N1-Heterocyclic pyrimidinediones as non-nucleoside inhibitors of HIV-1 reverse transcriptase

Article abstract of DOI:10.1016/j.bmcl.2010.01.086

A series of N1-heterocyclic pyrimidinediones were extensively evaluated as HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs). Inhibitor 1 is active against NNRTI-resistant viruses including RT mutant K103N. The co-crystal structure of inhibit

Full text of DOI:10.1016/j.bmcl.2010.01.086

Bioorganic & Medicinal Chemistry Letters 20 (2010) 1585–1588
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Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
N1-Heterocyclic pyrimidinediones as non-nucleoside inhibitors of HIV-1
reverse transcriptase
b
b
b
b
a
Michael L. Mitchell a, , Jong Chan Son , Ill Young Lee , Chong-Kyo Lee , Hae Soo Kim , Hongyan Guo ,
Jianhong Wang a, Jaclyn Hayes a, Michael Wang a, Amber Paul a, Eric B. Lansdon a, James M. Chen a,
Gene Eisenberg a, Romas Geleziunas a, Lianhong Xu a, Choung U. Kim a
*
a Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
b Korea Research Institute of Chemical Technology, PO Box 107, Yuseong, Daejeon 305-600, Republic of Korea
a r t i c l e i n f o
a b s t r a c t
Article history:
A series of N1-heterocyclic pyrimidinediones were extensively evaluated as HIV-1 non-nucleoside
reverse transcriptase inhibitors (NNRTIs). Inhibitor 1 is active against NNRTI-resistant viruses including
RT mutant K103N. The co-crystal structure of inhibitor 1 with HIV-1 RT revealed that H-bonds are formed
with K101 and K103. Efforts to improve the suboptimal pharmacokinetic profile of 1 resulted in the dis-
covery of compound 13, which represents the lead compound in this series with improved pharmacoki-
netics and similar potency as inhibitor 1.
Received 4 December 2009
Revised 11 January 2010
Accepted 13 January 2010
Available online 21 January 2010
Keywords:
Human immunodeficiency virus
Non-nucleoside
Ó 2010 Elsevier Ltd. All rights reserved.
Reverse transcriptase
Pyrimidinedione
The use of non-nucleoside reverse transcriptase inhibitors
(NNRTIs) for treatment of human immunodeficiency virus type 1
(HIV-1) infection has been well established.1 Despite active
research, there are only four marketed NNRTIs: efavirenz,2 nevira-
pine,3 delavirdine,4 and most recently, etravirine.5 Rapid emer-
gence of drug-resistant mutant viruses that were cross-resistant
to other NNRTIs limited the broad usage of this class of antiretro-
viral drugs. Efavirenz, the most prescribed NNRTI, is associated
with side effects that include perturbation of central nervous sys-
tem function and teratogenicity.6 Despite its improved resistance
profile, etravirine lacks the convenience of once-daily administra-
tion and is also associated with cutaneous and hypersensitivity
reactions. Thus, our goal was to identify an NNRTI that possessed
an improved safety profile with the convenience of once-daily dos-
ing that remained active against mutant viruses, especially the re-
verse transcriptase (RT) K103N mutant that is selected by
efavirenz.7 We herein report the synthesis and evaluation of N1-
pyridinyl pyrimidinediones as HIV-1 NNRTIs.
availability (Table 1). However, pharmacokinetics in three species
(rat, dog and monkey) suggested that once-daily dosing in humans
was unlikely. Incubation of 1 with human hepatocytes produced a
principal metabolite resulting from oxidation on the aminofluoro-
pyridyl moiety. Hydroxylation of the C5 isopropyl was also
observed.
Compound 1 was co-crystallized with HIV-1 reverse transcrip-
tase as shown in Figure 2.9 Hydrogen bonds are observed between
the NH of the pyrimidinedione and the backbone carbonyl of K101
An N-pyridinyl pyrimidinedione (KRV-2110, 1) was previously
identified as a potent NNRTI (Fig. 1).8 Antiviral profiling revealed
that compound 1 also exhibits potent antiviral activity against RT
Y181C and K103N mutant viruses. Detailed profiling of compound
1 indicated that it has moderate protein binding and high oral bio-
* Corresponding author. Tel.: +1 650 522 5185; fax: +1 650 522 5899.
E-mail addresses: mmitchell@gilead.com (M.L. Mitchell), james.mchen@yahoo.
com (J.M. Chen).
Figure 1. Structure of compound 1 (KRV-2110), efavirenz and etravirine.
0960-894X/$ - see front matter Ó 2010 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2010.01.086

