMP450, was synthesized by alkyla-
tion of 7 with m-nitrobenzyl bromide and NaH in DMF
to give a 58% yield of the bisalkylated cyclic urea.34
Deprotection (82% yield) with HCl in methanol followed
by hydrogenolysis (91% yield) with 10% Pd/C gave the
free base of 60. Treatment of the free base with
methanesulfonic acid provided 60. Cyclic ureas 3-55,
57-59, and 61 were synthesized using similar proce-
dures. A summary of the physical data is given in Table
1.
The nonsymmetrical cyclic urea 69 was synthesized
as shown in Scheme 2. Alkylation of cyclic urea 7 with
4.0 equiv of NaH and 1.1 equiv of â-naphthylmethyl
bromide in dry DMF under nitrogen gave a 23% chro-
matographed yield of monoalkylated product (monoalkyl-
ation:bisalkylation is 1.4:1.0). Second alkylation (31%
yield) of the monoalkylated product with 4 equiv of
4-picolyl chloride and 12 equiv of NaH in dry DMF
followed by HCl deprotection (100% yield) gave non-
symmetric cyclic urea 69. Nonsymmetric cyclic ureas
62-73 were synthesized by a similar procedure.
Deprotection of 7 with HCl in methanol followed by
treatment with triethyl orthoacetate and catalytic p-
toluenesulfonic acid in acetonitrile provided crystalline
unsubstituted cyclic urea 74 in 57% yield for the purpose
of X-ray structural determination of conformation.
Urea 75 was synthesized as shown in Scheme 3. (R)-
Phenylalaninol 4 was protected as MEM ether. Re-
moval of the N-Cbz protecting group with hydrogen and
5% Pd/C in ethanol gave the amine which was coupled
with CDI to form the urea. Benzylation of the urea with
benzyl bromide and sodium hydride in DMF followed
by deprotection with concentrated HCl and MeOH gave
compound 75 in 21% overall yield.
P 2/P 2′ Str u ctu r e-Activity Rela tion sh ip a n d Mo-
lecu la r Recogn ition . HIVPR is an attractive protein
to study the molecular recognition20 between macro-
molecules and small molecules, due to the abundance
of high-resolution crystal structures of the HIVPR-
inhibitor complexes.4 The study is further simplified
due to the C2-symmetric nature and small size (99
amino acids/monomer) of the HIVPR.4 We would like
to describe the P2/P2′ structure-activity relationship
and molecular recognition study in terms of enantio-
meric recognition, conformation, water displacement,
and preorganization.
compd
mp (°C)
formula
anal.
3
8
9
171-173
212-214
180-182
140-142
125-127
110-112
100-101
183-185
148-150
108-110
207
198-199
120-122
105-107
144-145
244-245
164-166
205-207
167-168
nd
196-197
210-212
215-216
227-228
242-243
120-122
171
151-153
104
nd
231-233
202-204
203
185
133
211
210
73
211
91
205
72
246
71
228
179
162
248
184
194-195
197
115-117
101-103
208 dec
198
150-152
78-80
172-174
175-178
80-92
90-92
94-96
118-120
105-107
199-201
nd
C21H26N2O3‚0.5H2O
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
HRMS
C,H,N
HRMS
HRMS
C,H,N
HRMS
C,H,N
HRMS
C,H,N
HRMS
HRMS
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
HRMS
HRMS
HRMS
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
HRMS
C,H,N
C,H,N
C,H,N
C,H,N
HRMS
C,H,N
C,H,N
C,H,N
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
23H30N2O3‚0.75H2O
25H34N2O3
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
27H38N2O3
29H42N2O3
31H46N2O3‚0.25H2O
33H50N2O3
25H34N2O5‚0.25H2O
27H38N2O5‚0.5H2O
29H42N2O7‚0.1CHCl3
27H38N2O3
29H42N2O3‚0.5H2O
31H46N2O3
33H50N2O3
35H54N2O3‚0.15CHCl3
31H46N2O3
25H30N2O3
27H34N2O3
29H38N2O3‚0.25H2O
27H34N2O5
25H26N2O3
27H34N2O3
29H38N2O3‚0.25H2O
31H42N2O3‚0.5H2O
33H46N2O3
31H44N2O3‚2H2O
33H36N2O3
31H32N4O3
31H32N4O3
31H32N4O3
41H38N2O3‚0.5H2O
41H38N2O3
C333H32N2O3F2‚1.5H2O
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
33H32N2O3F2‚0.67H2O
33H32N2O3F2
33H32N2O3Cl2‚0.75H2O
33H32N2O3Cl2‚0.67H2O
33H32N2O3Cl2‚H2O
33H32N2O3Br‚H2O
33H32N2O3Br‚0.5H2O
35H38N2O3‚-.5H2O
35H38N2O3‚H2O
35H32N2O3F6‚0.1CHCl3
35H32N2O3F6‚1.25H2O
35H38N2O5‚0.75H2O
35H38N2O5‚H2O
35H38N2O5
33H32N4O7‚0.33H2O
33H32N2O3I
35H38N2O5
35H38N2O5‚0.25H2O
33H34N2O3‚H2O
33H34N2O3‚0.5H2O
33H36N4O3‚2CH4O3S‚3H2O
35H38N2O5‚H2O
33H36N2O3‚1.5H2O
34H38N2O3‚1.25H2O
33H34N2O3‚1.5H2O
34H36N2O3‚1.25H2O
36H40N2O3‚0.25CHCl3
37H36N2O3
36H35N3O3‚H2O
36H35N3O3‚H2O
37H37N3O3‚0.1CH2Cl2
38H31N2O4‚0.5H2O
37H37N3O3
137-138
194-195
116
37H36N2O4‚0.25H2O
21H24N2O4‚0.25H2O
33H36N2O3‚0.25H2O
of N-(benzyloxycarbonyl)-(R)-phenylalaninol under
Swern18 conditions gave 84% yield of the corresponding
aldehyde. The aldehyde was then treated with VCl3‚
(THF)3 and zinc in methylene chloride at room temper-
ature19 to give diol 5 in 55% yield with a diastereomeric
purity of 98:2 (RSSR:RRRR) after purification. The diol
was protected by treatment with [2-(trimethylsilyl)-
Cyclic urea 3, with methyl substituents, inhibits HIV-
1PR with a Ki21 of 5700 nM as shown in Table 2. When

Cyclic HIV Protease Inhibitors
J ournal of Medicinal Chemistry, 1996, Vol. 39, No. 18 3517
Sch em e 2. Synthesis of Nonsymmetric Cyclic Ureasa
a
(a) 4 equiv of NaH, 1.1 equiv of â-naphthylmethyl bromide, DMF, separation; (b) 12 equiv of NaH, 4 equiv of 4-picolyl chloride, DMF;
(c) HCl, MeOH; (d) CH3C(OEt)3, p-TSA, CH3CN; (e) H2O.
Sch em e 3. Synthesis of Seco Compound
weight of this compound (434 g/mol) probably contrib-
utes to its excellent bioavailability. N-Morpholino-2-
ethyl cyclic urea 32, made to increase water solubility,
was found to be a poor binder. This is probably due to
the deleterious effect of the hydrophilic nitrogen in the
lipophilic region of the S2/S2′ pockets, as seen with
oxygen above.
Benzyl cyclic urea 33 showed a Ki of 3.0 nM, making
it an attractive side chain for analoging. Picolyl sub-
stituents were introduced as in 34-36, and 3-picolyl
cyclic urea 35 was found to be the best, with a Ki of only
3.2-fold weaker than that of the corresponding 33.
According to the X-ray structures,4 the S2/S2′ pockets
are very large. R-Naphthylmethyl was introduced at
P2/P2′ as in 37 and found to be a poor binder. On the
other hand, â-naphthylmethyl cyclic urea 38 was found
to be a subnanomolar inhibitor with a Ki of 0.31 nM.
However, the translation of Ki to IC90 for 38 is rather
poor, probably due to the extremely high lipophilicity
of the molecule (clogP23 9.2).
A series of regioisomeric halo (39-46), methyl (47,
48), trifluoromethyl (49,50), and methoxy (51-53) sub-
stituents were introduced on P2/P2′ benzyl side chains.
In general, the regioisomeric preference in decreasing
order is meta, para, and ortho. Several of the para-
isomers are within 2-3-fold of the meta-isomers in
terms of Ki. Nitro substitution at the meta-position as
in 54 gave a Ki of 2.8 nM. On the other hand, iodo
substitution at the meta-position gave a Ki of 0.42 nM,
making 55 the best binder in the m-halo series.
Modeling revealed that there are a few hydrogen bond
donors/acceptors, namely, the side chains and backbone
amides of Asp 29/29′ and Asp 30/30′, close to the meta-
and para-positions of the N-benzyl groups. Hydroxy and
hydroxymethyl groups were incorporated as in 56-59.
These compounds indeed have Ki values in the subna-
nomolar range. Moreover, because of the reduced
lipophilicity, the translation from Ki to IC90 is greatly
improved. For example, cyclic urea 56 (clogP and HPLC
log P are 4.8 and 3.6, respectively23) translates 2 orders
of magnitude better than other subnanomolar inhibitors
38 (clogP 9.2), 43 (clogP 8.3), and 55 (clogP 9.1). The
IC90’s of these cyclic ureas, 56-59, are in the range of
0.032-0.057 µM. These cyclic ureas are orally bioavail-
able with Cmax of 0.39-0.83 µM at 10 mg/kg in rats and
F% of 18-30.24 Among the hydroxy compounds, 56 has
the best oral bioavailability in dogs, with 37% oral
bioavailability and a Cmax of 2.8 µM at 10 mg/kg dose.
In addition to hydroxy groups, amino groups were also
the size of the alkyl group was increased incrementally
from methyl to n-heptyl as in 3 and 8-13, the optimal
size was found to be n-butyl (10) with a Ki of 1.4 nM.
Published X-ray structures4 revealed that the S2/S2′
pockets are essentially lipophilic except toward the edge
of the pockets near the entrance to the active site. The
hydrophobic residues lining the S2/S2′ pockets are Val
32/32′, Ile 47/47′, Gly 48/48′, Ile 50/50′, and Ile 84/84′.
