Design and synthesis of bicyclic pyrimidinone-based HCV NS3 protease inhibitors

Article abstract of DOI:10.1016/S0960-894X(03)00022-2

A series of bicyclic pyrimidinone-based HCV NS3 protease inhibitors was synthesized via selective C8 position functionalization. Substituted phenylamides and phenylureas were preferred in the S2 binding pocket.

Full text of DOI:10.1016/S0960-894X(03)00022-2

Bioorganic & Medicinal Chemistry Letters 13 (2003) 785–788
Design and Synthesis of Bicyclic Pyrimidinone-Based HCV NS3
Protease Inhibitors
Peter W. Glunz,* Brent D. Douty and Carl P. Decicco
Bristol-Myers Squibb Pharmaceutical Research Institute, PO Box 5400, Princeton, NJ 08543-5400, USA
Received 4 November 2002; revised 7 January 2003; accepted 10 January 2003
Abstract—A series of bicyclic pyrimidinone-based HCV NS3 protease inhibitors was synthesized via selective C8 position
functionalization. Substituted phenylamides and phenylureas were preferred in the S2 binding pocket.
# 2003 Elsevier Science Ltd. All rights reserved.
The hepatitisC virus(HCV) infectsan estimated 1–3%
of the world population. The clinical state of a propor-
tion of those infected individuals eventually progresses
to cirrhosis and hepatocellular carcinoma.1 The pre-
valence of this disease and its adverse outcome make it
the largest cause of liver transplantation. The current
treatment of HCV, based upon pegylated interferon-a
and the antiviral agent ribavirin, providesonly limited
sustained viral response and is accompanied by severe
side effects.2 New treatments for the disease exhibiting
improved success rates and side effect profiles are needed.
with the goal of interacting with the enzyme binding site
in ways unavailable to peptide-based inhibitors (see Fig.
1). Into a peptide boronic acid inhibitor,7 we incorpo-
rated a bicyclic pyrimidinone-based P2–P3 dipeptide
replacement8,9 and focused on projecting substituents
into the extended S2 binding pocket—a strategy shown
to increase potency in peptidic inhibitors of HCV NS3
protease.10 Towardsthisgoal, we have developed regio-
and stereoselective alkylation chemistry to functionalize
the C8-position of the bicyclic pyrimidinone core.11
Synthesis of the bicyclic pyrimidinone core was accom-
plished in an eight-step sequence according to the
method of Webber et al.,9 beginning with pyroglutamic
acid (1) (Scheme 1). N-Alkylation of Cbz-protected
intermediate 2, followed by amide coupling afforded
anilide 3. The 3-(trifluoromethyl)benzyl substituent was
found to be an optimal P4 substituent in a related pyr-
azinone-based inhibitor12 and was thus used in this ser-
ies. Anilide 3 served as a key intermediate for the
introduction of a variety of C8 substituents. Important
Newer strategies for combating HCV infection target
essential non-structural proteins of HCV. One such tar-
get is the HCV NS3 serine protease, which is responsible
for proteolytic processing of non-structural proteins
required for viral maturation. Functioning HCV NS3
hasbeen shown to be required for infection in a chim-
panzee model,3 thusvalidating the proteaes asa ther-
apeutic target and making it the focusof isgnificant
inhibitor design efforts.
Structural information and substrate requirements suggest
the challenge that inhibiting HCV NS3 protease poses. X-
ray crystal structures of the protease reveal a shallow, fea-
tureless binding pocket, with few opportunities for binding
interactions.4,5 Furthermore, substrates of ten or more
amino acidsare required for efficient enzymatic cleavage
and sequence specificity is quite broad.6 To overcome these
challenges, we undertook a peptidomimetic approach
Figure 1. Bicyclic pyrimidinone-based inhibitor designed to reach into
S2 via functionalization of C8 position.
*Corresponding author. Tel.:+1-609-818-5287; fax:+1-609-818-3331;
e-mail: peter.glunz@bms.com
0960-894X/03/$ - see front matter # 2003 Elsevier Science Ltd. All rights reserved.
doi:10.1016/S0960-894X(03)00022-2

