SAR of 3,4-dihydropyrido[3,2-d]pyrimidone p38 inhibitors

Article abstract of DOI:10.1016/j.bmcl.2003.08.059

Development for a class of potent 3,4-dihydropyrido(3,2-d)pyrimidone inhibitors of p38a MAP kinase is described. Modification of N-1 aryl and C-6 arylsulfide in 3,4-dihydropyrido(3,2-d)pyrimidone analogues for the interaction with the hydrophobic pockets

Full text of DOI:10.1016/j.bmcl.2003.08.059

Bioorganic & Medicinal ChemistryLetters 13 (2003) 3979–3982
SAR of 3,4-Dihydropyrido[3,2-d]pyrimidone p38 Inhibitors
Luping Liu,a,* John E. Stelmach,a Swaminathan R. Natarajan,a Meng-Hsin Chen,a
Suresh B. Singh,a Cheryl D. Schwartz,b Catherine E. Fitzgerald,b Stephen J. O’Keefe,b
Dennis M. Zaller,b Dennis M. Schmatzb and James B. Dohertya
aDepartments of Medicinal Chemistry, Merck Research Laboratories, PO Box 2000, Rahway, NJ 07065, USA
bDepartments of Inflamation Research, Merck Research Laboratories, PO Box 2000, Rahway, NJ 07065, USA
Received 2 July2003; revised 19 August 2003; accepted 27 August 2003
Abstract—Development for a class of potent 3,4-dihydropyrido(3,2-d)pyrimidone inhibitors of p38a MAP kinase is described.
Modification of N-1 aryl and C-6 arylsulfide in 3,4-dihydropyrido(3,2-d)pyrimidone analogues for the interaction with the hydro-
phobic pockets in p38 active site is also discussed.
# 2003 Elsevier Ltd. All rights reserved.
Tumor necrosis factor-a (TNF-a) and interleukin-1 (IL-
1) are proinflammatorycytokines produced in response
to infection and other cellular stresses. MAP kinase p38
is a keyplayer in the intracellular signal transduction
cascade required for the biosynthesis of the inflamma-
torycytokines IL-1 and TFN- a.1,2 The identification of
SB-2035801,3 as a p38 MAP kinase inhibitor led to the
development of trisubstituted imidazoles as promising
4ꢀ6
class of p38 antagonists byseveral groups.
Potent,
selective and functionally active pyrido-pyrimidones,
such as 1, derived from VX-745, have been previous
described.7 In this case, substitutents at the 7-position
enhanced activitythrough increased rigidi,ty pre-
orienting the aryl sulfide in a favorable disposition, and
possiblyformed a salt bridge with ASP-168 in p38
active binding site.8,9
carbonyl oxygen to form a hydrogen bond with amide
Met-109. The 2,4-difluoroaryl sulfide at C-6 position
penetrates into the hydrophobic pocket-1. The 2,6-
dichlorophenyl substituent at N-1 position is assumed
to occupythe hydrophobic pocket-2 in the active site.
X-raycrystallographic and mutagenesis studies of p38a
with trisubstituted imidazoles as molecular probes have
revealed keybinding interaction in the p38 active
site.10,11 The pyridine nitrogen forms a hydrogen bond
with the amide N–H of Met 109 and the aryl group
penetrating into a hydrophobic pocket not accessed by
ATP (Fig. 1). A mnemonic constructed to rationalize
the observed SAR in the imidazole series was utilized8
to predict the relative binding orientations of 1 in the
p38 active site. The primarycontact is made through the
In this communication, we would like to report SAR
efforts that help characterize hydrophobic pockets 1 and
2 in the enzyme active site with insights gleaned through
molecular modeling and X-ray crystallographic analysis.