The n-butyl group has the optimal length to form
hydrophobic interactions with most of these lipophilic
residues of the S2/S2′ pockets. The antiviral activity
in terms of IC90, the concentration of inhibitor resulting
in 90% inhibition of viral RNA production in HIV-1-
infected MT-2 cells, was determined by quantifying the
viral RNA with an oligonucleotide-based sandwich
hybridization assay.21 For this series of n-alkyl com-
pounds, 10 shows the lowest IC90. The translation of
Ki to IC90 also seems to be optimal for 10, relative to
the shorter or longer n-alkyls. The hydrophobic nature
of the S2/S2′ pockets was further demonstrated by the
2-3 orders of magnitude decrease in binding when
hydrophilic oxygens were inserted into the n-alkyl side
chains as in 14 (570×), 15 (690×), and 16 (30×)
compared with the corresponding n-alkyls 10, 11, and
13, respectively. Methyl branching along the n-alkyl
chains also decreases binding by 4.4-8.6-fold for 17-
20 relative to 9-12, respectively. Additional methyl
branching as in 22 decreases binding 3.0-fold further,
compared with 18. On the other hand, insertion of
double bonds in order to rigidify the alkyl groups
improves binding of 23 (1.5×), 24 (6.7×), 25 (6.7×), and
26 (18×) compared with 9, 17, 18, and 15, respectively.
Conversion of the allyl group to the alkynyl group (27)
loses 4.2-fold in binding.
In the cycloalkyl series, 28-31, cyclobutylmethyl
cyclic urea 29 was found to have the best Ki among the
cycloalkylmethyl cyclic ureas. The oral bioavailability
(F%) of cyclopropylmethyl cyclic urea 28 in rat was
determined to be 100% with a Cmax of 4.3 µM at 10 mg/
kg dose. In dog, the oral bioavailability is 48% with a
Cmax of 9.2 µM at similar dose. The low molecular

3518 J ournal of Medicinal Chemistry, 1996, Vol. 39, No. 18
Ta ble 2. Symmetric Cyclic Urea Inhibitors of HIVPR
Lam et al.
bioavailabilityc
Cmax (µM)
b
compd
P2/P2′
Kia (nM)
5700
100
8 (n ) 1)
1.4
1.6 (n ) 3)
4.6
260
800
1100
7700
49
12
IC90 (µM)
F%
3
8
9
methyl
>141
>132
54
n-ethyl
n-propyl
n-butyl
n-pentyl
n-hexyl
n-heptyl
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
0.68 (n ) 2)
1.5 (n ) 2)
>102
>96
CH2CH2OCH3
CH2CH2OCH2CH3
CH2CH2OCH2CH2OCH3
i-butyl
>114
>106
>94
>100
3.2
8.1
>95
>18
i-pentyl
i-hexyl
i-heptyl
i-octyl
neohexyl
allyl
7
30
110
36
5.2 (n ) 12)
4.7 (n ) 14)
7.6
2.7
49
2-methylpropen-3-yl
isoprenyl
CH2CH2OCHCH2
3-propynyl
7.3
1.8
60
22
2.1
0.87
>107
42
<0.4
cyclopropylmethyl
1.8 (n ) 49)
4.3
9.2 (dog)
100
48 (dog)
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
cyclobutylmethyl
cyclopentylmethyl
cyclohexylmethyl
N-morpholino-2-ethyl
benzyl
2-picolyl
3-picolyl
1.3
4.3
37
4000
3.0
145
9.7
90
1.0
1.7 (n ) 4)
0.2
>96 (n ) 2)
>91
0.83
1.3
49
8.8
98
16
3.9 (n ) 5)
5.5
0.71
0.60
11.3
1.3
4.5
1.2
8.1
2.4
4.3
7.8
7.2
22.9
1.3
7.6
0.97
3.0
0.057 (n ) 30)
4-picolyl
R-naphthylmethyl
â-naphthylmethyl
o-fluorobenzyl
m-fluorobenzyl
p-fluorobenzyl
o-chlorobenzyl
m-chlorobenzyl
p-chlorobenzyl
m-bromobenzyl
p-bromobenzyl
m-methylbenzyl
p-methylbenzyl
m-(trifluoromethyl)benzyl
p-(trifluoromethyl)benzyl
o-methoxybenzyl
m-methoxybenzyl
p-methoxybenzyl
m-nitrobenzyl
86
0.31 (n ) 3)
34
3.0
1.4
240
0.89
5.2
1.4
27
7.0
5.7
22
51
1,870
1.6
157
2.8
0.42
0.34 (n ) 91)
0.38
1.6
0.3
m-iodobenzyl
p-(hydroxymethyl)benzyl
(DMP323)
m-(hydroxymethyl)benzyl
p-hydroxybenzyl
m-hydroxybenzyl
0.78
2.8 (dog)
0.83
0.39
0.81
2.0 (dog)
2.25
11.2 (dog)
27
37 (dog)
18
22
30
16 (dog)
71
79 (dog)
57
58
59
0.14
0.12
0.12
0.038 (n ) 4)
0.032 (n ) 2)
0.054 (n ) 14)
60
61
m-(aminobenzyl)‚2CH3SO3H
(DMP450)
p-(HOCH2)benzyl
0.28
0.13
1650
51 (n ) 2)
(enantiomer of DMP323)
a
Ki values were measured as described,21 with 62.5-250 pM HIV-1PR dimer and four concentrations of inhibitor (0.1-10 000 nM,
b
depending on inhibitor); n ) 2 except as indicated. 56 has Ki ) 0.34 ( 0.16. Inhibition of viral replication was quantified in HIV-1
(RF)-infected MT-2 cells by measurement of viral RNA with an oligonucleotide-based sandwich hybridization assay;22 n ) 1 except as
indicated. 56 has IC90 of 0.057 ( 0.028 µM. c Bioavailability was determined in groups of rats, unless otherwise indicated (n ) 4/group),
dosed with compound in formulations containing propylene glycol, poly(ethylene glycol) 400, water at 10 mg/kg.24 The maximum plasma
concentration (Cmax) is the observed peak plasma concentration after an oral dose. Oral bioavailability (F%) was determined by the ratio
AUC(po)/AUC, where AUC is the area under the plasma concentration-time curve from time zero to infinity and is normalized for dose.
introduced as in 60 to provide another potent compound
(IC90 130 nM) with greatly improved oral bioavailability
in both rats and dogs. The oral bioavailability of 60 in
dogs was as high as 79%, with a Cmax of 11.2 µM at a
dose of 10 mg/kg.34
in Ki confirmed our modeling prediction during the
design stage that the RSSR stereochemistry as in 56 is
the preferred one. Based on modeling, cyclic urea 61
cannot project P2/P2′ into the corresponding S2/S2′
pockets.
Cyclic urea 56 has a Ki of 0.34 nM, while its enanti-
omer 61 has a Ki of 1650 nM. This 4900-fold difference
The cyclic urea scaffold is symmetric, designed to be
complementary to the C2-symmetric HIVPR.4 This

Cyclic HIV Protease Inhibitors
J ournal of Medicinal Chemistry, 1996, Vol. 39, No. 18 3519
Ta ble 3. Nonsymmetrical Cyclic Urea Inhibitors of HIVPR
intervening water molecule. The displacement of the
structural water was further confirmed by NMR ROESY
experiments of the complex of isotopically enriched
HIVPR-1/56.26 This water displacement is entropically
favorable,12 contributing to the high potency of the cyclic
ureas.
The displacement of the structural water by inhibitors
has been an area of active research.27,28 Recently the
Parke Davis28a-c and Upjohn28d-f groups had indepen-
dently discovered pyrone inhibitors based on random
screening of in-house chemical collections. These py-
rones have been confirmed to displace the structural
water based on X-ray studies of the complexes.28
bioavailc
b
compd
P2
Kia (nM) IC90 (µM) Cmax (µM)
38
62
63
64
65
66
67
68
69
70
71
72
73
â-naphthylmethyl
n-propyl
0.31 (n ) 3) 3.9 (n ) 5) 0.38
1.1
0.6
1.4
1.5
0.28
2.3
5.2
6.9
3.6
3.3
n-butyl
allyl
0.75
0.99
1.3
0.66
7.5
0.72
2.7
1.1
cyclopropylmethyl
cyclopentyl
benzyl
0.32
Attempts at preparing high-quality crystals of N-
unsubstituted cyclic urea for X-ray crystallographic
studies were unsuccessful. However, we were able to
obtain crystals of 74 where one of the hydroxyl groups
had been acetylated. The X-ray structure of 7429 shows
that the conformation of N-unsubstituted cyclic urea has
pseudodiequatorial benzyl and pseudodiaxial acetoxy
and hydroxyl groups (Figure 5). For the methyl-
substituted cyclic urea 3, the X-ray structure29 shows
that 3 has adopted the alternative ring conformation
with pseudodiaxial benzyl and pseudodiequatorial hy-
droxyl groups.
3-picolyl
4-picolyl
p-fluorobenzyl
p-(hydroxymethyl)benzyl 0.93
m-aminobenzyl
m-hydroxybenzyl
0.21
0.084
0.145
1.0
0.33
0.96
2.7 (dog)
a-c See footnotes a-c in Table 2.
provides the synthetic advantage in structure-activity
relationship studies as cyclic ureas with symmetric P2/
P2′ side chains can be prepared easily to find the best
P2/P2′ side chains. Subsequently, the best P2/P2′ side
chains can be combined to make cyclic ureas with
nonsymmetric P2/P2′ side chains. Nonsymmetric cyclic
ureas have the advantage of better solubility than
symmetric cyclic ureas. For example, the symmetric
cyclic ureas described above are in general poorly
soluble in chloroform, whereas nonsymmetric cyclic
ureas (vide infra) are more soluble in chloroform. We
next describe the study of an initial series of nonsym-
metric cyclic ureas containing a tight binding â-naph-
thylmethyl group as one of the P2/P2′ side chains as
shown in Table 3.
Nonsymmetric cyclic ureas 62-73 were prepared to
examine the effect of nonsymmetric P2/P2′ side chains
on Ki. In general, the Ki of the nonsymmetric cyclic
ureas falls within the range of the Ki constituted by the
two corresponding parent symmetric cyclic ureas. Only
70-72 are outside the range; however, even these
compounds are only 3-4-fold weaker. Cyclic urea 66
is an interesting compound. It is a combination of 11
(cyclopentylmethyl, Ki 4.3 nM) and 38 (â-naphthyl-
methyl, Ki 0.31 nM). It had a Ki of 0.28 nM, which is
identical with that of the tighter binder 38, even though
it contains a weaker cyclopentylmethyl group as one of
the P2 substituents.
