Structure-based design, synthesis, X-ray studies, and biological evaluation of novel HIV-1 protease inhibitors containing isophthalamide-derived P2-ligands

Article abstract of DOI:10.1016/j.bmcl.2015.05.052

We describe the design, synthesis and biological evaluation of a series of novel HIV-1 protease inhibitors bearing isophthalamide derivatives as the P2-P3 ligands. We have investigated a range of acyclic and heterocyclic amides as the extended P2-P3 ligan

Full text of DOI:10.1016/j.bmcl.2015.05.052

Bioorganic & Medicinal Chemistry Letters xxx (2015) xxx–xxx
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Structure-based design, synthesis, X-ray studies, and biological
evaluation of novel HIV-1 protease inhibitors containing
isophthalamide-derived P2-ligands
a
a
a
a
Arun K. Ghosh a, , Jun Takayama , Luke A. Kassekert , Jean-Rene Ella-Menye , Sofiya Yashchuk ,
Johnson Agniswamy b, Yuan-Fang Wang b, Manabu Aoki c, Masayuki Amano c, Irene T. Weber b,
Hiroaki Mitsuya c,d,e
⇑
a Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
b Departments of Biology and Chemistry, Georgia State University, Atlanta, GA 30303, USA
c Departments of Hematology and Infectious Diseases, Kumamoto University of Medicine, Kumamoto 860-8556, Japan
d Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD 20892, USA
e Center for Clinical Sciences, National Center for Global Health and Medicine, Shinjuku, Tokyo 162-8655, Japan
a r t i c l e i n f o
a b s t r a c t
Article history:
We describe the design, synthesis and biological evaluation of a series of novel HIV-1 protease inhibitors
bearing isophthalamide derivatives as the P2–P3 ligands. We have investigated a range of acyclic and
heterocyclic amides as the extended P2–P3 ligands. These inhibitors displayed good to excellent HIV-1
protease inhibitory activity. Also, a number of inhibitors showed very good antiviral activity in MT cells.
Compound 5n has shown an enzyme Ki of 0.17 nM and antiviral IC50 of 14 nM. An X-ray crystal structure
of inhibitor 5o-bound to HIV-1 protease was determined at 1.11 Å resolution. This structure revealed
important molecular insight into the inhibitor–HIV-1 protease interactions in the active site.
Ó 2015 Elsevier Ltd. All rights reserved.
Received 30 April 2015
Revised 19 May 2015
Accepted 21 May 2015
Available online xxxx
Keywords:
HIV-1 protease
Inhibitors
Design
Synthesis
Antiviral
Isophthalamide
HIV-1 protease inhibitors (PIs) are an important component of
highly active antiretroviral therapy (HAART).1,2 This treatment reg-
imen has had a major impact in improving the quality of life and
extending life expectancy of HIV/AIDS patients.3,4 In fact, recent
analyses have revealed that the mortality rates of HIV/AIDS
patients have become closer to general mortality rates due to
HAART and first-line HAART with protease inhibitor-based regi-
mens.5,6 Despite these advances, the development of potent and
more effective HIV-1 protease inhibitor drugs is essential for suc-
cessful long-term control of HIV-1 infection and AIDS.7,8 In our
continuing efforts toward the design and synthesis of nonpeptide
HIV-1 protease inhibitors with clinical potential, we reported a
variety of exceptionally potent PIs including darunavir (1, Fig. 1)
that incorporated structurally novel ligands and scaffolds targeting
the active site HIV-1 protease backbones.9–12 Our design of ligands
has focused on non-peptidic cyclic/heterocyclic structures that
mimic the biological mode of peptide bonds. In particular, we
designed a variety of cyclic ether and poly-ether derived function-
alities inherent to bioactive natural products.13,14 This led to the
development of structurally intriguing bis-THF, Cp-THF, Tp-THF,
and Tris-THF-derived exceptionally potent inhibitors with broad-
spectrum activity against multidrug-resistant HIV-1 variants.9–12
Recently, we reported a series of HIV-1 protease inhibitors
incorporating 3-hydroxy-2-alkyl or 3-hydroxy-2-alkoxy benzoic
acid derivatives as the P2-ligands.15,16 A representative example
is inhibitor 3. These inhibitors were designed by taking advantage
of the large hydrophobic pocket in the HIV-1 protease S1–S2 sub-
sites.16 The P2-ligands resemble 3-hydroxy-2-methyl benzamide
inherent to nelfinavir (4), an FDA approved drug. One of the impor-
tant features of inhibitor 3 is that the P2 ligand does not contain an
asymmetric center. Based upon this result, we have now investi-
gated isophthalamide-based P2-ligands in combination with
hydroxyethylamine sulfonamide isosteres. Our preliminary models
of such isophthalamide derivatives, based upon the X-ray structure
of nelfinavir-bound HIV-1 protease, revealed that both carboxam-
ide functionalities of the isophthalamide ligand can form hydrogen
bonds with the Gly-27 backbone carbonyl as well as with Asp-29
⇑
Corresponding author. Tel.: +1 765 494 5323; fax: +1 765 496 1612.