The general preparation procedures were summarized in
Scheme 1. We used a modified synthetic method as
reported before.8 Diazotization of amine 3 in HF-pyri-
dine gave 2-fluoropyridine moiety 4. NBS bromination
*Corresponding author. Tel.:+1-732-594-7744; fax:+1-732-594-8080;
e-mail: luping_liu@merck.com
0960-894X/$ - see front matter # 2003 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2003.08.059

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L. Liu et al. / Bioorg. Med. Chem. Lett. 13 (2003) 3979–3982
However, larger substituents should be tolerated in the
ortho position. This model is consistent with the
observed SAR in Table 1.
The data from p38a/b kinase assay8 (Table 1) shows
that meta- and para-substituted thiophenols gave low to
modest activities. The ortho-substituented compounds
23, 24 and 25 are less active compared to compound 18,
but compounds 14, 15 and 16 are more potent implying
methyl or chloro is preferred and there might be size or
electronic restrictions at this site. All meta-substituted
thiophenols, such as 20, 26, and 28 gave low to modest
activities. Substituents larger than a chlorine group in
the para position, such as 27 and 29, give reduced
activity. The experimental data from the p38a/b kinase
assayis thus consistent with the prediction from our
computer modeling studies. The 2,4-disubstituted thio-
phenols, such as 10, 11 and 12, showed significantly
improved activity.
Figure 1. Relative binding orientations of 11 to p38.
In order to further probe the size of hydrophobic
pocket 1, we adjusted the linker one carbon longer
between the aromatic group and the core ring. The
synthetic procedure for the linker modification is sum-
marized in Scheme 2. Treatment of 6 with 2,6-dichloro-
benzylisocyanates gave urea 30. Cyclization of 30 under
copper iodide catalysis yields 31. Replacement of fluor-
ine with a range of nucleophiles followed bydeprotection
byrefluxing in trifluoroacetic acid (containing 10–25%
anisole) gave the corresponding pyridine-urea analogues
32. (Scheme 2). The corresponding p38a/b data for the
products are summarized in Table 2.
Table 1. p38 Inhibitory activities for designed pyrido-pyrimidones:
C-6 arylsulfides
Compd
a
b
c
d
p38a
p38b
Scheme 1. Synthesis of 10: (a) 1.2 equiv NaNO2, HF-pyridine, 70%;
(b) 1.2 equiv NBS, 0.1 equiv Bz2O2, 80 ꢁC, CCl4, sun lamp, 1 h, 95%;
(c) 2 equiv PMB–NH2, CH2Cl2, 91%; (d) 1.5 equiv Ar–SH, 2 equiv
DIPEA, 1,4-dioxane, reflux, 4 h, 71%; (e) Ar–NCO, DIPEA, CH2Cl2,
82%; (f) 1.2 equiv CuI, 2 equiv DIPEA, DMF, 150 ꢁC, 2 h, 33%;
(g) TFA, 110 ꢁC, 80%.
IC50 (nM)
IC50 (nM)
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
Cl
F
Cl
Cl
Cl
Me
Br
NH2
H
Me
H
H
H
NH2
CF3
OMe
H
H
H
H
H
H
H
H
H
H
H
H
H
Cl
H
H
H
H
H
Cl
H
CF3
H
F
F
Cl
H
H
H
H
F
H
H
H
H
H
H
H
H
H
H
11
25
32
49
57
250
190
H
H
Cl
H
H
H
H
H
Me
Cl
F
Cl
H
H
H
H
H
H
H
50%@340
393
800
1480
1340
2370
980
47%@1250
74%@1000
1490
94
110
120
200
270
260
350
450
515
1420
1850
1990
2190
produced 5. Displacement of bromine with 4-methoxy-
benzyl amine gave 6. Replacement of fluorine with
thiophenol gave 7. Treatment of 7 with 2,6-dichloro-
phenyl isocyanate gave urea 8. Cyclization of 8 under
copper iodide catalysis yield 9. Deprotection byreflux-
ing in trifluoroacetic acid (containing 10-25% anisole)
gave the corresponding pyridine-urea analogue 10
(Scheme 1).