The translation of Ki to IC90 of all these nonsymmetric
cyclic ureas is 1-2 orders of magnitude better than the
parent symmetric 38. This is due to the fact that 38 is
too lipophilic (vide supra). We are currently actively
exploring nonsymmetric cyclic ureas.
The X-ray structure of the complex of 56 and HIV-
1PR was determined.25 As shown in Figure 3, the
complex displays reasonably symmetric binding be-
tween the inhibitor and protease. The benzyl alcohols
accept hydrogen bonds from the backbone NH of Asp
30/30′ and Asp 29/29′ as shown in Figure 4. The diols
form multiple hydrogen bonds with catalytic Asp 25/
25.26 The urea oxygen accepts two hydrogen bonds from
the backbone NH of Ile 50/50′. Thus, the inhibitor links
the protease catalytic aspartates to the flexible flaps via
a hydrogen bond network that does not include an
X-ray structures of other N-substituted cyclic ureas
have also been solved.29,30 They all share the same ring
conformation as 3. Extensive NMR studies of the ring
conformation of 60 in water had been performed. The
result indicates that the ring conformation of 60 in
water is similar to its solid-state X-ray conformation.
These NMR experiments are being described in detail
elsewhere.29
Figure 6 shows an overlap of bound and “unbound”
(small-molecule crystal structure2) 56. The similarity
of the two structures suggests that 56 is indeed highly
preorganized13 for binding. To further evaluate the
contribution of preorganization in the cyclic urea sys-
tem, the corresponding seco compound 75 was used for
comparison as shown in Figure 7. Cyclic urea 33 has a
Ki of 2.5 nM, whereas urea 75 has a Ki of 6700 nM. This
corresponds to a 4.8 kcal/mol gain in binding energy for
33 versus 75. This gain in binding energy reflects the
preorganization of the side chains and diols of the cyclic
urea structure relative to 75. In general, preorganiza-
tion includes, but is not limited to, conformational
entropic penality,13 hydrophobic collapse penalty,31 and
desolvation cost.13 In our case, it is not possible to
dissect these contributions. The above analysis was
performed based on the assumption that 75 binds in a
loose, relatively unstrained “pseudocyclic” conformation,
close to that of 33 but with the methylene carbons
bearing the hydroxy groups not in van der Waals
contacts. This binding mode is not unreasonable since
the diols would want to bind to the catalytic Asp 25/
25′.4 Nevertheless, this may or may not be the case.
The extended conformation of urea 75 may be the low-
energy binding conformation, whereas the loose
“pseudocyclic” conformation needed for comparison in
Figure 7 is a higher energy conformation. In this case,
the value of 4.8 kcal/mol as determined is not valid.
Obtaining the X-ray structure of a complex of 75 and
HIVPR can provide the answer.
In consideration of the overall pharmacokinetic and
safety parameters in animals, cyclic urea 56 was chosen
as the first clinical candidate and designated DMP323.32

3520 J ournal of Medicinal Chemistry, 1996, Vol. 39, No. 18
Lam et al.
F igu r e 3. X-ray structure of HIV-1PR dimer (brown/green) complexed with cyclic urea 56 (DMP323, white). Oxygen is colored
red and nitrogen colored blue. (Top) Front view showing the hydrogen-bonding network from the floor of the active site to the
flaps without the intervention of the structural water. (Bottom) C2-Axis view from the top showing the benzyl alcohol of 56
accepts two hydrogen bonds from Asp 29/29′ and Asp 30/30′.
F igu r e 4. Interatomic distances of cyclic urea 56 binding to
HIV-1PR as derived from the X-ray crystal structure. Dis-
tances are measured between heavy atoms in angstroms.
F igu r e 5. Small-molecule X-ray structures of unsubstituted
cyclic urea 74 showing pseudodiequatorial benzyl and pseudodi-
However due to the low aqueous solubility of 56 (6 µg/
mL), highly variable human oral bioavailability was
observed ranging from 0 to 4.6 µM at 1.5 g dose, with a
mean of 1.4 µM.33 This clinical trial was subsequently
axial diol substituents and of methyl-substituted cyclic urea
3 showing the alternate conformation, consistent with the
design hypothesis.

Cyclic HIV Protease Inhibitors
J ournal of Medicinal Chemistry, 1996, Vol. 39, No. 18 3521
which reduced the concentration of HIV viral RNA by 90%
from the level measured in an untreated infected culture was
designated the IC90. The cellular toxicity of compounds was
assayed by measuring the extent of MTT dye reduction in
uninfected MT-2 cell cultures grown for 3 days in the presence
of various concentrations of test compound. The compound
concentration which decreased the level of MTT dye reduction
by 50% was designated the TC50
. Only compounds which
displayed an antiviral IC90 concentration which was at least
3-fold less than the TC50 concentration were considered to have
a specific antiviral effect. Oral bioavailability was measured
as previously described.24,32c
Ch em ica l Meth od s. All procedures were carried out under
inert gas in oven-dried glassware unless otherwise indicated.
Proton NMR spectra were obtained on VXR or Unity 300 or
400 MHz instruments (Varian Instruments, Palo Alto, CA)
with TMS as an internal reference standard. Melting points
were determined on
a Mettler SP61 apparatus and are
F igu r e 6. Comparison of bound (white) and “unbound”
(brown) conformations of cyclic urea 56 showing the high
degree of preorganization.
uncorrected. Elemental analyses were performed by Quanti-
tative Technologies, Inc., Bound Brook, NJ . Mass spectra were
measured with a HP5988A mass spectrometer with particle
beam interface using NH3 for chemical ionization or a Finnigan
MAT 8230 mass spectrometer with NH3-DCI or VG TRIO 2000
for ESI. High-resolution mass spectra were measured on a
VG 70-VSE instrument with NH3 chemical ionization. Sepa-
ration of isomers was performed using supercritical fluid
chromatography with a Chiracel OD column (Daicel Chemical
Ind. Ltd.) and a 20% methanol-modified CO2 mobile phase.
Optical rotations were obtained on
a Perkin Elmer 241
polarimeter. Solvents and reagents were obtained from com-
mercial vendors in the appropriate grade and used without
further purification unless otherwise indicated. All compounds
were determined to be homogeneous by TLC, elemental
analysis, and/or HPLC. Phenylalaninol I, (R)-phenylmethyl
[2-hydroxy-1-(phenylmethyl)ethyl]carbamate, was obtained
from Synthetech, Inc. The optical rotation of the lot employed
in the following sequence was [R]25 +41° (c 1.0, EtOH).
D
(1R,2S,3S,4R)-Bis(p h en ylm et h yl)[2,3-Dih yd r oxy-1,4-
bis(p h en ylm eth yl)-1,4-bu ta n ed iyl]bis[ca r ba m a te] (5). A
solution of 52 mL of oxalyl chloride (0.59 mol) in 500 mL of
dichloromethane (CH2Cl2) was cooled to -78 °C, and 57 mL
of anhydrous dimethyl sulfoxide (0.81 mol) was added in 500
mL of CH2Cl2 over 1 h while the temperature was maintained
below -70 °C (caution: exothermic). Stirring was continued
at -78 °C for 0.5 h, and 125 g of (R)-N-Cbz-phenylalaninol (4)
(0.44 mol) was added in 800 mL of CH2Cl2 over 1 h, again
maintaining the temperature below -70 °C, followed by
stirring for 0.5 h at -78 °C. Triethylamine (244 mL) was
added in 300 mL of CH2Cl2 over 0.5 h followed by stirring for
2 h at -70 °C. Addition of 800 mL of 20% aqueous KHSO4
was followed by allowing the mixture to warm to room
temperature and addition of 300 mL of water. The aqueous
phase was separated and washed with 400 mL of CH2Cl2. The
combined organic layers from two such runs were washed with
1 L of saturated aqueous NaHCO3, 1 L of water, and 1 L of
saturated aqueous NaCl, dried over MgSO4, and concentrated
to 700 mL. Hexane (2 L) was added, the mixture was cooled
in an ice bath for 1 h, and the solids were filtered and washed
with cold hexane. After drying to constant weight at 40-50
°C, 209 g (84%) of a white solid was obtained: mp 82-83 °C;
F igu r e 7. Comparison of cyclic urea 33 and the seco com-
pound 74 showing a gain of 4.8 kcal/mol of binding energy upon
preorganizing the side chains and the diols.
terminated. DMP450, with excellent water solubility
(>170 mg/mL), was chosen as the second clinical
candidate, and the human pharmacokinetics were found
to be greatly improved, analogous to the animal models.
The results of the clinical study of DMP450 are being
described in detail elsewhere.34
Con clu sion
Cyclic ureas are in general potent inhibitors of HIVPR
for molecules of their size.5 The molecular recognition
features discussed above reveal that this is a result of
preorganization and high complementarity in terms of
conformation, stereochemistry, hydrophobic interac-
tions, hydrogen bondings, and water displacement. The
high potency results in relatively smaller size which
probably contributes to good oral bioavailability in rats
and dogs.14 We are continuing to explore nonsymmetric
cyclic HIVPR inhibitors in order to find candidates with
superior pharmacokinetic and efficacy profiles.
[R]25 +61.58° (c 0.406, MeOH); 1H NMR (CDCl3) δ 3.15 (d, J
D
) 7.0 Hz, 2H), 4.52 (q, J ) 7.0 Hz, 1H), 5.14 (s, 2H), 5.35 (br
d, J ) 6.0 Hz, 1H), 7.10-7.42 (m, 10H), 9.65 (br s, 1H). The
aldehyde, when pure, could be stored under inert atmosphere
without racemization or trimerization. Runs were pooled as
necessary for the following step.
Exp er im en ta l Section
Biologica l Meth od s. Inhibition of HIVPR was measured
by assaying the cleavage of a fluorescent peptide substrate
using HPLC.21 The antiviral potency of compounds was
assessed by measuring their effect on the accumulation of viral
RNA transcripts 3 days after infection of MT-2 cells with HIV-1
RF.22 Uninfected cells were incubated in microtiter plate wells
with serial dilutions of test compound in cell culture medium
for 30 min; then virus was added. After 3 days of culture at
37 °C and 5% CO2, infected cell cultures were lysed and the
levels of HIV RNA determined using a microtiter plate-based
hybridization assay. The concentration of test compound
A 4-necked reaction flask was charged with 467 g of
VCl3‚(THF)3 (1.25 mol) and 1 L of CH2Cl2 in a drybox, removed
from the drybox, and fitted with a reflux condenser, a nitrogen
bubbler, and a thermocouple. Zinc dust (54 g, 0.83 mol, also
weighed in the drybox) was added, and the temperature rose
to 40 °C. The prepared aldehyde (350 g, 1.2 mol) was added
rapidly in 700 mL of CH2Cl2, and the reaction mixture was
stirred overnight. A flask containing 6 L of water and 500
mL of concentrated HCl was warmed until the solution
reached about 65 °C. The reaction mixture was added by
addition funnel and CH2Cl2 collected in a cooled flask as it

3522 J ournal of Medicinal Chemistry, 1996, Vol. 39, No. 18
Lam et al.
distilled off. When addition was completed, the mixture was
allowed to cool to room temperature and the precipitate
collected and washed with water until colorless. The solid was
further washed with 1.2 L of ethanol followed by 1.2 L of
hexane. Two of the above runs were combined and recrystal-
lized by dissolving in hot THF and filtering away insoluble
material. Hexane was added and the mixture allowed to cool.