E-mail address: akghosh@purdue.edu (A.K. Ghosh).
http://dx.doi.org/10.1016/j.bmcl.2015.05.052
0960-894X/Ó 2015 Elsevier Ltd. All rights reserved.
Please cite this article in press as: Ghosh, A. K.; et al. Bioorg. Med. Chem. Lett. (2015), http://dx.doi.org/10.1016/j.bmcl.2015.05.052

2
A. K. Ghosh et al. / Bioorg. Med. Chem. Lett. xxx (2015) xxx–xxx
X
R
OMe
OH
OH
H
N
H
H
N
H
N
O
H
N
N
O
S
R
S
O
H
O
O
O
O
O
O
1, R = NH2 (Darunavir)
, R = OMe (TMC-126)
5 a-o
O
2
OMe
X
OH
OH
R
H
N
R1
N
OH
N
S
HO
HO
+
H2N
N
O
OH
O
O
S
O
O
O
R2
O
3
O
O
6
7a
R = OMe
7b R = CH2OH
H
H
N
H
N
NH2
NH
9b
X
H
9a
Me
X
O
N
H
S
HO
OMe
+
4
Me
(Nelfinavir)
O
N
8
O
O
NH
NH
9d
9c
OMe
Me
O
MeO
Me
BnO
OH
H
H
N
N
N
N
N
N
S
R
O
NH
10a-d
O
O
O
O
O
5 a-o
Me
NH2
NH2
HN
9f
9g
9h
Me
OMe
Scheme 1. General synthetic routes to inhibitors.
Figure 1. Structures of HIV-1 protease inhibitors 1–5.
BnO
HO
backbone amide NHs.17 Also, we speculated that appropriately
functionalized substituents can fill in the hydrophobic pocket in
the S2–S3 subsites. Interestingly, isophthalamide derivatives were
previously utilized in the design of BACE1 inhibitors, an aspartic
acid protease implicated in Alzheimer’s disease.18–20 However,
there is hardly any report of the use of isophthalamide-derived
P2 ligands in the design of HIV-1 protease inhibitors. Herein, we
report the design and synthesis of a series of potent HIV-1 protease
inhibitors incorporating substituted isophthalamide as the P2–P3
ligands. These inhibitors displayed excellent enzyme inhibitory
potency and a number of inhibitors exhibited excellent antiviral
activity. A high resolution X-ray structure of an inhibitor-bound
HIV-1 protease has been determined. The structure revealed
important molecular insight into the ligand-binding site
interactions.
Our general strategy for the synthesis of HIV-1 protease inhibi-
tors bearing isophthalamide derivatives as the P2–P3 ligands is
shown in Scheme 1. As shown, the designed inhibitors would be
synthesized by amide coupling of isophthalic acid derivative 6 with
the amine of the hydroxyethylamine sulfonamide isosteres (7a and
7b)21,22 to provide HIV-1 protease inhibitors. Various isophthalic
acid derivatives would be obtained by coupling of readily available
isophthalic monoacids 8 with various amines 9a–g and 10. Among
these, amines 9a–d are commercially available. Other amines were
synthesized as follows.
a, b
N
N
Boc
Boc
HO
EtO2C
11a
11b
(2R, 4R)
(2R, 4S)
12a
12b
(2R, 4R)
(2R, 4S)
c, d
11c (2S, 4R)
12c (2S, 4R)
11d
(2S, 4S)
12d
(2S, 4S)
BnO
BnO
d, e
N
OH
NH
O
O
O
O
MeO
MeO
BnO
13a
10a
10b
(2R, 4R)
(2R, 4S)
10c (2S, 4R)
10d
(2S, 4S)
N
N
OH
O
MeO
BnO
13b
BnO
OH
N
OH
13c
O
13d
MeO
O
O
MeO
Scheme 2. Reagents and conditions: (a) BnBr, NaH, DMF, 23 °C, 1 h; (b) LiBH4, THF,
23 °C, 2 h (80–85%); (c) MeI, NaH, THF, 23 °C, 12 h; (d) TFA, CH2Cl2, 0 °C, 2 h (65–
71%); (e) acid 8 (X = H), EDC, HOBT, i-Pr2NEt, CH2Cl2, 23 °C; (f) 1 N LiOH, THF, 23 °C,
2 h (67–82%).
