Evolution of anti-HIV drug candidates. Part 3: Diarylpyrimidine (DAPY) analogues

Article abstract of DOI:10.1016/S0960-894X(01)00412-7

The synthesis and anti-HIV-1 activity of a series of diarylpyrimidines (DAPYs) are described. Several members of this novel class of non-nucleoside reverse transcriptase inhibitors (NNRTIs) are extremely potent against both wild-type and a panel of clinically significant single- and double-mutant strains of HIV-1.

Full text of DOI:10.1016/S0960-894X(01)00412-7

Bioorganic & Medicinal Chemistry Letters 11 (2001) 2235–2239
Evolution of Anti-HIV Drug Candidates.
Part 3: Diarylpyrimidine (DAPY)Analogues
Donald W. Ludovici,a Bart L. De Corte,a,* Michael J. Kukla,a,* Hong Ye,a Chih Y. Ho,a
Mark A. Lichtenstein,a Robert W. Kavash,a Koen Andries,b Marie-Pierre de Bethune,c
Hilde Azijn,c Rudi Pauwels,c Paul J. Lewi,d Jan Heeres,d Lucien M. H. Koymans,d
Marc R. de Jonge,d Koen J. A. Van Aken,d Frederik F. D. Daeyaert,d Kalyan Das,e
Edward Arnolde and Paul A. J. Janssend
aJanssen Research Foundation, Welsh and McKean Roads, Spring House, PA 19477, USA
bJanssen Research Foundation, Turnhoutseweg 30, B-2340 Beerse, Belgium
cTIBOTEC, Generaal De Wittelaan L 11 B3, B-2800 Mechelen, Belgium
dJanssen Research Foundation, Center for Molecular Design, Antwerpsesteenweg 37, B-2350 Vosselaar, Belgium
eCenter for Advanced Biotechnology and Medicine and Rutgers University Chemistry Department, 679 Hoes Lane,
Piscataway, NJ 08854, USA
Received 5 September 2000; accepted 9 May 2001
Abstract—The synthesis and anti-HIV-1 activity of a series of diarylpyrimidines (DAPYs) are described. Several members of this
novel class of non-nucleoside reverse transcriptase inhibitors (NNRTIs) are extremely potent against both wild-type and a panel of
clinically significant single- and double-mutant strains of HIV-1. # 2001 Elsevier Science Ltd. All rights reserved.
The use of non-nucleoside reverse transcriptase inhibi-
tors (NNRTIs) such as RescriptorTM (delavirdine)1 and
ViramuneTM (nevirapine)2 for the treatment of acquired
immune deficiency syndrome (AIDS) has been well
established. NNRTIs have become key components in
combination regimens with nucleoside reverse tran-
scriptase inhibitors such as AZT and 3TC, and protease
inhibitors.3,4 The most recently approved NNRTI, Sus-
tivaTM (efavirenz), is active against many strains of the
virus that had evolved resistance to delavirdine and
nevirapine and it has quickly become part of key
combination therapies and even as a first line therapy.5
In the previous communication, we reported the dis-
covery of a group of diaryltriazines (DATAs) as a novel
class of NNRT inhibitors.7 While the structure–activity
relationship (SAR) of a variety of dichlorobenzyl-
triazines was being explored, synthesis of the three iso-
meric pyrimidine analogues [2a (R=H), 3 (R=H), and
4] of triazine 1 was pursued in an attempt to gain insight
into the importance of the central heterocycle. Synthesis
of pyrimidines 2a and 3 was accomplished as outlined in
Scheme 1. 2,4,6-Trichloropyrimidine 5 was reacted with
2,6-dichlorobenzylmagnesium chloride in diethyl ether
to afford 6 in excellent yield. Treatment of 6 with
ammonia in isopropanol resulted in a 1:1 mixture of
aminopyrimidines 7 (R=H) and 8 (R=H). The mixture
was treated with 4-cyanoaniline to yield equimolar
amounts of diaminopyrimidines 2a and 3.
As indicated in the previous two papers, our program in
NNRTIs led to the discovery of a series of acyclic imi-
doyl thioureas6 (ITUs) and a family of triazines7 with
excellent anti-HIV activity. We report in this paper the
discovery of a series of diarylpyrimidines (DAPYs) that
appear to be even more effective against wild-type and
various mutant strains of HIV-1.
The third isomer 4 was prepared by reacting amidine 9
with diethyl malonate in the presence of sodium eth-
oxide, resulting in the formation of pyrimidinedione 10
(Scheme 2).8 Conversion of 10 to the dichloropyr-
imidine with phosphorus oxychloride, followed by con-
secutive treatment with ammonia and 4-cyanoaniline,
led to the formation of the desired pyrimidine 4.
*Corresponding authors. Tel.: +1-215-628-5513; fax: +1-215-628-
4985; e-mail: bdecorte@prius.jnj.com; m-rkukla@erols.com
0960-894X/01/$ - see front matter # 2001 Elsevier Science Ltd. All rights reserved.
PII: S0960-894X(01)00412-7

