Orally bioavailable highly potent HIV protease inhibitors against PI-resistant virus

Article abstract of DOI:10.1016/j.bmcl.2005.08.072

Efforts directed to identifying potent HIV protease inhibitors (PI) have yielded a class of compounds that are not only very active against wild-type (NL4-3) HIV virus but also very potent against a panel of PI-resistant viral isolates. Chemistry and biol

Full text of DOI:10.1016/j.bmcl.2005.08.072

Bioorganic & Medicinal Chemistry Letters 15 (2005) 5311–5314
Orally bioavailable highly potent HIV protease inhibitors
against PI-resistant virus
Zhijian Lu,a,* Joann Bohn,a Tom Rano,a Carrie A. Rutkowski,b Amy L. Simcoe,b
David B. Olsen,b William A. Schleif,b Anthony Carella,b Lori Gabryelski,b Lixia Jin,c
Jiunn H. Lin,c Emilio Emini,b Kevin Chapmana and James R. Tataa
aDepartment of Basic Chemistry, Merck Research Laboratories, Rahway, NJ 07065, USA
bDepartment of Antiviral Research, Merck Research Laboratories, West Point, PA 19486, USA
cDepartment of Drug Metabolism, Merck Research Laboratories, West Point, PA 19486, USA
Received 14 June 2005; revised 8 August 2005; accepted 10 August 2005
Available online 3 October 2005
Abstract—Efforts directed to identifying potent HIV protease inhibitors (PI) have yielded a class of compounds that are not only
very active against wild-type (NL4-3) HIV virus but also very potent against a panel of PI-resistant viral isolates. Chemistry and
biology are described.
Ó 2005 Elsevier Ltd. All rights reserved.
The fast emerging resistance to the first generation of
HIV protease inhibitors, such as indinavir, nelfinavir,
saquinavir, and ritonavir, has been a substantial and
persistent problem in the treatment of AIDS. The need
for more potent and bioavailable protease inhibitors to
achieve more complete viral suppression has become ur-
gent. Furthermore, the alarming expression of viral
cross-resistance to multiple protease inhibitors under-
scores the necessity for chemotherapeutic agents that
are broadly active against a wide variety of HIV
mutations.1
The synthesis of these analogs is exemplified with the
best compound 9 (Scheme 1). Treatment of 1 with
LDA in THF at ꢀ78 °C followed by trapping with ethyl
Indinavir
S1'
S1
S3
OH
N
O
OH
H
N
N
N
O
NH
Our efforts in this area have been focused on reengineer-
ing the structure of indinavir that preserves its excellent
biological profile while improving the antiviral activity
against various resistant viral isolates. Previous work
highlighted the modifications at the S2 pocket by intro-
ducing N-CF3CH2 amide for a tert-butyl amide2 and at
the S30 pocket with aminochromanol moiety for amino-
indanol.3 In this communication, we report that modifi-
cations focused on the S10 and the S3 pockets have
afforded compounds with excellent potency against PI-
resistant virus. Figure 1 shows R1 and R2 are the focus
area under investigation.
S2
S3'
S3
R2
S1'
S1
R1
OH
N
OH
H
N
N
O
O
O
NH
CF3
S2
S3'
Keywords: HIV; Protease; Inhibitors.
*
Figure 1. Modifications of indinavir for R1 and R2 may lead to
improved potency against PI-resistant viral strains.
Corresponding author. Tel.: +1 732 594 4392; fax: +1 732 594
9473; e-mail: Zhijian_lu@merck.com
0960-894X/$ - see front matter Ó 2005 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2005.08.072