2750
66%@1000
3430
67@1000
Our binding model of 11 proposes a tight fit of the
thiophenol substituent in a hydrophobic pocket 1. The
model suggests that no large substituents will be toler-
ated in the para and meta position of the thiophenol.
CF3
H
-S-4-F-Ph
51%@10,000 31%@10,000
1815 66%@80,000
ꢀ6%@10,000 6%@10,000
H

L. Liu et al. / Bioorg. Med. Chem. Lett. 13 (2003) 3979–3982
3981
Molecular modeling studies suggested an additional
hydrogen bonding interaction with residue Y35 of p38
maybe possible if a suitable hydrogen bond acceptor
was present in the para position of the phenyl. A methyl
ester substituent 56 in the para position did produce a
slight increase activityover the parent compound 60. A
para acetyl moiety 57 also produced a slight increase in
activityover the parent 60. Amide analogues 59 and 61
produced same or attenuated activityespeciallyfor
amides derived from larger amines.
In summary, we have described the results of optimiza-
tion from our investigation for both hydrophobic
Table 3. p38 Inhibitory activities for designed pyrido-pyrimidones:
N-1 arylsulfides
Scheme 2. Synthesis of 32: (a) Ar-NCO, DIPEA, CH2Cl2, 82%; (b) 1.2
equiv CuI, 2 equiv DIPEA, DMF, 150 ꢁC, 2 h, 35%; (c) BnNH2 (or
HSBn), DIPEA, 1,4-dioxane, 160 ꢁC, 14 h, 48%; (d) TFA, 110 ꢁC, 80%.
Table 2. p38 Inhibitoryactivities for 32–39
Compd R1
R2
R3
p38a
p38b
X
IC50 (nM)
IC50 (nM)
Compd
X
R
R0
p38a
p38b
39
40
41
Cl COOMe
Me
Et
Me
36
38
47
250
200
80%@300
IC50 (nM)
IC50(nM)
Cl
Cl
H
COMe
32
33
34
35
36
37
38
NH
NH
NH
NH
S
H
F
H
Cl
H
F
H
F
Cl
Cl
H
F
OMe
113
340
980
42%@1000
12%@1000
15%@1000
13%@1000
6%@1000
3%@1000
42
Cl
H
F
48
86%@2000
14%@1000
9%@1000
42%@1000
21%@1000
ꢀ8%@1000
43
44
Cl
Cl
H
NO2
Me
Me
54
66
270
66%@1000
S
S
H
45
46
Cl
H
H
COOMe
OMe
80
67%@1000
66%@1000
950
Me
100
47
48
Cl
Me
H
H
CF3
H
110
180
As we predicted, because of limited space in hydro-
phobic pocket 1, especiallythe tight fit in the para-
position of the aromatic group, the p38a/b data for the
compounds 36, 37 and 38 in Table 2 have much lower
activities comparing with the corresponding compounds
in Table 1. Moreover, bigger para-substituent R0 of the
aromatic group in both substituted benzyl amines, such
as 32, 33, 34, 35, and benzyl thioethers, such as 36, 37,
38, gave lower activities. Those observations further
identified the tight fit in hydrophobic pocket 1 for the
phenyl group.
52%@1000 Cl
49
50
51
52
53
54
55
Cl
Cl
CF3
H
Cl
230
56%@1000
CH2OH 46%@1000 23%@1000
COONH2 46%@1000 10%@1000
Cl
H
Cl
H
NH2
OH
29%@1000 11%@1000
20%@1000 16%@1000
Me
Cl
H
H
COOH 14%@1000 0%@1000
Ph
H
H
28%@1000 16%@1000
Investigation of hydrophobic pocket 2 has been per-
formed bytesting a series of analogues with different
substituents in the N-1 aromatic ring. As demonstrated
in Table 3, compounds possessing ortho substituted
phenyl were dramatically more potent than the corre-
sponding ortho unsubstituted 64. It appears that the
primaryrole of the ortho substituent is to maintain an
appropriate orientation of the phenyl substituent.