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D. W. Ludovici et al. / Bioorg. Med. Chem. Lett. 11 (2001) 2235–2239
Scheme 1. (a) 2,6-Dichlorobenzylmagnesium chloride, Et2O, 0 ꢀC, 90%; (b) RNH2, iPrOH, quant.; (c) 4-cyanoaniline, melt at 160 ꢀC, 73%.
Of the three isomeric pyrimidines, 2a and 3 were as
effective as the triazine in inhibiting the LAI strain of
HIV-1. Interestingly, among the three, only 2a was
effective in inhibiting several key mutant strains. When
compared to triazine 1, pyrimidine 2a was more active
against several clinically relevant mutant strains (Table 1).
We were also interested in synthesizing the pyrimidine
with hydrogen at the 6-position. Molecular modeling,
based on crystal structures of HIV-1 RT complexed
with molecules from the DATA series, indicated that
this modification might be useful. Unfortunately, all
attempts to prepare 2-(4-cyanoanilino)-4-(2,6-dichloro-
benzyl)pyrimidine by reacting 2,6-dichlorobenzyl mag-
nesium chloride with 2,4-dichloropyrimidine failed. As
the introduction of the 2,4,6-trimethylanilino sub-
stituent in the triazine series had resulted in improved
activity against the wild type and a number of mutant
strains,7 we decided to prepare 2-(4-cyanoanilino)-4-
(2,4,6-trimethylanilino) pyrimidine 13a (Ar-Y=2,4,6-
trimethylanilino)as outlined in Scheme 3.
We then embarked on an extensive SAR study of 2
with the goal of finding analogues that were active
against as many clinically relevant HIV-1 mutant strains
as possible, especially those that were resistant to the
important treatment alternative, SustivaTM
.
In our studies with the ITU and DATA series, we had
found that the para-cyanoaniline ‘eastern aromatic
wing’ (Wing I in the terminology used in describing
HIV-1 RT/NNRTI complex structures10) was optimum.
Consequently, we focused our efforts on varying the
amino and dichlorobenzyl moieties. Keeping the 2,6-
dichlorobenzyl unchanged, we introduced a variety of
amine substituents at the 4-position of the pyrimidine
ring as outlined in Scheme 1. Replacement of the NH2
by a variety of bulkier amines (RNH, R variable) did
not result in an improvement of activity against the wild
type, and the inhibition profile for most mutant HIV-1
strains was poor (data not shown).
We were pleasantly surprised to observe that removal of
the amine (i.e., no substitution) resulted in a compound
(13a) that was nearly as potent as 2a. Based on this
observation, compound 12 became an ideal substrate
for exploration of the SAR of the ‘western aromatic
wing’ (Wing II in HIV-1 RT/NNRTI crystal struc-
tures10), and a variety of aromatic nucleophiles were
reacted with this intermediate (Scheme 3). Anilines were
introduced by reaction with the hydrochloride salt of
12, whereas the oxygen and sulfur analogues were pre-
pared by reaction of 12 with sodium phenolates and
sodium thiolates.
In this series, the compounds containing the 4-cyano-
2,6-dimethylphenoxy and 4-cyano-2,6-dimethylanilino
Table 1. Inhibition of HIV-1 (IC50, mM)9
Compd
X
Y
Z
LAI
100I
103N 181C
188L
1
2a
3
N
N
CH
N
N
N
N
CH
N 0.006 0.398 0.040 0.200 0.316
CH 0.001 0.299 0.012 0.175 0.071
N
N
0.010
96.6
33.3
>100 >100
Scheme 2. (a) Diethyl malonate, NaOEt in EtOH, 76%; (b) POCl3;
82%; (c) NH3/iPrOH, 62%, (d) 4-cyanoaniline, 64%.
4
0.452 >100 >100 >100 >100