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M. L. Mitchell et al. / Bioorg. Med. Chem. Lett. 20 (2010) 1585–1588
Table 1
Evaluation of pyrimidinedione NNRTI’s
Compound
R
EC50 (nm)a WT fold change
% Protein Bindingb
Human MS t1/2 (min)c
t1/2 (h)
Dog PKd
Vss (L/kg)
WT
Y181C
K103N
% F
Efavirenz
Efavirenz
—
—
1.1
1.6
2.6
2.6
35
0.9
99.9
99.8
98
140
ND
8.87
ND
1.6
ND
13.3e
1
9
3.4
4.5
6.7
8.2
1.6
7.3
93.6
93.3
45
51
3.3
ND
1.8
ND
96e
ND
10
13
12.4
6.2
12
16
1.9
2.4
94.2
87.7
Stable
281
4.9
4.7
1.94
1.61
41.5f
80g
ND = not determined.
a
Values are means of at least two experiments in MT-2 cells.
Values determined from HSA column.
Values determined by incubating with human microsomes; half-life greater than 395 min is reported as stable.
Pharmacokinetic values determined from IV (0.5 mg/kg) or PO solution dosing in beagle dogs in triplicate.
%F determined with 4 mg/kg oral dose.
b
c
d
e
f
%F determined with 0.5 mg/kg oral dose.
%F determined with 2 mg/kg oral dose.
g
as well as the NH2 of the aminofluoropyridyl moiety and the back-
bone carbonyl of the K103 residue.
Analogs of compound 1 were designed to block the oxidation of
the aminofluoropyridine as shown in Scheme 1. Compound 1 was
synthesized starting from 3,5-dichloro-2,4,6-trifluoro-pyridine
(2a) that was next converted to 3a via dibenzyl malonate displace-
ment and mono-decarboxylation. Hydrogenolysis of benzyl ester
3a gave the corresponding acid and decarboxylation with concom-
itant bromination provided bromide 4a. Bromide displacement
with sodium benzoate, chloride removal via hydrogenolysis, and
benzoate ester cleavage gave 2,6-difluoro-4-hydroxymethyl pyri-
dine 5a. Displacement of a fluoride with p-methoxybenzylamine,
mesylation of the hydroxyl group, coupling with pyrimidinedione
core 78 and deprotection furnished compound 1.
Compound 9 was prepared similarly to compound 1 starting
from 3-chloro-2,4,5,6-tetrafluoro-pyridine (2b). Compound
9
would be expected to potentially block and/or slow down oxida-
tion of the aminofluoropyridyl moiety, but no significant improve-
ment in microsomal stability was observed. Potency of 9 against
wild type and RT Y181C viruses was similar to 1 but compound
9 was less potent against RT K103N virus. We speculate that the
ortho substitution may perturb the hydrogen bond formed be-
tween –NH2 and the carbonyl of residue 103, either by electronic
effects or torsional restriction.
Next, we investigated whether oxidation of the pyridyl nitrogen
was contributing to the metabolic instability. To specifically ad-
dress this issue, the corresponding phenyl analog lacking the pyr-
idine nitrogen was prepared. The resulting compound showed only
marginal improvement in microsomal stability.
The evidence assembled thus far indicated that the NH2 in 1
was responsible for the microsomal instability. To test this hypoth-
esis, difluoropyridine 10, in which the amino group was replaced
with fluoride (Scheme 2), was synthesized. Compound 10 proved
to be more stable in both dog and human microsomes compared
to 1. However, in contrast to the in vitro observations, the half-life
of compound 10 in dogs was only marginally improved relative to
1. To reconcile this inconsistency, compound 10 was incubated in
Figure 2. Compound 1 bound in the NNRTI binding pocket of HIV-1RT (2.3Å
resolution).