The synthesis of various proline derivatives 10a–d is shown in
Scheme 2. The synthesis of all four optically active hydroxyl proline
derivatives 11 was carried out as described by Baker and co-work-
ers.23 Protection of the hydroxyl group as the benzyl ether followed
by LiBH4 reduction of the ethyl ester provided respective primary
alcohol 12a–d in excellent yields. These alcohols were converted
to methyl ethers by treatment with NaH in THF for 30 min at
23 °C followed by addition of methyl iodide and stirring for 12 h.
Methyl ethers were obtained in good yield. Removal of the Boc-
group by exposure of the Boc-derivatives to trifluoroacetic acid
(TFA) in CH2Cl2 at 0 °C for 2 h afforded proline derivatives 10a–d
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A. K. Ghosh et al. / Bioorg. Med. Chem. Lett. xxx (2015) xxx–xxx
3
in excellent yields. These proline derivatives were then coupled
with isophthalic acid methyl ester 8 (X = H) in the presence of
EDC, HOBt, and i-Pr2NEt to provide the corresponding amide
derivative. Saponification of the methyl ester with aqueous lithium
hydroxide afforded acid derivatives 13a–d in very good yields.
The synthesis of oxazole derivatives 9e and 9f is shown in
Scheme 3. Commercially available oxazole 14 was treated with
NaN3 in DMF and heated to 120 °C for 2 h to provide the corre-
sponding azide in 59% yield. Catalytic hydrogenation of azide using
10% Pd–C in the presence of Boc2O afforded the corresponding Boc-
derivative in near quantitative yield. Reduction of the ester with
calcium borohydride afforded alcohol 15 in excellent yield.24
Reaction of alcohol 15 with NaH and MeI in THF for 6 h at 23 °C
resulted in the formation of methyl ether and N-methylation to
provide 16 in moderate yield. Removal of the Boc-group by expo-
sure to TFA in CH2Cl2 at 0 °C for 3 h provided amine 9e in near
quantitative yield. Alcohol 15 was converted to methyl oxazole
17 in a two-step sequence involving mesylation of alcohol 15 with
mesyl chloride and pyridine at 0–23 °C for 4 h followed by reduc-
tion of the resulting mesylate with NaBH4 in HMPA to provide 17.
Removal of the Boc-group by exposure of 17 to TFA in CH2Cl2 pro-
vided amine 9f in excellent yield. Amine 9e was coupled with
isophthalic acid methyl ester 8 (X = H) using EDC, HOBt and in
the presence of i-Pr2NEt to furnish the corresponding amide
derivative. Saponification of the methyl ester with aqueous lithium
hydroxide afforded acid 18a in very good yield. Similarly, acid 8
was coupled with oxazolylmethyl amine 9f to provide the corre-
sponding amide. The resulting amide was methylated using NaH
and MeI in THF for 6 h to provide the corresponding amide.
Saponification of the methyl ester with aqueous lithium hydroxide
afforded acid 18b. For the synthesis of dimethyloxazole derivatives
18c,d, the corresponding known oxazolylmethyl amine 9g was
coupled with acids 8 (X = H, Me).19 The resulting amides were
methylated with NaH and MeI to provide the corresponding N-
methyl derivatives. Saponification of the methyl ester afforded
acids 18c and 18d (50–55% yield for the 3-steps).
Synthesis of HIV-1 protease inhibitors 5a–o containing isoph-
thalamide as the P2 ligands is shown in Scheme 4. Coupling of var-
ious carboxylic acids 19a–c with amine 9a using EDC and HOBt in
the presence of i-Pr2NEt afforded the corresponding amide deriva-
tive 20a–c in good yields (50–60%). For the synthesis of N-methyl
amine derivatives, methyl esters 20a–c were reacted with NaH and
MeI in THF at 0–23 °C for 6 h to provide the corresponding N-
methyl derivatives 21a–c. Saponification of the resulting methyl
esters with aqueous lithium hydroxide afforded carboxylic acids
22a–c in good yields (90–95%). For the synthesis of inhibitor 5a,
methyl ester 20a was saponified and the resulting acid was
coupled with amine 7 using EDC and HOBt in the presence of
i-Pr2NEt to afford amide 5a in 65% yield. In the synthesis of
inhibitors 5b–d, amide derivatives 20a–c were methylated with
NaH and MeI to provide the corresponding N-methyl amides.