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P. W. Glunz et al. / Bioorg. Med. Chem. Lett. 13 (2003) 785–788
Scheme 1. Reagents and conditions: (a) eight steps, ref 9; (b) NaH, mCF3–BnBr, TBAI; (c) aniline, EDCI, HOAt, NaHCO3 (74%, two steps); (d)
LiHMDS, MeI; (e) LiHMDS, trisyl azide (83%, two steps); (f) Boc2O, DMAP, CH3CN (100%); (g) LiOH, H2O2; (h) EDCI, HOAt, (1R)-1-ami-
nopropyl boronic acid pinanediol ester (75%, two steps); (i) H2, Pd–C, MeOH (100%); (j) PhNCO, CH2Cl2 (40%).
featuresof thisintermediate are the anilide, which
serves as a synthetically convenient, protected car-
boxylic acid and preventsC a deprotonation/alkyl-
ation,13 and the tertiary substitution of the C3 amine,
which facilitatesdeprotonation of the C8 position.
C6 carboxamide in 83% overall yield for the two-step
sequence. The stereochemical outcome, as determined
by nOe studies, is consistent with the trans selectivity
observed in alkylations of N-protected pyroglutamic
acid esters.14,15 The carboxylic acid functionality was
revealed by conversion of the amide to an imide, fol-
lowed by hydrolysis of the imide to the acid. The acid
wascoupled with (1 R)-1-aminopropyl boronic acid
pinanediol ester, prepared according to the method of
Matteson et al.16,17 The azide functionality wasreduced
to the amine via hydrogenolysis with concomitant Cbz
removal. Treatment of amine 6 with phenyl isocyanate
afforded phenyl urea-based inhibitor 7a. In addition, a
series of amides and a carbamate were prepared by
treatment of amine 6 with variousacid chloridesor
An initial series of inhibitors, based upon a C8 amino
group designed to project a substituent into the exten-
ded S2 pocket, wassynthesized beginning with phenyl-
amide 3. Deprotonation of 3 (LiHMDS, 2.0 equiv)
followed by quenching of the resultant dianion with MeI
givesa trans/cis mixture (ꢀ2:1) of C8 mono-alkylation
products. A second deprotonation followed by treat-
ment with trisyl azide installed the quaternary center of
intermediate 4 in which the azide isoriented trans to the
Scheme 2. Reagents and conditions: (a) LiHMDS, MeI; (b) LiHMDS, allyl bromide (48%, two steps); (c) RuCl3, NaIO4; (d) Cs2CO3, BnBr (42%,
two steps); (e) Boc2O, DMAP, CH3CN (93%); (f) LiOH, H2O2 (100%); (g) EDCI, HOAt, (1R)-1-aminopropyl boronic acid pinanediol ester (52%);
(h) H2, Pd–C, MeOH (100%); (i) PhNH2, HATU, DIEA (54%).

P. W. Glunz et al. / Bioorg. Med. Chem. Lett. 13 (2003) 785–788
787
phenyl chloroformate (see Table 1). A series of sub-
stituted phenyl urea-based inhibitors (7f–z) waspre-
pared by treatment of amine 6 with substituted phenyl
isocyanates (Table 2).
oxidation of the allyl group to the acid (RuCl3, NalO4),
followed by benzylation afforded the acetate function-
ality with the desired trans stereochemistry, protected as
the benzyl ester (10). Asin the previousexample, the C-
terminal acid wasrevealed and coupled with (1 R)-1-
aminopropyl boronic acid pinanediol ester to provide
protected intermediate 11. Hydrogenation unmasked
the carboxylate group, which wascoupled with a series
of aminesto provide trans substituted amides 12a–j
(Table 3).
A second series of bicyclic pyrimidinone-based inhibi-
torswasprepared that incorporatesan acetate group at
the C8 position, designed to project a substituent into
the S2 pocket (Scheme 2). To obtain the trans-disposed
acetate moiety, it was necessary to proceed through the
intermediacy of an allyl substituent (intermediate 9),
which was readily installed with the desired trans
stereochemistry via alkylation of bicyclic pyrimidinone
3 with allyl bromide. Attemptsto directly intsall the
acetate group via alkylation with tert-butyl bromoace-
tate afforded predominantly cis substitution relative to
the C6 carboxamide asdetermined by nOe. Subsequent
IC50 values18 determined for the initial series of bicyclic
pyrimidinone inhibitors( Table 1) show a preference for
a phenyl urea substituent (7a) in the S2 pocket over
benzyl urea 7b, amides 7c and 7d, or phenyl carbamate
7e. The phenyl urea hasapproximately a 10-fold effect
on inhibition relative to C8-unsubstitued analogue 8
(prepared by coupling of 2 with (1R)-1-aminopropyl
boronic acid pinanediol ester, hydrogenation,
and reductive amination with 3-(trifluoromethyl)
benzaldehyde).
Table 1. Inhibition of HCV NS3 protease by C8-nitrogen linked
bicyclic pyrimidinonesa
IC50 determinations for the substituted phenyl ureas are
listed in Table 2. The most potent HCV NS3 protease
inhibitorsin thisseriesare
ortho alkyl esters 7m and 7p,
which are approximately 10-fold more potent than the
unsubstituted phenyl urea (7a). Moving this substitutent
to either the meta (7n and 7q) or para (7r) positions
results in a significant loss in inhibition, as does remov-
ing the alkyl group to give ortho carboxylate 7o. Potent
inhibitors are also obtained with alkoxy substitution at
the ortho position (7i, 7j and 7k) or a meta methylsulfa-
nyl group (7t). Substitution at the para position dimin-
ishes inhibitory activity relative to the unsubstituted
phenyl urea.
Compd
R1
R2
IC50, mM
8
H
H
7.0
0.79
1.2
3.4
2.4
1.4
7a
7b
7c
7d
7e
Me
Me
Me
Me
Me
–NH(CO)NHPh
–NH(CO)NHCH2Ph
–NHCOPh
–NHCOCH2Ph
–NHCO2Ph
aEach IC50 isthe average of two determinations.
Inhibition determinationsfor the
trans substituted
amides, listed in Table 3, follow trendsobserved in the
phenyl urea series. The unsubstituted phenylamide (12a)
is4-fold more potent than the correpsonding phenyl
urea 7a. Preferences are seen for the methyl ester and
alkoxy substituents at the ortho position (compounds
Table 2. Inhibition of HCV NS3 protease by substituted phenyl
ureasa
Table 3. Inhibition of HCV NS3 protease by trans substituted C8
amidesa
Compd
R
IC50 (mM)
R
IC50 (mM)
7a
7f
7g
7h
7i
7j
7k
7l
Ph
0.70
0.18
0.37
1.10
0.36
0.16
0.30
4.74
0.08
1.77
6.40
7p o-(CO2Et)Ph
7q m-(CO2Et)Ph
7r p-(CO2Et)Ph
0.10
1.55
1.10
0.71
0.13
2.36
30
0.50
1.03
0.78
0.27
o-NO2Ph
o-ClPh
p-ClPh
o-MeOPh
o-EtOPh
o-PhOPh
p-PhOPh
o-(CO2Me)Ph
m-(CO2Me)Ph
o-(CO2H)Ph
7s
7t
o-MeSPh
m-MeSPh
p-MeSPh
o-PhPh
Compd
R
IC50 (mM)
R
IC50 (mM)
7u
7v
7w
7x
7y
7z
12a
12b
12c
12d
12e
Ph
0.17
0.10
0.20
2.53
0.09
12f
1-Naphthyl
0.17
0.44
0.15
0.18
1.46
o-(CO2Me)Ph
o-MeOPh
o-NO2Ph
12g 1-Isoquinolinyl
12h o-(CONH2)Ph
12i o-(CONHMe)Ph
12j o-(CONMe2)Ph
m-FPh
p-FPh
7m
7n
7o
o-MePh
1-Naph
m-MeSPh
aEach IC50 isthe average of two determinations.
aEach IC50 isthe average of two determinations.