A total of 374 g (55%) of 5 as a white crystalline solid was
recovered: mp 211-213 °C; SCF chromatographic analysis
solution was added 5.48 mL (8.22 mmol) of DIBAL-H (1.5 M
in toluene) dropwise, and the mixture was allowed to warm
to room temperature and stir overnight. The mixture was then
washed with cold 5% HCl, water, saturated sodium bicarbon-
ate, and brine and dried with MgSO4. Evaporation of solvent
followed by flash chromatography with 20% ethyl acetate in
methylene chloride gave 1.18 g (43%) of aldehyde as a gum:
MS m/z 739 (M + 1, 100).
The aldehyde (1.00 g, 1.35 mmol) was dissolved in 10 mL of
ethanol and treated with 65 mg of sodium borohydride. The
mixture was refluxed for 3 h. After cooling, the mixture was
partitioned between ether and water. The ether phase was
washed twice with water and brine and dried with magnesium
sulfate. The resulting benzyl alcohol was used with no
purification.
showed 98% 1R,2S,3S,4R isomer and 2% 1R,2R,3R,4R isomer;
1
[R]25 +12.5° (c 0.042, MeOH; H NMR (DMSO) δ 2.65-2.80
D
(m, 4H), 3.25 (br s, 2H), 4.12-4.26 (m, 2H), 4.55 (br s, 2H),
4.90 (ABd, J ) 15.0 Hz), 4.93 (ABd, J ) 15.0 Hz), 6.84 (d, J )
8.0 Hz, 2H), 7.00-7.35 (m, 20H); MS m/z 569 (M + 1, 100);
HRMS (M + 1) calcd 569.2651, found 569.2644. Anal.
(C34H36N2O6) C, H, N.
The benzyl alcohol (0.87 g, 1.17 mmol) was dissolved in 10
mL of methanol and 10 mL of 4 M HCl in dioxane. After
stirring overnight, the solvent was evaporated and the residue
purified by chromatography (3% methanol in ethyl acetate)
to give 0.49 g (64% in two steps) of 56 as a white solid: mp
(4R,5S,6S,7R)-H exa h yd r o-5,6-b is[[2-(t r im et h ylsilyl)-
eth oxy]m eth oxy]-4,7-bis(p h en ylm eth yl)-2H-1,3-d ia zep in -
2-on e (6). To a solution of 40 g (70 mmol) of diol 5 in 150 mL
of dry DMF under nitrogen was added 37 mL (211 mmol) of
[2-(trimethylsilyl)ethoxy]methoxy chloride (SEMCl) followed
by 38 mL (230 mmol) of diisopropylethylamine. The mixture
was heated at 50 °C for 48 h. After cooling, the mixture was
partitioned between CH2Cl2 and 5% HCl. The organic phase
was washed with saturated NaHCO3, water, and brine and
dried with MgSO4. The solvent was removed and the residue
purified by chromatography (30% ethyl acetate/hexane) to give
53 g (91%) of a white solid: mp 53-54 °C; 1H NMR (CDCl3) δ
0.05 (s, 18H), 0.95-1.00 (m, 4H), 2.70-2.80 (m, 4H), 3.40-
3.60 (m, 4H), 3.75-4.05 (m, 3H), 4.15 (q, J ) 7.5 Hz, 1H), 4.60-
5.05 (m, 10H), 7.0-7.4 (m, 20H); MS (DCI) m/z 847 (M + NH4,
100); HRMS (M + 1) calcd 829.4280, found 829.4281. Anal.
(C46H64N2O8Si2) C, H, N.
1
197 °C; H NMR (CD3OD) δ 2.93 (d, J ) 15 Hz, 2H), 2.90-
3.05 (m, 4H), 3.53 (br s, 2H), 3.68 (br d, 2H), 4.57 (s, 4H), 4.75
(d, J ) 15 Hz, 2H), 7.05-7.35 (m, 18H); MS (CI) m/z 567 (100,
M + 1); [R]25 +103° (c 0.598, EtOH). Anal. (C35H38N2O5) C,
D
H, N.
Method A was used to make cyclic ureas 57-61.
Meth od B. (4R,5S,6S,7R)-Hexa h yd r o-5,6-d ih yd r oxy-
1,3-d im et h yl-4,7-b is(p h en ylm et h yl)-2H -1,3-d ia zep in -2-
on e (3). Following the same procedure for 56 with SEM-
protected cyclic urea 6 and methyl iodide as the alkylating
1
agent, one can obtain 3 as a white solid: mp 170-174 °C; H
NMR (CDCl3) δ 2.58 (s, 6H), 2.80-3.10 (m, 4H), 2.90 (s, 2H),
3.52 (d, J ) 9.0 Hz, 2H), 4.02 (br s, 2H); MS (CI) m/z 355 (100,
M + 1). Anal. (C21H26N2O3‚0.5H2O) C, H, N.
The white solid (8.2 g, 9.9 mmol) and 1 g of 10% Pd/C in
100 mL of ethyl acetate/methanol (1:1) was stirred under
hydrogen overnight. TLC showed complete hydrogenolysis.
The catalyst was filtered off through a Celite pad, and the
solvent was removed to give 5.3 g of the diamine as a colorless
gum. The diamine was dissolved in 50 mL of dry CH2Cl2 under
nitrogen. Pyridine (1.5 mL, 19 mmol) and 1.9 g (11 mmol) of
1,1′-carbonyldiimidazole in 50 mL of CH2Cl2 were added, and
the mixture was stirred overnight and then washed with 5%
HCl, saturated NaHCO3, and brine and dried with MgSO4. The
solvent was removed and the residue chromatographed to give
3.1 g (52% in two steps) of cyclic urea 6 as a white solid: mp
Method B was also used to make cyclic ureas 4-55.
(4R,5S,6S,7R)-Hexa h yd r o-5,6-d ih yd r oxy-1,3,4,7-tetr a -
k is(p h en ylm eth yl)-2H-1,3-d ia zep in -2-on e (33). Following
method B for 3 with benzyl chloride as alkylating agent, one
can obtain benzyl cyclic urea 33 as a white solid: mp 171 °C;
1H NMR (CDCl3) d 1.60 (br s, 1H), 2.35 (br s, 1H), 2.98-3.10
(m, 6H), 3.57 (br d, J ) 15 Hz, 2H), 3.60 (br s, 2H), 7.10-7.40
(m, 20H); MS (CI) m/z 507 (100, M + 1); [R]25 +141 (c 0.922,
D
MeOH). Anal. (C33H34N2O3) C, H, N.
(4R,5S,6S,7R)-Hexa h yd r o-5,6-d ih yd r oxy-1,3-bis[[3-(h y-
d r oxym eth yl)p h en yl]m eth yl]-4,7-bis(p h en ylm eth yl)-2H-
1,3-d ia zep in -2-on e (57). Following method A for 56 with
3-cyanobenzyl chloride as alkylating agent, one can obtain
benzyl alcohol 57 as a white solid: mp 245-247 °C; 1H NMR
(CD3OD) δ 2.80-3.15 (m, 4H), 3.10 (d, J ) 15 Hz, 2H), 3.60
(br s, 2H), 3.62 (br s, 2H), 4.85 (d, J ) 15 Hz, 2H), 7.00-7.90
1
74-75 °C; H NMR (CDCl3) δ 0.05 (s, 18H), 0.90 (t, J ) 7.5
Hz, 4H), 2.85-2.95 (m, 4H), 3.50-3.70 (m, 4H), 3.65 (s, 2H),
3.90 (t, J ) 7.5, 2H), 4.06 (s, 2H), 4.66 (d, J ) 7.5 Hz, 2H),
4.75 (d, J ) 7.5 Hz, 2H), 7.15-7.30 (m, 10H); MS (DCI) m/z
587 (M + 1, 100); HRMS (M + 1) calcd 587.3337, found
587.3353. Anal. (C31H50N2O5Si2) C, H, N.
(m, 18H); MS (CI) m/z 567 (100, M + 1). Anal. (C35H38
N2O5‚0.25H2O) C, H, N.
-
(4R,5S,6S,7R)-H exa h yd r o-5,6-b is[(2-m et h oxyet h oxy)-
m eth oxy]-4,7-bis(ph en ylm eth yl)-2H-1,3-diazepin -2-on e (7).
Following the same procedure for 6, one can obtain (methoxy-
ethoxy)methyl (MEM)-protected cyclic urea 7 in 62% yield from
5 and MEM chloride as a colorless oil: 1H NMR (CDCl3) δ
2.80-3.00 (m, 4H), 3.34 (s, 6H), 3.38-3.50 (m, 6H), 3.64 (s,
2H), 3.90 (t, J ) 8.0 Hz, 2H), 4.26 (s, 2H, NH), 4.75 (ABd, J )
7.5 Hz, 2H), 4.80 (ABd, J ) 7.5 Hz, 2H), 7.18-7.35 (m, 10H);
MS (ESI) m/z 503 (M + 1, 100); HRMS (M + 1) calcd 503.2757,
found 503.2772.
Rep r esen ta tive P r oced u r es for N-Su bstitu ted Cyclic
Ur ea s: Meth od A. (4R,5S,6S,7R)-Hexa h yd r o-5,6-d ih y-
d r oxy-1,3-bis[[4-(h yd r oxym eth yl)p h en yl]m eth yl]-4,7-bis-
(p h en ylm eth yl)-2H-1,3-d ia zep in -2-on e (56, DMP 323). To
a solution of 5.50 g (10.9 mmol) of MEM-protected cyclic urea
7 in 50 mL of dry dimethylformamide was added 2.60 g (65.6
mmol) of 60% sodium hydride in mineral oil. The mixture was
stirred for 15 min and cooled to 0 °C, and 8.58 g (43.8 mmol)
of 4-cyanobenzyl bromide in DMF was added. The mixture
was stirred at 0 °C for 15 min and at room temperature for 2
h and then hydrolyzed with water and extracted with ether
to give an oil that was purified by flash chromatography using
15% ethyl acetate in methylene chloride. This yielded 3.2 g
(40%) of the nitrile as a semisolid: MS m/z 733 (M + 1, 100).