Saponification of the methyl ester provided acids 22a–c. Coupling
of acids 22a,b with amine 7 provided inhibitors 5b and 5c.
Synthesis of inhibitor 5d was accomplished by coupling of acid
22c with amine 7 followed by treatment of the resulting amide
with TFA in CH2Cl2 for 6 h to provide 5d. For the synthesis of inhi-
bitors 5e–g, isophthalic acid methyl ester 8 (X = H) was coupled
with amines 9b–d. The resulting esters were saponified and the
acids were coupled with amine 7. For the synthesis of inhibitors
5h–k, proline derivatives 13a–d were coupled with amine 7 and
the resulting amide derivatives were hydrogenated using 10%
Pd–C in a mixture of EtOAc and ethanol. Inhibitors 5l–o were syn-
thesized by coupling of acids 18a–d with amine 7a or 7b.21,22
X
X
HO
MeO2C
H
N
a
OMe
OMe
HO
OMe
N
N
a - c
H
N
Cl
O
O
O
19a
O
O
O
Boc
X = H
20a
b
X = H
14
15
19b X = OMe
20b X = OMe
d
19c
X = N(Me)-Boc
X
20c
X = N(Me)-Boc
f, g
X
MeO
Me
Me
Me
N
Me
N
N
N
N
N
Me
N
c
H
N
OH
O
O
16
Boc
Boc
O
O
O
22a
O
17
X = H
21a
X = H
e
e
22b X = OMe
21b X = OMe
22c
X = N(Me)-Boc
X
21c
X = N(Me)-Boc
MeO
Me
H
N
NH2
OMe
O
9f
O
9e
Me
R2
OH
+
H2N
Ph
a, d, e
N
O
N
OH
O
R1
S
O
7
O
MeO
22a-c
,
N
O
Me
N
N
Me
N
13a-d , 18a-d
OH
OH
OH
N
O
X
18a
18b
O
O
O
O
O
OMe
R2
N
OH
Me
H
N
Me
O
Me
O
N
R1
S
N
Me
N
Me
N
O
O
O
O
OH
Ph
5a-o
Me
18c
Me
18d
O
O
O
(structures in Tables 1 and 2)
Scheme 3. Reagents and conditions: (a) NaN3, DMF, 120 °C; (b) H2, Pd/C, Boc2O,
EtOAc; (c) NaBH4, CaCl2, EtOH/THF (3:2), (58% 3-steps); (d) MeI, NaH, THF (51%); (e)
TFA, CH2Cl2, 0 °C (99%); (f) MsCl, pyridine, CH2Cl2 (46%); (g) NaBH4, HMPa (66%).
Scheme 4. Reagents and conditions: (a) EDCl, HOBT, DIPEA, CH2Cl2; (b) MeI, NaH,
DMF; (c) 1 N LiOH, THF, 23 °C, 2 h; (d) TFA, CH2Cl2 (90%); (e) H2, 10% Pd–C, EtOAc/
EtOH (1:1), 23 °C, 2 h (90–95%).
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A. K. Ghosh et al. / Bioorg. Med. Chem. Lett. xxx (2015) xxx–xxx
Standard EDC and HOBt coupling afforded the various amides in
55–65% yield.
morpholine and N-methylpiperazine in inhibitors 5f and 5g
resulted in over 10-fold improvement of protease inhibitory activ-
ity (entries 6 and 7). Both inhibitors 5f and 5g showed very good
antiviral activity as well.