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Z. Lu et al. / Bioorg. Med. Chem. Lett. 15 (2005) 5311–5314
formate gave aldehyde 2 in 82% yield. Wittig–Horner
reaction of 2 afforded ester 3 in excellent yield. Hydroge-
nation of 3 gave a saturated ester which was subsequent-
ly hydrolyzed to an acid. The acid was coupled with
aminochromanol and the resulting coupling product
was protected to give compound 4 in 51% overall yield.
Compound 4 was treated with 1 M LiN(TMS)2 and
trapped with allyl bromide at ꢀ25 °C to afford 5 in
75% yield. The epoxide 6 was obtained in 58% yield
by treatment of 5 with NIS in a mixture of EtOAc
and aqueous NaHCO3 followed by NaOMe in EtOAc
at room temperature. The epoxide ring opening with
compound 7 in i-PrOH under reflux conditions afforded
compound 8 in 33% yield. Final deprotection of 8 with
HCl in ether and MeOH gave compound 9 in 47% yield.
The synthesis of all analogs described herein, was car-
ried out in a similar fashion as illustrated in Scheme 1.
All final products were isolated by preparative TLC
and characterized by 1H NMR and LC–MS (ESI).
The preparation of the intermediate 7 was similar to
the chemistry described elsewhere.4
ally they are 5–30-fold more potent than indinavir. The
similar potencies of these compounds have made it hard
to differentiate them from each other by just comparing
their wild-type IC50 and CIC95 (Table 1). Our discussion
for the SAR therefore will be focused instead on the re-
sults from their viral spread assay6 in Table 2. Among
the compounds tested (9–22), compounds 9 and 16 are
extremely potent and they are the best against all mutant
viruses listed (CIC95 < 7.8 nM cross the board). These
two compounds are the regio-isomers of the pyridylthi-
ophene at R1. With the same R1, compounds 9–13 pres-
ent an interesting SAR at R2 site. All five groups at R2
were used before in different series.4,7 We try to examine
how these groups respond to the pyridylthiophene moi-
ety at the R1. gem-Dimethyl-2-(4-chlorophenyl)-1,3-oxa-
zol-5-yl moiety (9) is the best in all five groups. gem-
Dimethyl-2-(4-chlorophenyl)-1,3-thiazol-2-yl
group
(10) also displays excellent antiviral activity and is only
slightly less potent against mutant V-18C than com-
pound 9. The other three, furan analog 11, thiophene
analog 12, and thiazole analog 13, are active against mu-
tant virus but less potent than 9 and 10. It is worth not-
ing that a CF3 group in the thiazole analog 13 causes a
loss of potency for both IC50 and CIC95 (Tables 1 and
2). Compound 15 is another very potent compound
against mutant virus.
The biological activity of the synthesized compounds is
shown in Tables 1 and 2. The compounds were tested for
their ability to inhibit the protease enzyme (IC50) and to
inhibit the spread of viral infection in MT4 human T-
lymphoid cells using NL4-3 virus (CIC95).5 The results
indicate that all compounds 9–22 are very potent against
wild-type protease enzyme and NL4-3 virus, and gener-
Introduction of a chlorine atom at the pyridylthiophene
ring (17) resulted in a potent protease inhibitor with
N
H
CO2Et
c,d,e
O
a
N
b
N
N
N
S
O
S
S
S
O
1
O
2
3
4
N
N
N
S
S
S
Cl
f
O
N
OH
g
O
O
O
O
h
N
N
N
N
N
7
O
O
O
O
O
O
O
HN
F3C
5
6
8
N
Cl
S
O
Cl
N
O
i
N
N
OH
NH
HO
H
N
N
N
O
O
HN
F3C
O
O
HN
F3C
7
9
Scheme 1. Reagents and conditions: (a) LDA, THF, ꢀ78 °C, ethylformate, 82%; (b) triethyl phosphonoacetate, NaH, THF, 0 °C, 92%; (c) H2, Pd/C,
MeOH, rt; (d) NaOH, MeOH/H2O; (e) aminochromanol, EDC, HOBT, Et3N, CH2Cl2, rt, 2-methoxy propene, 10-camphorsulfonic acid, CH2Cl2,
51% overall; (f) 1 M LiN(TMS)2, allyl bromide, THF, ꢀ25 °C, 75%; (g) NIS, EtOAc/NaHCO3, 0 °C to rt; NaOMe, EtOAc, rt, 58% overall;
(h) i-PrOH, reflux, 33%; (i) HCl in ether, MeOH, 47%.