D. W. Ludovici et al. / Bioorg. Med. Chem. Lett. 11 (2001) 2235–2239
2237
substituents (13b and 13c) consistently displayed strong
potency against most single mutants tested (Table 2),
and also had the best activity against the HIV-1 mutants
tested. However, the activity of these compounds
against the double mutants, particularly the
100I+103N mutant, was only moderate and in the
micromolar range. We then set out to explore the effect
of substitution on C-5 of the pyrimidine nucleus. In this
series, the 4-cyanoanilino group in the 2-position was
not varied, and the substituents in the 4-position were
limited to 2,4,6-trimethylanilino, 4-cyano-2,6-dimethyl-
anilino, and 4-cyano-2,6-dimethylphenoxy. The 5-bro-
mopyrimidine 15 was synthesized by halogenation of 12
with NBS in chloroform, followed by treatment with 4-
cyanoaniline (Scheme 3). 5-Bromopyrimidines 15a and
15c were further converted to the corresponding 5-eth-
ynyl (16),11 5-vinyl (17),12 and 5-phenylpyrimidines (18)13
using well documented transition metal catalysis chem-
istry. 5-Cyanopyrimidines 19a and 19b were obtained by
treatment of 15a and 15c with cuprous cyanide in dime-
thylformamide.14 The 5-chloropyrimidines (20a–c), 5-
methylpyrimidines (21a and 21b), and 5-nitropyrimidine
(22) were obtained from the corresponding commercially
available 2,4,5-trichloropyrimidine, thymine, and 5-
nitrouracil, respectively, applying chemistry as outlined
in Scheme 3. 5-Aminopyrimidine 23 was obtained by
hydrogenation (H2/10% Pd on C) of 5-nitropyrimidine
22. The acetylated aminopyrimidine 24 was obtained by
treatment of 23 with acetic anhydride in acetone.
The introduction of a substituent in the 5-position of
the pyrimidine clearly resulted in improved activity
against most strains tested. With the exception of the 5-
nitro analogue 22, these compounds displayed excellent
activity against HIV-1 wild-type and single mutants
(Table 3). We were also delighted to see that, in parti-
cular, the 5-bromo derivatives 15a and 15b displayed
strong potency against double mutants 100I+103N and
103N+181C.
The NH2 functionality was also reintroduced in the 6-
position of the pyrimidine for comparison with 15b. The
synthetic scheme followed was similar to the one
described for the synthesis of 4 (Scheme 4). Base cata-
lyzed condensation of 4-cyanophenyl guanidine 2615
and diethyl malonate resulted in formation of pyr-
imidinedione 27. Conversion of 27 to the corresponding
5-bromo-2,4-dichloro derivative 28 was accomplished
using phosphorus oxychloride, followed by bromina-
tion.16 Reaction of 28 with 4-cyano-2,6-dimethyl phe-
nolate and ammonia resulted in formation of target
compound 25.
Scheme 3. (a) 4-Cyanoaniline, diglyme; (b) POCl3; (c) Ar-YH
(Y=NH) or Ar-YÀNa+ (Y=O, S), 1,4-dioxane; (d) NBS, CHCl3; (e)
16: TMS–acetylene, Pd(Ph3P)2Cl2, CuI, Et3N, 3%; (f) 17: tetravinyltin,
Pd(PPh3)4, 1,4-dioxane, 12%; (g) 18: PhSn(Bu)3, Pd(PPh3)4, 1,4-diox-
ane, 23%; (R) 19a and 19b: CuCN, DMF, 17 and 24%, respectively.
Table 2. Inhibition of HIV-1 (IC50, mM)9
Compd
R
Y
LAI
100I
103N
181C
188L
100I+103N
103N+181C
13a
13b
13c
13d
13e
13f
13g
13h
13i
13j
13k
13l
13m
13n
13o
2,4,6-triMe
2,6-diMe-4-CN
2,6-diMe-4-CN
2,6-diMe-4-Br
2,6-diMe-4-Br
2,6-diMe-4-(HCC)
2,4,6-triMe
N
O
N
O
S
0.0010
0.0011
0.0004
0.0029
0.0057
0.0055
0.0036
0.0029
0.0006
0.0007
0.0007
0.0010
0.0021
0.0007
0.0023
0.018
0.073
0.034
0.113
0.174
0.185
0.054
0.022
0.015
0.014
0.212
0.060
0.327
0.0030
0.076
0.0043
0.0027
0.0019
0.0047
0.039
0.012
0.012
0.0030
0.0057
0.0030
0.028
0.0075
0.037
0.0071
0.059
0.068
0.171
0.025
0.038
0.015
0.010
0.061
0.018
0.019
0.0034
0.017
0.048
0.019
0.0078
0.079
0.044
0.050
0.020
0.055
0.064
0.099
0.260
0.086
0.115
>100
0.069
>10
0.798
1.086
2.371
3.890
4.188
4.786
8.2
>10
>10
>10
>10
0.044
0.094
0.037
0.217
0.354
0.793
nd
1.1
nd
nd
nd
O
S
2,4,6-triMe
O
N
N
N
N
N
N
N
2,4-diBr-6-F
2,4,6-triCl
2,6-diMe
2,4-diCl-6-Me
2,6-diMe-4-Cl
2,6-diBr-4-Me
2,6-diMe-4-Br
0.013
0.013
0.0030
0.012
nd
>10
>100
>100
0.401
0.133
0.150
nd: not determined.