56
57
58
59
60
61
Cl COOMe
Cl
Cl
Me
Cl
Cl
Cl
9
73
210
220
220
250
1230
Cl
Cl
COMe
H
16
19
23
25
80
Cl COONH2
Cl
H
F
Cl CONH–
(CH2)2ꢀ
NME2
62
63
64
Cl
Cl
H
COOH
H
H
Cl
H
H
96
69
600
530
530
26%@10,000
Substituents with active proton at the ortho position, such
as 50, 51, 52, 53, 54, were not tolerated. Bulkygroup,
such as 55, will also dramaticallyreduce the activity.

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L. Liu et al. / Bioorg. Med. Chem. Lett. 13 (2003) 3979–3982
pocket 1 and hydrophobic pocket 2 in p38 binding site
for 3,4-dihydropyrido[3,2-d]pyrimidones. In order to fit
hydrophobic pocket 2, the best aromatic groups in the
N-1 position should have 2,6-disubstituents with size
similar to chlorine, such as methyl. The para position in
those aromatic rings have bigger space and possibly
produce an additional hydrogen binding interaction
with Y35 of p38 to increase activity, such as 56 and 57.
As for the hydrophobic pocket 1, the optimized sub-
stituents in aromatic ring are also ortho chlorine or
methyl group. The space in para and meta positions are
verysmall, onlyfluorine and proton can fit in. Com-
pounds 9, 10, 56, 57, 58, 59 and 60 are the best com-
pounds in this analogues with p38a IC50 <30 nM. All
of those best compounds have optimized substituents in
the aromatic rings.
5. Badger, A. M.; Olivera, D.; Talmadge, J. E.; Hanna, N.
Circ. Shock 1989, 27, 51.
6. (a) Gallagher, T. F.; Seibel, G. L.; Kassis, S; Laydon, J. T.;
Blumenthal, M. J.; Lee, J. C.; Lee, D.; Boehm, J. C.; Fier-
Thompson, S. M.; Abt, J. W.; Sorenson, M. E.; Smietana,
J. M.; Hall, R. F.; Garigipati, R. S.; Bender, P. E.; Erhard,
K. F.; Krog, A. J.; Hofmann, G. A.; Sheldrake, P. L.;
McDonnell, P. C.; Kumar, S.; Young, P. R.; Adams, J. L.
Bioorg. Med. Chem. 1997, 5, 49. (b) Liverton, N. J.; Butcher,
J. W.; Claiborne, C. F.; Claremon, D. A.; Libby, B. E.;
Ngyuen, K. T.; Pitzenberger, S. M.; Selnick, H. G.; Smith,
G. R.; Tebben, A.; Vacca, J. P.; Varga, S. L.; Agarwal, L.;
Danheck, K.; Forsyth, A. J.; Fletcher, D. S.; Frantz, B.;
Hanlon, W. A.; Harper, C. F.; Hofsess, S. J.; Kostura, M.;
Lin, J.; Luell, S.; O’Neil, E. A.; Orevillo, C. J.; Pang, M.;
Parsons, J.; Rolondo, A.; Sahly, Y.; Visco, D. M.; O’Keefe,
S. J. J. Med. Chem. 1999, 42, 2180. (c) Collis, A. J.; Foster,
M. L.; Halley, F.; Maslen, C.; Mclay, I. M.; Page, M. P.;
Redford, E. J.; Souness, J. E.; Wilsher, N. E. Bioorg. Med.
Chem. 2001, 693.
7. (a) Bemis, G. W.; Salituro, F. G.; Duffy, J. P.; Harrington,
E. M. US Patent 2000, 6, 080. (b) Salituro, F.; Bemis, G.;
Cochran, J. Intl. Patent, 1999, WO 99/64400.