Z. Lu et al. / Bioorg. Med. Chem. Lett. 15 (2005) 5311–5314
Table 1. Influence of substituents on in vitro potency of HIV protease inhibitors
5313
R2
R1
N
OH
OH
H
N
N
O
O
O
NH
F3C
Compound
R1
R2
IC50 (nM)
0.02
CIC95 (nM) NL4-3
N
N
N
N
N
N
N
9
<7.8
<7.8
15.6
15.6
26.0
<7.8
<7.8
<7.8
<7.8
O
S
Cl
Cl
Cl
Cl
S
S
S
S
S
O
O
S
10
11
12
13
14
15
16
17
0.04
0.03
O
0.05
S
S
0.07
N
F3C
0.05
N
O
O
O
O
Cl
N
N
N
0.02
N
N
Cl
Cl
Cl
<0.02
<0.02
Cl
N
S
S
O
18
0.11
0.08
0.03
0.04
0.03
0.59
<7.8
15.6
15.6
<7.8
<7.8
50
N
F
N
N
N
N
N
O
O
O
O
19
O
S
S
O
Cl
N
20
Cl
Cl
Cl
21
N
22
Indinavir

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Z. Lu et al. / Bioorg. Med. Chem. Lett. 15 (2005) 5311–5314
Table 2. Potency (CIC95) (nM) against PI-resistant viral isolate
constructs in the viral spread assay
and another compound 15 shows a decent bioavailabil-
ity in both dogs and rats.
Compound NL4-3 4X Virus
Viral isolates
V-18C
K-60C
>1000
Q-60C
>1000
References and notes
Indinavir
50
400
>1000
<7.8
31.3
125
9
10
11
12
13
14
15
16
17
18
19
20
21
22
<7.8
<7.8
15.6
15.6
26.0
<7.8
7.8
<7.8
<7.8
15.6
15.6
125
<7.8
<7.8
1. (a) Vacca, J. P.; Condra, J. H. Drug Discov. Today 1997, 2,
261; (b) Kempf, D. J.; Sham, J. L. Curr. Pharm. Design
1996, 2, 225; (c) Vacca, J. P.; Dorsey, B. D.; Schlief, W. A.;
Levin, R. B.; MeDaniel, S. L.; Derke, P. L.; Zugay, J.;
Quintero, J. C.; Blanhy, 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.; Vastag, K.; Ostovic,
D.; Anderson, P. S.; Emini, E. A.; Huff, J. R. Proc. Natl.
Acad. Sci. U.S.A. 1994, 91, 4096; (d) Condra, J. H. Drug
Resist. Updates 1998, 1, 1; (e) Boden, D.; Markowits, M.
Antimicrob. Agents Chemother. 1998, 42, 2775.
<7.8
<7.8
31.3
31.3
<7.8
<7.8
<7.8
<7.8
125
<7.8
31.3
31.3
93.8
15.6
<7.8
<7.8
<7.8
125
125
375
31.3
<7.8
<7.8
<7.8
15.6
31.3
31.3
15.6
62.5
62.5
31
<7.8
7.8
<7.8
15.6
62.5
125
7.8
15.6
15.6
<7.8
<7.8
<7.8
15.6
125
62.5
31.3
62.5
62.5
250
62.5
125
2. Duffy, J. L.; Kevin, N. J.; Kirk, B. A.; Chapman, K. T.;
Schleif, W. A.; Olsen, D. B.; Stahlhut, M.; Rutkowski, C.
A.; Kuo, L. C.; Jin, L.; Lin, J. H.; Emini, E. A.; Tata, J. R.
Bioorg. Med. Chem. Lett. 2002, 12, 2423.
15.6
3. Cheng, Y.; Zhang, F.; Rano, T. A.; Lu, Z.; Chapman, K. T.;
Schleif, W. A.; Olsen, D. B.; Stahlhut, M.; Rutkowski, C. A.;
Kuo, L. C.; Jin, L.; Lin, J. H.; Emini, E. A.; Tata, J. R. Bioorg.
Med. Chem. Lett. 2002, 12, 2419; For other synthesis of
aminochromanol, see: (a) Ghosh, A. K.; Mckee, S. P.;
Sanders, W. M. Tetrahedron Lett. 1991, 32, 711; (b) Davies, I.
W.; Taylor, M.; Marcoux, J.-F.; Matty, L.; Wu, J.; Hughes,
D.; Reider, P. J. Tetrahedron Lett. 2000, 41, 8021.
4. Zhang, F.; Chapman, K. T.; Schleif, W. A.; Olsen, D. B.;
Stahlhut, M.; Rutkowski, C. A.; Kuo, L. C.; Jin, L.; Lin, J.
H.; Emini, E. A.; Tata, J. R. Bioorg. Med. Chem. Lett.
2003, 13, 2573.
5. Vacca, J. P.; Dorsey, B. D.; Schleif, 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.; Vastag, K.; Ostovic, D.; Anderson, P.