2238
D. W. Ludovici et al. / Bioorg. Med. Chem. Lett. 11 (2001) 2235–2239
Table 3. Inhibition of HIV-1 (IC50, mM)9
Compd
R1
Y
R2
R3
LAI
100I
103N
181C
188L
100I+103N
103N+181C
15a
15b
15c
16
17
18
19a
19b
20a
20b
20c
21a
21b
22
23
24
2,6-diMe-4-CN
2,6-diMe-4-CN
2,4,6-triMe
2,4,6-triMe
2,4,6-triMe
2,4,6-triMe
2,6-diMe-4-CN
2,4,6-triMe
2,6-diMe-4-CN
2,6-diMe-4-CN
2,4,6-triMe
2,6-diMe-4-CN
2,4,6-triMe
2,6-diMe-4-CN
2,6-diMe-4-CN
2,6-diMe-4-CN
2,6-diMe-4-CN
N
O
N
N
N
N
N
N
N
O
N
N
N
O
O
O
O
Br
Br
Br
HCC
Vinyl
Ph
CN
CN
Cl
—
—
—
—
—
—
—
—
—
—
—
—
—
—
—
—
NH2
0.0004
0.0014
0.0055
0.0042
0.0025
0.024
0.0005
0.0010
0.0012
0.0014
0.0027
0.0008
0.0017
0.018
0.0010
0.0019
0.0014
0.032
0.063
0.0010
0.0070
0.0066
0.011
0.028
0.035
nd
0.091
0.063
0.0052
0.0075
0.017
0.016
0.012
0.121
0.016
0.031
0.0033
0.316
2.512
0.040
0.0004
0.0014
0.0073
0.0062
0.0058
nd
0.0026
0.0034
0.0009
0.0026
0.0060
0.0017
0.0026
0.010
0.0013
0.0033
0.0012
6.310
2.512
0.040
0.0096
0.022
0.036
0.043
0.036
nd
0.076
0.040
0.014
0.034
0.032
0.012
0.012
0.304
0.0093
0.030
0.0070
10.000
1.995
0.0020
0.0033
0.0059
0.027
0.042
0.029
nd
0.0086
0.077
0.0047
0.0048
0.034
0.016
0.018
0.782
0.0057
0.0084
0.0046
>100
1.259
0.158
0.037
0.049
0.348
0.071
>100
nd
0.032
0.025
0.283
0.042
0.106
nd
0.312
nd
0.181
nd
0.144
0.138
0.319
>10
>100
>10
0.282
0.205
0.019
nd
0.069
0.038
0.138
0.162
0.053
0.194
0.014
0.030
0.0043
>100
19.953
0.040
Cl
Cl
Me
Me
NO2
NH2
NHAc
Br
25
Nevirapine
Delavirdine
Efavirenz
nd
>10
nd: not determined.
tested. A number of compounds from this series are
being considered for clinical evaluation.
Acknowledgements
A number of people have been instrumental in this
work. Thanks go to our colleagues in the JRF-CMD for
many stimulating discussions and suggestions;17 to
Diane Gautier and Greg Leo for help with NMR spec-
tral analyses; to Theo Thielemans for continuously
updating extremely organized data presentations; to Bill
Leister, Kim Strauss, and Brian Rafferty for numerous
analyses and sample purifications; to Inge Dierynck and
Kurt Hertogs (TIBOTEC) for the construction of
mutant HIV-1 strains; and to Art Clark and others at
CABM and Rutgers University and to Stephen Hughes
and his colleagues at NIH-NCI for their help with the
structural studies.
Scheme 4. (a) Diethyl malonate, NaOEt in EtOH, 76%; (b) POCl3;
86%; (c) Br2, NaHCO3, H2O, MeOH, 78%; (d) sodium 4-cyano-2,6-
dimethylphenolate, N-methyl-pyrrolidone, 1,4-dioxane, 45%; (e) NH3/
iPrOH, 41%.
Compound 25 proved to be even more potent than any
other compound synthesized in this series. In fact, 25
inhibits all HIV-1 mutant strains tested with IC50 values
less than 20 nM, including the 100I+103N mutant,
References and Notes
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.
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both the wild type and the single and double mutants

D. W. Ludovici et al. / Bioorg. Med. Chem. Lett. 11 (2001) 2235–2239
2239
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