The nitrile (2.74 g, 3.74 mmol) was dissolved in 15 mL of
dry toluene under nitrogen and cooled to -78 °C. To this
(4R,5S,6s,7R)-Hexa h yd r o-5,6-d ih yd r oxy-1,3-bis[(4-h y-
d r oxyp h en yl)m eth yl]-4,7-bis(p h en ylm eth yl)-2H-1,3-d ia z-
ep in -2-on e (58). Following method A for 56 with 3-(ben-
zyloxy)benzyl chloride as alkylating agent, one can obtain
bisalkylated cyclic urea. The benzyl protecting groups were
removed by hydrogenolysis in the presence of 10% Pd/C, and
the MEM protecting groups were removed by the standard
procedure to give phenol 58 as a white solid: mp 115-117
°C; 1H NMR (CD3OD) δ 2.83 (d, J ) 11 Hz, 2H), 2.95-3.05
(m, 4H), 3.60 (br s, 2H), 3.62 (br s, 2H), 4.65 (d, J ) 11 Hz,
2H), 6.75 (d, J ) 8 Hz, 4H), 6.96 (d, J ) 8 Hz, 4H), 7.10-7.40
(m, 8H); MS (CI) m/z 539 (5, M + 1), 182 (100). Anal.
(C33H34N2O5‚0.5H2O) C, H, N.
(4R,5S,6S,7R)-Hexa h yd r o-5,6-d ih yd r oxy-1,3-bis[(3-h y-
d r oxyp h en yl)m eth yl]-4,7-bis(p h en ylm eth yl)-2H-1,3-d ia z-
ep in -2-on e (59). Following the procedure for the synthesis
of 58 with 4-(benzyloxy)benzyl chloride as alkylating agent,
one can obtain phenol 59 as a white solid: mp 101-103 °C;
1H NMR (CD3OD) δ 2.83 (d, J ) 11 Hz, 2H), 2.95-3.20 (m,
4H), 3.60 (br s, 2H), 3.62 (br s, 2H), 4.70 (d, J ) 11 Hz, 2H),
6.60 (d, J ) 8 Hz, 2H), 6.64 (s, 2H), 6.67 (d, J ) 8 Hz, 2H),
7.10-7.40 (m, 12H); MS (CI) m/z 539 (2, M + 1), 142 (100).
Anal. (C33H34N2O5‚0.5H2O) C, H, N.
(4R,5S,6S,7R)-Hexa h yd r o-5,6-d ih yd r oxy-1,3-bis[(3-a m i-
n op h en yl)m eth yl]-2H-1,3-d ia zep in -2-on e, Bism eth a n e-

Cyclic HIV Protease Inhibitors
J ournal of Medicinal Chemistry, 1996, Vol. 39, No. 18 3523
su lfon ic Acid Sa lt (60, DMP 450). The synthesis of 60 is
described in detail in ref 34.
(11.5 g, 48.1 mmol) and carbonyldiimidazole (3.9 g, 24.1 mmol)
were dissolved in 200 mL of dry THF under nitrogen and
stirred at room temperature overnight until the reaction was
completed. The mixture was evaporated and partitioned
between CH2Cl2 and water. The organic phase was washed
with water twice, dried with MgSO4, and evaporated to give
11.6 g of crude urea. The crude urea (2.52 g, 5.0 mmol) was
benzylated with 5.13 g (30 mmol) of benzyl bromide and 1.2 g
(83 mmol) of 60% NaH in mineral oil in anhydrous DMF under
nitrogen. The reaction was completed overnight as monitored
by TLC.
(4S,5R,6R,7S)-Hexa h yd r o-5,6-d ih yd r oxy-1,3-bis[[4-(h y-
d r oxym eth yl)p h en yl]m eth yl]-4,7-bis(p h en ylm eth yl)-2H-
1,3-d ia zep in -2-on e (61). Following method A for 56, one can
prepare the corresponding enantiomer 61 as a white solid: mp
1
198 °C; H NMR (CD3OD) δ 2.93 (d, J ) 15 Hz, 2H), 2.90-
3.05 (m, 4H), 3.53 (br s, 2H), 3.68 (br d, 2H), 4.75 (d, J ) 15
Hz, 2H), 7.05-7.35 (m, 18H); MS (CI) m/z 567 (100, M + 1);
[R]25 -101° (c 0.466, EtOH). Anal. (C35H38N2O5‚H2O) C, H,
D
N.
The final reaction mixture was poured into ice/water and
extracted with EtOAc. The organic phase was washed with
water six times, dried with MgSO4, and evaporated to dryness.
The crude product was chromatographed (hexane/EtOAc, 1:1)
to give 2.03 g of a light colored oil. The oil (1.1 g, 1.6 mmol)
was dissolved in 200 mL of methanol and 40 mL of concen-
trated HCl added slowly. The mixture was allowed to stir
overnight and poured into ice/saturated NaHCO3. The crude
product was chromatographed (CH2Cl2/MeOH, 100:1) to give
300 mg (21% overall yield) of urea diol 75 as a solid: mp 116
°C; 1H NMR (CDCl3) δ 2.88 (d, J ) 6.0 Hz, 4H), 3.48-3.70 (m,
6H), 3.75 (d, J ) 15 Hz, 2H), 4.18 (d, J ) 15 Hz, 2H), 4.82 (br
s, 2H), 7.00-7.35 (m, 10H); MS (CI) m/z 509 (M + 1, 100);
HRMS calcd 509.2804, found 509.2799; [R]25D +80.0° (c 0.015,
MeOH). Anal. (C33H36O3N2‚0.25H2O) C, H, N.
(4R,5S,6S,7R)-Hexa h yd r o-5,6-d ih yd r oxy-1-(4-p yr id yl-
m eth yl)-3-(â-n a p h th ylm eth yl)-4,7-bis(p h en ylm eth yl)-2H-
1,3-d ia zep in -2-on e (69). To a mixture of 2.03 g (50.9 mmol)
of 60% NaH in mineral oil (washed with hexane) in 20 mL of
dry DMF under nitrogen was added a solution of 6.40 g (12.7
mmol) of di-MEM-protected cyclic urea 7. The mixture was
stirred at room temperature for 10 min. A solution of 3.16 g
(14.0 mmol) of 2-(bromomethyl)naphthylene was added and
the mixture stirred at room temperature for 8 h. The reaction
was quenched with methanol and partitioned between ethyl
acetate and water. The organic phase was washed with water
and brine and dried with MgSO4. After rotovaping, 7.5 g of a
residue was obtained and chromatographed with a gradient
of EtOAc and hexane to give 1.77 g (23%) of mononaphthyl-
methyl cyclic urea (MS m/z 643 (M + 1), 100), 1.51 g (16%) of
bis(naphthylmethyl) cyclic urea, and 2.31 g (36%) of starting
material.
Ack n ow led gm en t. We would like to thank Dr.
J oseph C. Calabrese for solving the small-molecule
crystal structures and Mrs. Beverly C. Cordova for
running the RNA cell assays. We also thank Drs. Alex
J ohnson, George L. Trainor, Soo S. Ko, and Paul S.
Anderson and the HIVPR working group for their
valuable contributions to the HIVPR program.
The mononaphthylmethyl cyclic urea was alkylated with 4
equiv of 4-picolyl chloride and 12 equiv of NaH at room
temperature for 2 weeks following method A to give 31% yield
of MEM-protected 4-picolyl cyclic urea. Similar acid depro-
tection (100% yield) followed by preparative TLC (70% EtOAc/
1
hexane) gave 69 as a white solid: mp 118-120 °C; H NMR
(CDCl3) δ 2.90-3.40 (m, 4H), 2.98 (d, J ) 15 Hz, 1H), 3.25 (d,
J ) 15 Hz, 1H), 3.65 (br d, 2 H), 4.95 (d, J ) 15 Hz, 1H), 5.07
(d, J ) 15 Hz, 1H), 7.05-7.35 (m, 17H), 7.67 (d, J ) 7.5 Hz,
2H), 8.15 (d, J ) 7.5 Hz, 2H); MS (CI) m/z 558 (100, M + 1).
Anal. (C35H38N2O5‚H2O) C, H, N.
Su p p or tin g In for m a tion Ava ila ble: Elementary analy-
sis, high-resolution mass spectra, and X-ray crystallographic
data (12 pages). Ordering information is given on any current
masthead page.
(4R,5S,6S,7R)-Hexa h yd r o-5-a cetoxy-6-h yd r oxy-4,7-bis-
(p h en ylm et h yl)-2H -1,3-d ia zep in -2-on e (74). Di-MEM-
protected cyclic urea 7 (50.2 g, 0.1 mol) was dissolved in MeOH
(250 mL) and cooled in an ice bath to 0 °C. HCl (g) was
bubbled into the solution for 10 min, and the mixture was
stirred at 0 °C for 1 h. The mixture was concentrated at room
temperature on a rotary evaporator to give the diol as a white
solid. The resulting diol was suspended in acetonitrile (300
mL) and treated with 34.5 g (0.2 mol) of triethyl orthoacetate
and 0.5 g of p-toluenesulfonic acid. The suspension was stirred
until TLC analysis showed all the diol was consumed and
formation of the ortho ester was complete. Then 50 mL of
water was added and the mixture stirred for 30 min until all
the ortho ester was converted to the monoacetate. The mixture
was concentrated on a rotary evaporator to give a solid residue.
The resulting residue was recrystallized from ethyl acetate to
give 21 g (57%) of 74 as a white solid: mp 194-195 °C; 1H
NMR (CDCl3) δ 2.08 (s, 3H), 2.64-2.83 (m, 3H), 2.86 (d, J )
8.0 Hz, 2H), 3.56 (q, J ) 4.4 Hz, 1H), 3.79 (t, J ) 7.7 Hz, 1H),
3.92 (br t, J ) 7.7 Hz, 1H), 4.80 (d, J ) 4.4 Hz, 1H), 7.19-7.12
(m, 4H), 7.33-7.21 (m, 6H); 13C NMR (CDCl3) δ 21.27, 38.45,
38.88, 51.35, 53.75, 57.56, 72.57, 120.44, 127.69, 127.82,
Refer en ces
(1) For recent reviews, see: (a) Debouck, C. The HIV-1 Protease as
a Therapeutic Target for AIDS. AIDS Res. Human Retroviruses
1992, 8, 153-164. (b) Katz, R. A.; Skalka, A. M. Annu. Rev.