S.; Emini, E. A.; Huff, J. R. Proc. Natl. Acad. Sci. U.S.A.
1994, 91, 4096.
only a slight loss of potency against viral isolate V-18C
(17 vs 16). The analogs of 3-(5-methyl-2-furyl)-4-methyl-
pyridine moiety (18–22) are generally potent but less ac-
tive than other compounds (9–17). We noticed that the
V-18C viral isolate was one of the toughest viral isolates
and most of our compounds performed less satisfactori-
ly against it. Given their excellent antiviral activity
against mutant virus, pyridylthiophene analog 9, and
pyridylfuran analog 15 were chosen to test the oral bio-
availability in animal models. At the dose of 2 mpk po,
compound 9 showed moderate bioavailability (7.3%)
with a reasonable PK profile (Table 3). Additionally,
compound 15 had decent oral bioavailability (F = 42%
in dog and 14% in rat, see Tables 3 and 4 for PK data
in dog and rat). Unfortunately, both 9 and 15 were po-
tent (IC50 < 1lM) inhibitors of CYP 3A4, 2D6, and
2C9.
6. For the genotype of these isolates and their susceptibility to
protease inhibitors, see (a) Condra, J. H.; Holder, D. J.;
Schleif, W. A.; Blahy, O. M.; Danovich, R. M.; Gabyelski, L.
J.; Graham, D. J.; Laird, D.; Quintero, J. C.; Rhodes, A.;
Robbins, H. L.; Roth, E.; Shivaprakash, M.; Yang, T.;
Chodakewitz, J. A.; Deutsch, P. J.; Leavitt, R. Y.; Massari,
F. E.; Mellors, J. W.; Squires, K. E.; Steigbigel, R. T.;
Teppler, H.; Emini, E. A. J. Virol. 1996, 70, 8270; (b) Olsen,
D. B.; Stahlhut, M. W.; Rutkowski, C. A.; Schock, H. B.;
vanOlden, A. L.; Kuo, L. C. J. Biol. Chem. 1999, 274, 23699.
7. (a) Kim, R. M.; Rouse, E. A.; Chapman, K. T.; Schleif, W.
A.; Olsen, D. B.; Stahlhut, M.; Rutkowski, C. A.; Kuo, L.
C.; Jin, L.; Lin, J. H.; Emini, E. A.; Tata, J. R. Bioorg. Med.
Chem. Lett. 2004, 14, 4651(b) Manuscripts in preparation.
In summary, we have shown that replacement of phenyl
group at the S10 of Indinavir with various aryl heterocy-
cles along with modifications at the S3 pocket can signif-
icantly impact the inhibitory potency of the compounds
against the HIV protease enzyme. All compounds dis-
cussed above display much better antiviral activity
against mutant isolates than does indinavir. Specifically,
nearly a half dozen compounds (9, 10, and 15–17) show
substantially better potency (low nanomolar) against the
viral spread of both the wild-type virus (NL4-3) and a
number of PI-resistant variants of HIV. One of the best
compounds (9) shows moderate bioavailability in rats
Table 3. Pharmacokinetics in rats for compounds 9 and 15 (n = 4)
Compound
Dose (po dose mpk)
Cmax (lM)
AUC (lM h)
F (%)
t1/2 (min)
CL (ml/min/kg)
9
15
2
10
0.052
0.18 (sd = 0.07)
0.36
0.29 (sd = 0.12)
7.3
14
48
48
111
98
Table 4. Pharmacokinetics in dogs for compound 15 (n = 2)
Compound
Dose (po dose mpk)
10
Cmax (lM)
AUC (lM h)
F (%)
t1/2 (min)
CL (ml/min/kg)
23
15
2.1 (sd = 1.51)
0.39 (sd = 0.31)
42
60