788
P. W. Glunz et al. / Bioorg. Med. Chem. Lett. 13 (2003) 785–788
12b and 12c, repsectively) aswell asa methyluslfanyl
group at the meta position (12e). Primary and second-
ary carboxamidesat the ortho position (12h and 12i) are
tolerated, whereasa tertiary amide ( 12j) isnot. In con-
trast to the trends observed in the urea series, an ortho
nitro substituent (12d) results in a 15-fold loss in activity
relative to the unsubstituted phenylamide. Inhibitors
prepared based upon the cis substitution pattern (pre-
pared via alkylation of intermediate 3 with tert-butyl
bromoacetate) displayed flat SAR, which is consistent
with molecular modeling that predictsthe C8 usb-
stituent to be solvent exposed in the cis system.
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In summary, we have developed potent, non-peptide
HCV NS3 protease inhibitors based upon a bicyclic
pyrimidinone scaffold. Interaction with the S2 binding
pocket by these inhibitors via urea- and amide-based
linkerscontributed isgnificantly to inhibition of the
enzyme. To access the extended S2 binding pocket of
the enzyme and make these binding interactions, we have
developed alkylation chemistry to regio- and stereo-
selectively functionalize the bicyclic pyrimidinone ring
system at the C8 position. This chemistry allows late-
stage modification of the C8 position of the scaffold with-
out necessitating resynthesis of the bicyclic pyrimidinone
core for each analogue (i.e., pyrrolidinone alkylation, fol-
lowed by elaboration to the bicyclic pyrimidinone).
Acknowledgements
14. Ezquerra, J.; Pedregal, C.; Rubio, A.; Yruretagoyena, B.;
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J. B. J. Org. Chem. 1994, 59, 4327.
We thank Lorraine Gorey-Feret and JamesL. Meek for
IC50 determinations, Laurine G. Galya and Thomas H.
Scholz for NMR structural determinations, and Pro-
fessor David Evans for helpful discussions.
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References and Notes
18. In vitro inhibition assays were performed as described in
the following reference: Priestley, E. S.; DeLucca, I.; Ghavimi,
B.; Erickson-Viitanen, S.; Decicco, C. P. Bioorg. Med. Chem.
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