Biochem. 1994, 63, 133-173.
(2) (a) Kohl, N. E.; Emini, E. A.; Schleif, W. A.; Davis, L. J .;
Heimbach, J . C.; Dixon, R. A. F.; Scolnick, E. M.; Sigal, I. S.
Active Human Immunodeficiency Virus Protease is Required for
Viral Infectivity. Proc. Natl. Acad. Sci. U.S.A. 1988, 85, 4686-
4690. (b) Peng, C.; Ho, B. K.; Chang, T. W.; Chang, N. T. Role
of Human Immunodeficiency Virus Type 1-Specific Protease in
Core Protein Maturation and Viral Infectivity. J . Virol. 1989,
63, 2550-2556.
(3) (a) Vella, S. HIV Therapy Advances. Update on a Proteinase
Inhibitor. AIDS 1994, 8 (Suppl. 3), S25-29. (b) Pollard, R. B.
Use of Proteinase Inhibitors in Clinical Practice. Pharmaco-
therapy 1994, 14, 21S-29S. (c) Vacca, J . P.; Dorsey, B. D.;
Schlief, W. A.; Levin, R. B.; McDaniel, S. L.; Darke, P. L.; Zugay,
J .; Quintero, J . C.; Blahy, O. M.; Roth, E.; Sardana, V. V.;
Schlabach, A. J .; Graham, P. I.; Condra, J . H.; Gotlib, L.;
Holloway, M. k.; Lin, J .; Chen, I.-W.; Ostovic, D.; Anderson, P.
S.; Emini, E. A.; Huff, J . R. An Orally Bioavailable Human
Immunodeficiency Virus Type-1 Protease Inhibitor. Proc. Natl.
Acad. Sci. U.S.A. 1994, 91, 4096-4100. (d) Wei, X.; Ghosh, S.
K.; Taylor, M. E.; J ohnson, V. A.; Emini, E. A.; Deutsch, P.;
Lifson, J . d.; Bonhoeffer, S.; Nowak, M. A.; Hahn, B. H.; Saag,
M. S.; Shaw, G. M. Viral Dynamics in Human Immunodeficiency
Virus Type 1 Infection. Nature 1995, 373, 117-122. (e) Kempf,
D.; Marsh, K. C.; Denissen, J . F.; McDonald, E.; Vasavanonda,
S.; Flentge, C. A.; Green, B. G.; Fino, L.; Park, C. H.; Kong, X.-
P.; Wideburg, N. E.; Saldivar, A.; Ruiz, L.; Kati, W. M.; Sham,
H. L.; Robins, T.; Stewart, K. D.; Hsu, A.; Plattner, J . J .; Leonard,
J . M.; Norbeck, D. W. ABT-538 is a Potent Inhibitor of Human
Immunodeficiency Virus Protease with High Oral Bioavailability
in Humans. Proc. Natl. Acad. Sci. U.S.A 1995, 92, 2484-2488.
(f) Ho, D. D.; Neumann, A. U.; Perelson, A. S.; Chen, W.;
Leonard, J . M.; Markowitz, M. Rapid Turnover of Plasma Virions
and CD4 Lymphocytes in HIV-1 Infection. Nature 1995, 373,
123-126. (g) Kitchen, V. S.; Skinner, C.; Ariyoshi, K.; Lane, E.
A.; Duncan, I. B.; Burckhardt, J .; Burger, H. U.; Bragman, K.;
Pinching, A. J .; Weber, J . N. Safety and Activity of Saquinavir
in HIV Infection. Lancet 1995, 345, 952-955.
129.39, 129.50, 136.40, 136.80, 164.41, 170.31. Anal. (C21H24
-
N2O4‚0.25H2O) C, H, N.
[R-(R*,R*)]-N,N′-Bis[2-h ydr oxy-1-(ph en ylm eth yl)eth yl]-
N,N′-bis(p h en ylm eth yl)u r ea (75). A solution of 28.5 g (0.1
mol) of (R)-N-Cbz-phenylalaninol (4), 18.7 g (0.15 mol) of (2-
methoxyethoxy)methyl chloride (MEMCI), and 26.1 mL (0.15
mol) of diisopropylethylamine in 200 mL of dry methylene
chloride was stirred at room temperature overnight. TLC
showed no starting material. The reaction mixture was
washed with water, dried with MgSO4, and evaporated to
dryness to give 37.9 g of crude MEM ether as a brown oil.
To a solution of 18.7 g (50 mmol) of the crude MEM ether
in 200 mL of ethanol was added 3.7 g of 5% Pd/C. The mixture
was treated with 1 atm of hydrogen for 2 h until TLC showed
no starting material. The mixture was filtered and evaporated
to dryness to give 11.9 g of crude diamine. The crude diamine

3524 J ournal of Medicinal Chemistry, 1996, Vol. 39, No. 18
Lam et al.
(4) (a) Wlodawer, A.; Erickson, J . W. Structure-based Inhibitors of
HIV-1 Protease. Annu. Rev. Biochem. 1993, 62, 543-585. (b)
Appelt, K. Crystal Structures of HIV-1 Protease-inhibitor Com-
plexes. Perspect. Drug Discovery Des. 1993, 1, 23-48.
pounds. In Structural Biology of Viruses; Chiu, W., Ed.; Oxford
Press: Oxford, 1996. (c) Comment by Klunder, J . M. Nonpeptide
Cyclic Urea Inhibitors of HIV Protease. Chemtracts-Org. Chem.
1994, 7, 82-87.
(5) (a) Kempf, D. J .; Norbeck, D. W.; Codacovi, L. M.; Wang, X. C.;
Kohlbrenner, W. E.; Wideburg, N. E.; Paul, D. A.; Knigge, M.
F.; Vasavanonda, S.; Craig-Kennard, A.; Saldivar, A.; Rosen-
brook, W.; Clement, J . J .; Plattner, J . J .; Erickson, J . Structure-
Based, C2 Symmetric Inhibitors of HIV Protease. J . Med. Chem.
1990, 33, 2687-2689. For reviews, see: (b) Norbeck, D. W.;
Kempf, D. J . HIV Protease Inhibitors. Annu. Rep. Med. Chem.
1991, 26, 141-160. (c) Tomasselli, A. G.; Howe, W. J .; Sawyer,
T. K.; Wlodawer, A.; Heinrikson, R. L. The Complexities of
AIDS: An Assessment of the HIV Protease as a Therapeutic
Target. Chim. Oggi 1991, 6-27. (d) Huff, J . R. HIV Protease:
A Novel Chemotherapeutic Target for AIDS. J . Med. Chem.
1991, 34, 2305-2314. (e) Martin, J . A. Recent Advances in the
Design of HIV Proteinase Inhibitors. Antiviral Res. 1992, 17,
265-278. (f) Thaisrivaongs, S. HIV Protease Inhibitors. Annu.
Rep. Med. Chem. 1994, 29, 133-144. (g) Kempf, D. J . Progress
in the Discovery of Orally Bioavailable Inhibitors of HIV
Protease. Perspect. Drug Discovery Des. 1994, 2, 427-436. (h)
Gait, M. J .; Karn, J . Progress in Anti-HIV Structure-based Drug
Design. TiBTECH 1995, 13, 430-437. (i) West, M. L.; Fairlie,
D. P. Targeting HIV-1 Protease. A Test of Drug-design Meth-
odologies. TiPS 1995, 16, 67-74. (j) De Clercq, E. Toward
Improved Anti-HIV Chemotherapy: Therapeutic Strategies for
Intervention with HIV Infections. J . Med. Chem. 1995, 38,
2491-2517. (k) Boehme, R. E.; Borthwick, A. D.; Wyatt, P. G.
Antiviral Agents. Annu. Rep. Med. Chem. 1995, 30, 139-149.
(6) (a) J acobsen, H.; Yasargil, K.; Winslow, D. L.; Craig, J . C.; Krohn,
A.; Duncan, I. B.; Mous, J . Characterization of Human Immu-
nodeficiency Virus Type 1 Mutants with Decreased Sensitivity
to Proteinase Inhibitor Ro 31-8959. Virology 1995, 206, 527-
534. (b) Markowitz, M. M.; Mo, H.; Kempf, D. J .; Norbeck, D.
W.; Bhat, T. N.; Erickson, J . W.; Ho, D. Selection and Analysis
(12) Dunitz, J . D. The Entropic Cost of Bound Water in Crystals and
Biomolecules. Science 1994, 264, 670.
(13) (a) Cram, D. J . Preorganization-From Solvents to Spherands.
Angew. Chem., Int. Ed. Engl. 1986, 25, 1039-1057. (b) Cram,
D. J . The Design of Molecular Hosts, Guests and Their Com-
plexes. Science 1988, 240, 760-767.
(14) (a) Hamilton, H. W.; Steinbaugh, B. A.; Stewart, B. H.; Chan,
O. H.; Schmid, H. L.; Schroeder, R.; Ryan, M. J .; Keiser, J .;
Taylor, M. D.; Blankley, C. J .; Kaltenbronn, J . S.; Wright, J .;
Hicks, J . Evaluation of Physicochemical Parameters Important
to the Oral Bioavailability of Peptide-like Compounds: Implica-
tions for the Synthesis of Renin Inhibitors. J . Med. Chem. 1995,
38, 1446-1455. (b) Kim, E. E.; Baker, C. T.; Dwyer, M. D.;
Murcko, M. A.; Rao, B. G.; Tung, R. D.; Navia, M. A. Crystal
Structure of HIV-1 Protease in complex with VX-478, a Potent
and Orally bioavailable Inhibitor of the Enzyme. J . Am. Chem.
Soc. 1995, 117, 1181-1182.
(15) March, J . Advanced Organic Chemistry, 3rd ed.; Wiley: New
York, 1985; p 125.
(16) (a) J ohnson, F. Allylic Strain in Six-Membered Rings. Chem.
Rev. 1968, 68, 375-413. (b) Hoffmann, R. W. Flexible Molecules
with Defined Shape-Conformational Design. Angew. Chem., Int.
Ed. Engl. 1992, 31, 1124-1134.
(17) Lam, P. Y. S.; J adhav, P. K. Unpublished data.