8. Natarajan, S. R.; Wisnoski, D. D.; Singh, S. B.; Stelmach,
J. E.; O’Neill, E. A.; Schwartz, C. D.; Thompson, C. M.;
Fitzgerald, C. E.; O’Keefe, S. J.; Kumar, S.; Hop, C. E. C. A.;
Zaller, D. M.; Schmatz, D. M.; Doherty, J. B. Bioorg. Med.
Chem. Lett. 2003, 13, 273.
References and Notes
1. Lee, J. C.; Laydon, J. T.; McDonnell, P. C.; Gallagher,
T. F.; Kumar, S.; Green, D.; McNulty, D.; Blumenthal, M. J.;
Heys, J. R.; Landvatter, S. W.; Stricker, J. E.; McLaughlin,
M. M.; Siemens, J. R.; Fisher, S. M.; Livi, G. P.; White, J. R.;
Adams, J. L.; Young, P. R. Nature 1994, 372, 739.
2. Han, J.; Lee, J. D.; Bibbs, L.; Ulevitch, R. J. Science 1994,
265, 808.
3. (a) Badger, A. M.; Griswold, D. E.; Kapadia, R.; Blake, S.;
Swift, B. A.; Hoffman, S. J.; Stroup, G. B.; Webb, E.; Reie-
man, D. J.; Gowen, M.; Boehm, J. C.; Adams, J. L.; Lee, J. C.
Arthritis Rheum. 2000, 43, 175. (b) Griego, S. D.; Weston,
C. B.; Adams, J. L.; Tal-Singer, R.; Dillon, S. B. J. Immunol.
2000, 165, 5211. (c) Fullerton, T.; Sharma, A.; Prabhakar, U.;
Tucci, M.; Boike, S.; Davis, H.; Jorkasky, D.; Williams, W.
Clin. Pharmacol. Ther. 2000, 67, 114.
9. Stelmach, J. E.; Liu, L.; Patel, S. B.; Pivnichny, J. E.; Sca-
pin, G.; Singh, S.; Hop, C. E. C. A.; Wang, Z.; Strauss, J. R.;
Cameron, P. M.; Nichols, E. A.; O’Keefe, S. J.; O’Neill, E. A.;
Scmatz, D. M.; Schwartz, C. D.; Thompson, C. M.; Zaller,
D. M.; Doherty, J. B. Med. Chem. Lett. 2003, 13, 277.
10. Wang, Z. L.; Canagarajah, B. J.; Boehm, J. C.; Kassis, S.;
Cobb, M. H.; Young, P. R.; Abdel-Meguid, S.; Adams, J. L.;
Goldsmith, E. J. Structure 1998, 6, 1117.
4. (a) Badger, A. M.; Bradbeer, J. N.; Votta, B.; Lee, J. C.;
Adams, J. L.; Griswold, D. E. J. Pharmacol. Exp. Ther. 1996,
279, 1453. (b) Adams, J. L.; Boehm, J. C.; Gallagher, T. F.;
Kassis, S.; Webb, E. F.; Hall, R.; Sorenson, M.; Garigipati,
R.; Griswold, D. E.; Lee, J. C. Bioorg. Med. Chem. Lett. 2001,
11, 2867.
11. (a) Wilson, K. P.; McCaffrey, P. G.; Hsiao, K.; Pazhani-
samy, P.; Galullo, V.; Bemis, G. W.; Fitzgibbon, M. J.; Caron,
P. R.; Murcko, M. A.; Su, M. S. S. Chem. Biol. 1997, 4, 423.
(b) Gum, R. J.; McLaughlin, M. M.; Kumar, S.; Wang, Z. L.;
Bower, M. J.; Lee, J. C.; Adams, J. L.; Livi, G. P.; Goldsmith,
E. J.; Young, P. R. J. Biol. Chem. 1998, 272, 15605.