M. L. Mitchell et al. / Bioorg. Med. Chem. Lett. 20 (2010) 1585–1588
1587
Scheme 1. Reagents and conditions: (a) (i) dibenzyl malonate, NaH, DMF; (ii) DMSO/H2O, 130 °C, 75%; (b) H2, Pd/C, THF, 78–89%; (c) HgO, Br2, chlorobenzene, 145 °C, 75–
80%; (d) NaOBz, DMF, 66–81%; (e) H2 (50 psi), Pd/C, EtOH, 61%; (f) NaOMe, MeOH, 95–98%; (g) PMBNH2, 125 °C, 90–94%; (h) methanesulfonyl chloride, triethylamine, CHCl3;
(i) 7, K2CO3, LiI, DMF, 32–55%; (j) CAN, ACN/H2O, 77%.
Figure 3. Comparison of PO PK for compounds 1 (4 mg/kg) and 13 (2 mg/kg) in
Scheme 2. Reagents and conditions: (a) methanesulfonyl chloride, triethylamine,
beagle dogs.
CHCl3; (b) 7, potassium carbonate, lithium iodide, DMF, 32%; (c) N-bromosuccin-
imide, benzoyl peroxide, CCl4, reflux, 28%; (d) sodium benzoate, DMF, 79%; (e)
sodium methoxide, MeOH, 94%.
pound 1. It represents an improvement in microsomal stability,
fresh human hepatocytes which showed that the difluoropyridyl
pharmacokinetic parameters while maintaining most of the antivi-
moiety of compound 10 underwent oxidative defluorination fol-
ral potency of compound 1 against wild type virus. However, the
lowed by glutathione adduct formation.
As a result of this observation, the stability of monofluoropyri-
justed antiviral potency, was insufficient to support once-daily
dine 13 was also evaluated in fresh human hepatocytes. Compound
13 did not form glutathione adducts in vitro and showed improved
microsomal stability and a longer half-life compared to compound
1. Compound 13 retained most of the potency against wild type
and RT K103N viruses but displayed diminished potency against
half-life of 13, as shown in Figure 3, together with its plasma ad-
dosing in humans.
Our parallel effort on N1-alkyl pyrimidinediones generated
more promising results. Thus, research efforts were shifted to focus
on the N1-alkyl pyrimidinedione series which is reported in the
following Letter.10
RT Y181C virus.
Since incubation of compound 1 with microsomes resulted in
C5 hydroxylation, we substituted the isopropyl group for ethyl
and tert-butyl in an attempt to blunt metabolism. Although we ob-
served a modest improvement of in vitro and in vivo stability for
the C5 ethyl analog, both ethyl and tert-butyl analogs were less po-
tent against mutant viruses, in particular RT Y181C. The increased
volume of the Y181C NNRTI binding pocket in the vicinity of the C5
substituent may explain why these compounds are less potent
against the RT Y181C mutant virus.
Thus, the C5 isopropyl may provide the best balance of hydro-
phobic interactions with the NNRTI binding pocket and transla-
tional freedom to give the superior potencies against wild type
and mutant viruses.5
Acknowledgements
The authors wish to thank Gerry Rhodes, Manoj Desai, Nilima
Kutty, Candra Lancaster, and Stephanie Leavitt for their
contributions.
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