(18) Omura, K.; Swern, D. Oxidation of Alcohols by “Activated”
Dimethylsulfoxide. A Preparative, Steric and Mechanistic Study.
Tetrahedron 1978, 34, 1651-1660.
(19) (a) Freuidenberger, J . H.; Konradi, A. W.; Pedersen, S. F.
Intermolecular Pinacol Cross Coupling of Electronically Similar
Aldehydes. An Efficient and Stereoselective Synthesis of 1,2-
Diols Employing a Practical Vanadium(II) Reagent. J . Am.
Chem. Soc. 1989, 111, 8014-8016. (b) Kempf, D. J .; Sowin, T.
J .; Doherty, E. M.; Hannick, S. M.; Codavoci, L.; Henry, R. F.;
Green, B. E.; Spanton, S. G.; Norbeck, D. W. Strereocontrolled
Synthesis of C2-Symmetric and Pseudo-C2-Symmetric Diamino
Alcohols and Diols for Use in HIV Protease Inhibitors. J . Org.
Chem. 1992, 57, 5692-5700.
(20) Roberts, S. M., Ed. Molecular Recognition: Chemical and
Biochemical Problems II; Royal Society of Chemistry: Cam-
bridge, 1992.
(21) Erickson-Viitanen, S.; Klabe, R. M.; Cawood, P. G.; O’Neal, P.
L.; Meek, J . L. Potency and Selectivity of Inhibition of Human
Immunodeficiency Virus Protease by a Small Nonpeptide Cyclic
Urea, DMP323. Antimicrob. Agents Chemother. 1994, 38, 1628-
1634.
of Human Immunodeficiency Virus Type
1 Variants with
Increased Resistance to ABT-538, a Novel Protease Inhibitor.
J . Virol. 1995, 69, 701-706. (c) Condra, J . H.; Schlelf, W. A.;
Blahy, O. M.; Gabryelski, L. J .; Graham, D. J .; Quintero, J . C.;
Rhodes, A.; Robbins, H. L.; Roth, E.; Shivaprakash, M.; Titus,
D.; Yang, T.; Teppler, H.; Squires, K. E.; Deutsch, P. J .; Emini,
E. A. In Vivo Emergence of HIV-1 Variants Resistant to Multiple
Protease Inhibitors. Nature 1995, 374, 569-571. (d) Ridky, T.;
Leis, J . Development of Drug Resistance to HIV-1 Protease
Inhibitors. J . Biol. Chem. 1995, 270, 29621-29623.
(7) (a) Swain, A. L.; Miller, M. M.; Green, J .; Rich, D. H.; Schneider,
J .; Kent, S. B. H.; Wlodawer, A. X-ray Crystallographic Structure
of a Complex Between a Synthetic Protease of Human Immu-
nodeficiency Virus 1 and a Substrate-based Hydroxyethylamine
Inhibitor. Proc. Natl. Acad. Sci. U.S.A. 1990, 87, 8805-8809.
(b) Erickson, J .; et al. Design, Activity, and 2.8 A Crystal
Structure of a C2 Symmetric Inhibitor Complexed to HIV-1
Protease. Science 1990, 249, 527-532.
(8) (a) Rahuel, J .; Priestle, J . P.; Grutter, M. G. The Crystal
Structures of Recombinant Glycosylated Human Renin Alone
and in Complex with a Transition State Analog Inhibitor. J .
Struct. Biol. 1991, 107, 227-236. (b) Dhanaraj, V.; Dealwis, C.
G.; Frazao, C.; Badasso, M.; Sibanda, B. L.; Tickle, I. J .; Cooper,
J . B.; Driessen, H. P. C.; Newman, M.; Aguilar, C.; Wood, S. P.;
Blundell, T. L.; Hobart, P. M.; Geoghegan, K. F.; Ammirati, M.
J .; Danley, D. E.; O’Connor, B. A.; Hoover, D. J . X-ray Analyses
of Peptide-Inhibitor Complexes Define the Structural Basis of
Specificity for Human and Mouse Renins. Nature 1992, 357,
466-472.
(9) (a) Lam, P. Y. S.; Eyermann, C. J .; Hodge, C. N.; J adhav, P. K.;
Ru, Y.; Bacheler, L. T.; Meek, J . L.; Otto, M. J .; Rayner, M. M.;
Wong, N. Y.; Chang, C. H.; Wever, P. C.; J ackson, D. A.; Sharpe,
T. R.; Erickson-Viitanen, S. De Novo Design and Discovery of
Potent, Nonpeptidal HIV-1 Protease Inhibitors. 205th ACS
National Meeting, Mar. 28-Apr 2, 1993; Division of Med. Chem.,
No. 96. (b) Lam, P. Y. S.; Eyermann, C. J .; Hodge, C. N.; J adhav,
P. K.; Delucca, G. V. Substituted Cyclic Carbonyls and Deriva-
tives Thereof Useful as Retroviral Protease Inhibitors. PCT
Patent Application WO 9307128, 1993. (c) Lam, P. Y. S.; J adhav,
P. K.; Eyermann, C. J .; Hodge, C. N.; Ru, Y.; Bacheler, L. T.;
Meek, J . L.; Otto, M. J .; Rayner, M. M.; Wong, N. Y.; Chang, C.
H.; Wever, P. C.; J ackson, D. A.; Sharpe, T. R.; Erickson-Vitanen,
S. Rational Design of Potent, Bioavailable, Nonpeptide Cyclic
Ureas as HIV Protease Inhibitors. Science 1994, 263, 380-384.
(10) (a) J adhav, P. K.; Woerner, F. J . Synthesis of C2-Symmetric
HIV-1 Protease Inhibitors from D-Mannitol. Bioorg. Med. Chem.
Lett. 1992, 2, 353-356. (b) J adhav, P. K.; McGee, L. R.; Shenvi,
A.; Hodge, C. N. 1,4-Diamine-2,3-dihydroxybutanes. U.S. Patent
5,294,720, Mar. 15, 1994.
(22) Bacheler, L. T.; Paul, M.; J adhav, P. K.; Otto, M.; Stone, B.;
Miller, J . An Assay for HIV RNA in Infected Cell Lysates, and
Its Use for the Rapid Evaluation of Antiviral Efficacy. Antiviral
Chem. Chemother. 1994, 5 (2), 111-121.
(23) clogP was calculated using Pomona’s MedChem Software Release
3.32. For cyclic urea 27, the clogP of 9.2 probably has a
significant amount of error since clogP calculation is not too
accurate at the high end. HPLC log P was measured by J . Gerry
Everlof using a C18 column and methanol/water eluant.
(24) Wong, N. Y.; Burcham, D. L.; Saxton, P. L.; Erickson-Viitanen,
S.; Grubb, M. F.; Quon, C. Y.; Huang, S.-M. A Pharmacokinetic
Evaluation of HIV Protease Inhibitors, Cyclic Ureas, in Rats and
Dogs. Biopharm. Drug Dispos. 1994, 15, 535-544.
(25) The complete macromolecular crystallographic method is de-
scribed in detail in: Chang, C. H.; Schadt, M. C.; Lewandowski,
F. A.; DeLoskey, R.; Duke, J .; Calabrese, J . C.; Lam, P. Y. S.;
J adhav, P. K.; Eyermann, C. J .; Hodge, C. N.; Weber, P. C. Three
Dimensional Structures of the HIV-1 Protease Complexed with
Novel Non-Peptide, Cyclic Urea-Containing Inhibitors. Manu-
script in preparation.
(26) (a) Grzesiek, S.; Bax, A.; Nicholson, L. K.; Yamazaki, T.;
Wingfield, P.; Stahl, S. J .; Eyermann, C. J .; Torchia, D. A.;
Hodge, C. N.; Lam, P. Y. S.; J adhav, P. K.; Chang, C.-H. NMR
Evidence for the Displacement of a Conserved Interior Water
Molecule in HIV Protease by a Non-Peptide Cyclic Urea-Based
Inhibitor. J . Am. Chem. Soc. 1994, 116, 1581-1582. (b)
Yamazaki, T.; Nicholson, L. K.; Torchia, D. A.; Wingfield, P.;
Stahl, S. J .; Kaufman, J . D.; Eyermann, C. J .; Hodge, C. N.; Lam,
P. Y. S.; Ru, Y.; J adhav, P. K.; Chang, C.-H.; Weber, P. C. NMR
and X-ray Evidence That the HIV Protease Catalytic Aspartyl
Groups Are Protonated in the Complex Formed by the Protease
and a Non-Peptide Cycyclic Urea-Based Inhibitor. J . Am. Chem.
Soc. 1994, 16, 10791-10792. (c) Nicholson, L. K.; Yamazaki,
T.; Torchia, D. A.; Grzesiek, S.; Bax, A.; Stahl, S. J .; Kaufman,
J . D.; Wingfield, P. T.; Lam, P. Y. S.; J adhav, P. K.; Hodge, C.
N.; Domaille, P. J .; Chang, C.-H. Flexibility and Function in
HIV-1 Protease. Struct. Biol. 1995, 2 274-280. (d) Yamazaki,
T.; Hinck, A. P.; Wang, Y.-X.; Nicholson, L. K.; Torchia, D. A.;
Wingfield, P.; Stahl, S. J .; Kaufman, J . D.; Chang, C.-H.;
(11) (a) Eyermann, C. J .; et al. To be published. (b) Hodge, C. N.;
Straatsma, T. P.; McCammon, J . A.; Wlodawer, A. Molecular
Modelling in the Discovery and Optimization of Lead Com-

Cyclic HIV Protease Inhibitors
J ournal of Medicinal Chemistry, 1996, Vol. 39, No. 18 3525
Domaille, P. J .; Lam, P. Y. S. Three Dimensional Solution
Structure of the HIV-1 Protease Complexed with DMP323, a
Novel Cyclic Urea-type Inhibitor, Determined by Nuclear Mag-
netic Resonce Spectroscopy. Protein Sci. 1996, 5, 495-506.
(27) (a) Chenera, B.; DesJ arlais, R. L.; Finkelstein, J . A.; Eggleston,
D. S.; Meek, T. D.; Tomaszek, T. A.; Dryer, G. B. Nonpeptide
HIV Protease Inhibitors Designed to Replace a Bound Water.
Bioorg. Med. Chem. Lett. 1993, 3, 2717-2722. (b) Wild, H.;
Hansen, J .; Lautz, J .; Paessens, A. Preparation of 5-Oxodibenzo-
(a,d)cyclohepta-1,4-diene Derivatives as Antiretroviral Agents.