HIV-1 protease inhibitory potency of all inhibitors was first
evaluated using assay protocol reported by Toth and Marshall.25
Compounds that showed potent enzyme inhibitory Ki values were
then evaluated in an antiviral assay. The results of isophthalamide-
derived inhibitors are shown in Tables 1 and 2. As can be seen,
N-alkylated amides are more potent than the secondary amide
inhibitor 5a (entry 1). Interestingly, N-methyl amide derivative
5b showed 5-fold enhanced potency over 5a (entry 2). In inhibitors
5c and 5d, we examined the effect of polar substituents at the
3-position of isophthalamide (entries 3 and 4). As it turned out,
neither the hydrogen bond donor nor acceptor group improved
potency over unsubstituted derivative 5b. Dipropyl amide 5e was
less effective than N-methyl amide 5b. Compound 5e was evalu-
ated in antiviral assay using MT-2 cells exposed to HIV-1 LAI.26
However, it showed no appreciable antiviral activity. Substitution
of N-methyl-N-propyl amide in 5b with cyclic amines such as
We then examined various proline-derived isophthalamide
derivatives. These results are shown in Table 2. Both donor and
acceptor functionalities were introduced to form hydrogen bonds
in the S2–S3 subsites. We explored all four possible diastereomers
of hydroxyproline ligand. As shown, the 2-(R)-methoxymethyl con-
figuration is preferred (entries 2 and 4) over 2-(S)-diastereomers in
inhibitors 5h and 5j (entries 1 and 3). The effect of the C-4 hydroxy
stereochemistry was not very pronounced. Inhibitors 5h, 5i and 5k
showed moderate antiviral activity. We then examined various oxa-
zolylmethyl-derived P3-ligands in inhibitors 5l–o. Inhibitors 5l and
5m(entries5 and6)exhibitedcomparableHIV-1proteaseinhibitory
activity, indicating minor contribution of the methoxy functionality
in inhibitor 5m. Inhibitor 5m displayed an antiviral IC50 value of
25 nM. Inhibitors 5n and 5o containing dimethyloxazole derivatives
Table 1
Enzyme inhibitory and antiviral activity of inhibitors 5a–g
a,b
Entry
Inhibitor structure
Ki
IC50
(nM)
OMe
OMe
OH
H
N
H
N
1
N
25.1
nt
S
S
O
O
O
O
O
5a
OH
Ph
Me
N
H
N
N
2
3
5.1
nt
nt
O
O
O
Ph
5b
OMe
OMe
Me
N
OH
H
N
20.4
N
S
O
O
O
O
Ph
5c
Me
NH
OMe
OMe
Me
N
OH
H
N
4
157.7
12.4
nt
N
S
S
O
O
O
O
O
Ph
5d
OH
H
N
N
N
5
6
7
>1000
O
O
O
Ph
5e
OMe
O
OH
H
N
N
N
0.42
25
S
O
O
O
O
Ph
5f
Me
OMe
N
OH
H
N
N
N
O
0.54
45
S
O
O
O
Ph
5g
a
Darunavir (1) exhibited Ki = 16 pM, antiviral IC50 = 3 nM.
nt = not tested.
b
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A. K. Ghosh et al. / Bioorg. Med. Chem. Lett. xxx (2015) xxx–xxx
5
Table 2
Enzyme inhibitory and antiviral activity of inhibitors 5h–o
a,b
Entry
Inhibitor structure
Ki
IC50
178
(nM)
HO
OMe
OH
H
1
2.85
N
N
N
S
S
S
S
MeO
O
O
O
O
O
O
O
5h
Ph
HO
OMe
OMe
OH
H
N
2
3
4
N
N
0.27
1.5
389
MeO
O
O
O
Ph
5i
HO
OH
H
N
N
N
>1000
MeO
O
O
O
Ph
5j
HO
OMe
OH
OH
H
N
N
N
0.27
190
MeO
O
O
O
Ph
5k
Me
N
Me
N
OH
H
5
6
0.63
0.31
nt
N
N
O
S
O
O
O
O
Ph
5l
OMe
N
OMe
Me
OH
H
25
N
N
N
O
S
O
O
O
O
Ph
5m
OMe
O
N
Me
N
OH
H
N
N
7
8
0.17
0.21
14
31
S
O
O
O
O
O
Ph
5n
Me
OMe
O
N
Me
N
OH
H
N
N
S
O
O
O
Ph
5o
a
Darunavir (1) exhibited Ki = 16 pM, antiviral IC50 = 3 nM.
nt = not tested.
b
showed enhanced potency over methyloxazole derivative in inhibi-
tor 5l. However, incorporation of 3-methyl on the isophthalic phenyl
ring (entry 8) resulted in reduction of enzyme affinity and antiviral
activity. Inhibitor 5n displayed very potent antiviral activity
(IC50 = 14 nM). To obtain molecular insight into the inhibitor–HIV-
1 protease interactions, we have determined the X-ray crystal struc-
ture of the related inhibitor 5o and HIV-1 protease complex.