EP 589322-A1, 1994. (c) Randad, R. S.; Pan, W.; Gulnik, S. V.;
Burt, S.; Erickson, J . W. De Novo Design of Nonpeptidic HIV-1
Protease Inhibitors: Incorporation of Structural Water. Bioorg.
Med. Chem. Lett. 1994, 4, 1247-1252. (d) Vara Prasad, J . V.
N.; et al. Novel Series of Achiral, Low Molecular Weight, and
Potent HIV-1 Protese Inhibitors. J . Am. Chem. Soc. 1994, 116,
6989-6990. (e) Peyman, A.; Stahl, W.; Wagner, K.; Ruppert,
D.; Budt, K.-H. Non-Peptide-Based Inhibitors of Human Immu-
nodeficiency Virus-1 Protease. Bioorg. Med. Chem. Lett. 1994,
4, 2601-2604. (f) J adhav, P. K.; Woerner, F. J . Synthesis of
8-Membered Cyclic Sulfamides: Novel HIV-1 Protease Inhibi-
tors. Tetrahedron Lett. 1995, 36, 6383-6386. (g) Sham, H. L.;
Zhao, C.; Stewart, K. D.; Betebenner, D. A.; Lin, S.; Park, C. H.;
Kong, X.-P.; Rosenbrook, W., J r.; Herrin, T.; Madigan, D.;
Vasavanonda, S.; Lyons, N.; Molla, A.; Saldivar, A.; Marsh, K.
C.; McDonald, E.; Wideburg, N. E.; Denissen, J . F.; Robins, T.;
Kempf, D. J .; Plattner, J . J .; Norbeck, D. W. A Novel, Picomolar
Inhibitor of Human Immunodeficiency Virus Type 1 Protease.
J . Med. Chem. 1996, 39, 392-397. (h) Nugiel, D. A.; J acobs,
K.; Worley, T.; Patel, M.; Kaltenbach, R. F., III; Meyer, D. T.;
J adhav, P. K.; De Lucca, G. V.; Smyser, T. E.; Klabe, R. M.;
Bacheler, L. T.; Rayner, M. M.; Seitz, S. P. Preparation and SAR
of Novel P1/P1′ Substituted Cyclic Urea Based HIV-1 Protease
Inhibitors. J . Med. Chem. 1996, 39, 2156-2169.
(28) (a) Lunney, E. A.; Hagen, S. E.; Domagala, J . M.; Humblet, C.;
Kosinski, J .; Tait, B. D.; Warmus, J . S.; Wilson, M.; Ferguson,
D.; Hupe, D.; Tummino, P. T.; Baldwin, E. T.; Bhat, T. N.; Liu,
B.; Erickson, J . W. A Novel Nonpeptide HIV-1 Protease Inhibi-
tor: Elucidation of the Binding Mode and Its Application in the
Design of Related Analogs. J . Med. Chem. 1994, 37, 2664-2677.
(b) Prasad, J . V. N. V.; Para, K. S.; Lunney, E. A.; Ortwine, D.
F.; Dunbar, J . B.; Ferguson, D.; Tummino, P. J .; Hupe, D.; Tait,
B. D.; Domagala, J . M.; Humblet, C.; Bhat, T. N.; Liu, B.; Guerin,
D. M. A.; Baldwin, E. T.; Erickson, J . W.; Sawyer, T. K. Novel
Series of Achiral, Low Molecular Weight, and Potent HIV-1
Protease Inhibitors. J . Am. Chem. Soc. 1994, 116, 6989-6990.
(c) Prasad, J . V. N. V.; Para, K. S.; Tummino, P. J .; Ferguson,
D.; McQuade, T. J .; Lunney, E. A.; Rapundalo, S. T.; Batley, B.
L.; Hingorani, G.; Domagala, J . M.; Gracheck, S. J .; Bhat, T.
N.; Liu, B.; Baldwin, E. T.; Erickson, J . W.; Sawyer, T. K.
Nonpeptidic Potent HIV-1 Protease Inhibitors: (4-Hydroxy-6-
phenyl-2-oxo-2H-pyran-3-yl)thiomethanes That Span P1-P2′
Subsites in a Unique Mode of Active Site Binding. J . Med.
Chem. 1995, 38, 898-905. (d) Thaisrivongs, S.; Tomich, P. K.;
Watenpaugh, K. D.; Chong, K.-T.; Howe, W. J .; Yang, C.-P.;
Strohbach, J . W.; Turner, S. R.; McGrath, J . P.; Bohanon, M. J .;
Lynn, J . C.; Mulichak, A. M.; Spinelli, P. A.; Hinshaw, R. R.;
Pagano, P. J .; Moon, J . B.; Ruwart, M. J .; Wilkinson, K. F.; Rush,
B. D.; Zipp, G. L.; Dalga, R. J .; Schwende, F. J .; Howard, G. M.;
Padbury, G. E.; Toth, L. N.; Zhao, Z.; Koeplinger, K. A.; Kakuk,
T. J .; Cole, S. L.; Zaya, R. M.; Piper, R. C.; J effrey, P. Structure-
Based Design of HIV Protease Inhibitors: 4-Hydroxycoumarins
and 4-Hydroxy-2-pyrones as Nonpeptidic Inhibitors. J . Med.
Chem. 1994, 37, 3200-3204. (e) Romines, K. R.; Watenpaugh,
K. D.; Tomich, P. K.; Howe, W. J .; Morris, J . K.; Lovasz, K. D.;
Mulichak, A. M.; Finzel, B. C.; Lynn, J . C.; Horng, M.-M.;
Schwende, F. J .; Ruwart, M. J .; Zipp, G. L.; Chong, K.-T.; Dolak,
L. A.; Toth, L. N.; Howard, G. M.; Rush, B. D.; Wilkinson, K. F.;
Possert, P. L.; Dalga, R. J .; Hinshaw, R. R. Use of Medium-Sized
Cycloalkyl Rings to Enhance Secondary Binding: Discovery of
a New Class of Human Immunodeficiency Virus (HIV) Proteases
Inhibitors. J . Med. Chem. 1995, 38, 1884-1891. (f) Thais-
rivongs, S.; Watenpaugh, K. D.; Howe, W. J .; Tomich, P. K.;
Dolak, L. A.; Chong, K.-T.; Tomich, C.-S.; Tomasselli, A. G.;
Turner, S. R.; Strohbach, J . W.; Mulichak, A. M.; J anakiraman,
M. N.; Moon, J . B.; Lynn, J . C.; Horng, M.-M.; Hinshaw, R. R.;
Curry, K. A.; Rothrock, D. J . Structure-Based Design of Novel
Protease Inhibitors: Carboxamide-Containing 4-Hydroxycou-
marins and 4-Hydroxy-2-pyrones as Potent Nonpeptidic Inhibi-
tors. J . Med. Chem. 1995, 38, 3624-3637. (g) Romines, K. R.;
Watenpaugh, K. D.; Howe, W. J .; Tomich, P. K.; Lovasz, K. D.;
Morris, J . K.; J anakiraman, M. N.; Lynn, J . C.; Horng, M.-M.;
Chong, K.-T.; Hinshaw, R. R.; Dolak, L. A. Structure-Based
Design of Nonpeptidic HIV Protease Inhibitors from a Cyclooc-
tylpyranone Lead Structure. J . Med. Chem. 1995, 38, 4463-
4473.
(29) Hodge, C. N.; Ru, Y.; Aldrich, P. E.; Lam, P. Y. S.; J adhav, P.
K.; DeLucca, G. V.; Kaltenbach, R. F., III; Chang, C. H.;
Fernandez, C. H.; Holler, E. E.; Woerner, F. J .; Calabrese, J .
C.; Daneker, W. K.; Emmett, G. C. Calculated and Experimental
Conformations of Cyclic Urea Inhibitors of HIV Protease.
Manuscript in preparation.
(30) Small-molecule crystal structures solved by J . C. Calabrese of
E. I. DuPont de Nemours & Co. Inc. See Supporting Information
for complete methods and coordinates.
(31) Rich, D. H. Effect of Hydrophobic Collapse on Enzyme-Inhibitor
Interaction. Implication for the Design of Peptidal Mimetics.
In Perspectives in Medicinal Chemistry; Testa, B.; Kyburz, E.,
Fuhrer, W., Giger, R., Eds.; VCH: New York, 1993; pp 15-25.
(32) (a) Otto, M. J .; Reid, C. D.; Garber, S.; Lam, P. Y. S.; Scarnati,
H.; Bacheler, L. T.; Rayner, M. M.; Winslow, D. L. Rational
Design of Potent, Bioavailable, Nonpeptide Cyclic Ureas as HIV
Protease Inhibitors. Antimicrob. Agents Chemother. 1993, 37,
2606-2611. (b) Rayner, M. M.; Cordova, B. C.; Meade, R. P.;
Aldrich, P. E.; J adhav, P. K.; Ru, Y.; Lam, P. Y. S. DMP323, a
Nonpeptide Cyclic Urea Inhibitor of Human Immunodeficiency
Virus (HIV) Protease, Specifically and Persistently Blocks
Intracellular Processing of HIV gag Polyprotein. Antimicrob.
Agents Chemother. 1994, 38, 1635-1640. (c) Grubb, M. F.;
Wong, Y. N.; Burcham, D. L.; Saxton, P. L.; Quon, C. Y.; Huang,
S.-M. Pharmacokinetics of HIV Protease Inhibitor DMP323 in
Rats and Dogs. Drug Metab. Dispos. 1994, 22, 709-712.
(33) Shum, L. I.; Winslow, D. L.; Kornhauser, D. M.; et al. Unpub-
lished data. The metabolic instability of the benzyl alcohol of
DMP323 was also of concern.
(34) Hodge, C. N.; Aldrich, P. E.; Bacheler, L. T.; Chang, C.-H.;
Eyermann, C. J .; Grubb, M. F.; J ackson, D. A.; J adhav, P. K.;
Korant, B.; Lam, P. Y. S.; Maurin, M. B.; Meek, J . L.; Otto, M.
J .; Rayner, M. M.; Sharpe, T. R.; Shum, L.; Winslow, D. L.;
Erickson-Viitanen, S. DMP450: An Orally Bioavailable Cyclic
Urea Inhibitor of the HIV Protease. Chem. Biol. 1996, 3, 301-
314. Avid Pharmaceutical Co. (Philadelphia, PA) has recently
acquired the option to license DMP450.
J M9602571