The crystal structure of 5o-bound HIV-1 was refined using
X-ray data at 1.11 Å resolution. The overall protease structure
showed similarity to that of the complex with darunavir27 with
which may result from crystallographic packing.28 Most of
the interactions of the inhibitor with protease residues in
the active site cavity are comparable to those of the protease–
darunavir complex.27 The major differences are due to the
dimethyl-oxazolylmethyl isophthalamide group in place of the
bis-tetrahydrofuranyl (bis-THF) urethane in darunavir. The long
P2–P3 ligand is positioned between the side chains of Asp29 and
Arg80 on one side and the carbonyl oxygen of Gly48 on the opposite
site, while forming a water-mediated hydrogen bond with the car-
bonyl oxygen of Pro810 (not shown in Fig. 2). A new hydrogen bond
is formed between the amide nitrogen of Asp29 and one of the car-
bonyl oxygen of isophthalamide ligand. Also, C–H. . .O interactions
are evident between the carbonyl oxygen of Gly48 and amide
an RMSD of 0.21 Å for C
corresponding C atoms are 0.9 Å for residue 78–79, 0.6 Å for flap
residues 48 and 51 and 0.9 Å for the N-terminal residue 30 and 40,
a atoms. The largest differences between
a
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A. K. Ghosh et al. / Bioorg. Med. Chem. Lett. xxx (2015) xxx–xxx
Figure 2. Stereoview of the X-ray structure of inhibitor 5o (green)-bound HIV-1 protease (PDB code: 4ZIP). All strong active site hydrogen bonding interactions of inhibitor 5o
with HIV-1 protease are shown as dotted lines.
methyl in the P2 ligand, producing a shift in the flap regions 47–56.
The five-membered oxazole ring at the distal end of the P2 group
rotates into two alternative conformations. The major conforma-
tion of the oxazole ring forms hydrophobic interactions with the
side chains of Leu230 and Val820. The minor conformation of the
Japan (Monbu Kagakusho), a Grant for Promotion of AIDS
Research from the Ministry of Health, Welfare, and Labor of
Japan, and the Grant to the Cooperative Research Project on
Clinical and Epidemiological Studies of Emerging and Reemerging
Infectious Diseases (Renkei Jigyo) of Monbu-Kagakusho. The
authors would like to thank the Purdue University Center for
Cancer Research, which supports the shared NMR and mass spec-
trometry facilities.
ring forms C–H...p stacking interactions with the guanidinium moi-
ety of Arg80. These extended interactions of the long P2 group are
expected to stabilize the inhibitor in the binding site. The methyl-
benzene moiety of the P2 ligand forms C–H. . .
p interactions with
Ala28 on one side of the binding site and van der Waals contacts
Supplementary data
with Ile500, Val32, Ile47 and Ile84 on the other side.
In summary, we have designed and synthesized a series of novel
HIV-1 protease inhibitors and evaluated their enzyme inhibitory
and antiviral activity. We designed these inhibitors based upon
the X-ray structures of inhibitor–HIV-1 protease complexes. The
inhibitors incorporated isophthalamide-derived P2–P3 ligands to
interact with the HIV-1 protease active site in the S2 and S3 sub-
sites. We have investigated a variety of acyclic, cyclic, and hetero-
cyclic amide derivatives. In particular, we examined substituted
prolines and oxazoles which contain hydrogen bond donor and
acceptor groups for specific interactions in the S3 subsite. A
number of inhibitors exhibited excellent enzyme inhibitory and
antiviral activity. Inhibitor 5n containing isophthalamide dimethy-
loxazolylmethyl amide displayed an enzyme Ki of 0.14 nM and
antiviral IC50 value of 14 nM in MT cells. To obtain molecular
insight into the inhibitor’s binding properties in the HIV-1 protease
active site, we determined the X-ray structure of 5o-bound HIV-1
at 1.11 Å resolution. Our structural analysis revealed that one of
the carboxamide NH formed a strong hydrogen bond with Gly27
carbonyl group of HIV-1 protease. The other carbonyl oxygen
was involved in hydrogen bonding with Asp 29 NH in the S2 sub-
site. Further design and improvement of inhibitor properties utiliz-
ing this molecular insight are in progress.
Supplementary data associated with this article can be found, in
the online version, at http://dx.doi.org/10.1016/j.bmcl.2015.05.
052.
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This research was supported by the National Institutes of
Health (Grant GM53386, A.K.G. and Grant GM62920, I.T.W.). X-
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to 90 K at SER-CAT (22-ID beamline), Advanced Photon Source, Argonne
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and 256 water molecules. The coordinates and structure factors for the
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Data Bank with code: 4ZIP.
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Please cite this article in press as: Ghosh, A. K.; et al. Bioorg. Med. Chem. Lett. (2015), http://dx.doi.org/10.1016/j.bmcl.2015.05.052