Synthesis of 5-substituted benzyl-2,4-diamino pyrimidine derivatives as c-Fms kinase inhibitors

Article abstract of DOI:10.1016/j.cclet.2010.06.023

A serials of novel 5-substituted benzyl-2,4-diamino pyrimidine derivatives have been synthesized and evaluated as inhibitors of c-Fms kinase by the standard MTT method. The results showed that compound 15,5-[3-methoxy-4-(pyridine-3-yl)benzyl]-2,4-diamino pyrimidine, had an IC₅₀ of 1.45μmol/L in inhibiting the proliferation of M-CSF-dependent myeloid leukemia cells in mice (NFS-60), which was similar with GW2580, a selective inhibitor of c-Fms kinase.

Full text of DOI:10.1016/j.cclet.2010.06.023

Available online at www.sciencedirect.com
Chinese Chemical Letters 21 (2010) 1318–1321
www.elsevier.com/locate/cclet
Synthesis of 5-substituted benzyl-2,4-diamino pyrimidine
derivatives as c-Fms kinase inhibitors
Li Bao Xu a, Wei Sun a, Hong Ying Liu b, Li Li Wang b, Jun Hai Xiao b,
*
,
b
Xiao Hong Yang a, , Song Li
*
a School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China
b Laboratory of Computer-Aided Drug Design & Discovery, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
Received 23 March 2010
Abstract
A serials of novel 5-substituted benzyl-2,4-diamino pyrimidine derivatives have been synthesized and evaluated as inhibitors of
c-Fms kinase by the standard MTT method. The results showed that compound 15,5-[3-methoxy-4-(pyridine-3-yl)benzyl]-2,4-
diamino pyrimidine, had an IC50 of 1.45 mmol/L in inhibiting the proliferation of M-CSF-dependent myeloid leukemia cells in mice
(NFS-60), which was similar with GW2580, a selective inhibitor of c-Fms kinase.
# 2010 Jun Hai Xiao. Published by Elsevier B.V. on behalf of Chinese Chemical Society. All rights reserved.
Keywords: C-Fms kinase inhibitors; Synthesis; 2,4-Diamino pyrimidine
The macrophage colony-stimulating factor-1 receptor (c-Fms, also known as M-CSFR, CSF-1R, or Fms) is
encoded by the c-fms proto-oncogene and is the exclusive receptor for its ligand, colony-stimulating factor-1 (CSF-1
or macrophage colony-stimulating factor, M-CSF), which regulates proliferation, differentiation and survival of cells
of the mononuclear phagocyte lineage [1,2]. Recent studies have demonstrated a direct correlation between tumor-
associated macrophage numbers and tumor progression [3,4] and between synovial macrophage numbers and disease
severity in rheumatoid arthritis [5]. Hence the inhibition of c-Fms appears to be of therapeutic value in treating
diseases such as rheumatoid arthritis as well as certain cancers where macrophages are pathogenic. This hypothesis is
also well-supported by the biological studies conducted with CSF-1 deficient mice [6,7].
A recent publication described the identification of 5-substituted benzyl-2,4-diamino pyrimidine compound
GW2580 as c-Fms kinase specific inhibitors. GW2580 can completely inhibit human c-Fms kinase in vitro, whereas it
was inactive against 26 other kinases. It is a useful probe for the elucidation of the regulation mechanism of c-Fms
kinase in normal and pathological processes [8]. But the structure-activity relationships (SAR) of this chemotype have
not been reported. Herein we designed a serial compounds based on the structure of GW2580, the analysis of c-Fms
kinase binding site and the rule of bioisosterism. The generic structures of designed compounds are in Scheme 1 as
compound 5. The aromatic ring A of compound 5 was retained for keeping the hydrogen bonds between the ligand and
the binding site. The aromatic ring B was substituted by methoxyl group and bromine in different positions to
investigate the SAR of ring B. The aromatic ring C has hydrophobic interaction with the receptor, so the methyl group
* Corresponding authors.
E-mail addresses: xiaojh@nic.bmi.ac.cn (J.H. Xiao), xiaohongyang88@126.com (X.H. Yang).
1001-8417/$ – see front matter # 2010 Jun Hai Xiao. Published by Elsevier B.V. on behalf of Chinese Chemical Society. All rights reserved.
doi:10.1016/j.cclet.2010.06.023

[(Scheme_1)TD$FIG]
L.B. Xu et al. / Chinese Chemical Letters 21 (2010) 1318–1321
1319
Scheme 1. Reagents and conditions: (a) K2CO3, KI, DMF, 90 8C, 82%; (b) 3-morpholinopropionitrile, NaOCH3, DMSO, 75 8C; (c) aniline
hydrochloride, isopropanol, reflux, 45–55%; (d) guanidine hydrochloride, NaOCH3, ethanol, reflux, 90%.
was introduced to replace methoxyl group to enhance the hydrophobic effect. Heteroaromatic rings were also
introduced to increase the structural diversity of ring C. Thus two categories of compounds, 5-substituted benzyl-2,4-
diaminepyrimidine and 5-substituted benzyl-2-mercapto-4-aminopyrimidine were designed and synthesized. Their
1
structures were confirmed by H NMR and FAB-MS.
The general synthetic route of all designed compounds was illustrated in Scheme 1. Substituted benzaldehyde 3 was
synthesized by alkylation of the corresponding substituted hydroxybenzaldehyde 1 in the presence of K2CO3/KI in DMF
solution at 90 8C. Condensation of 3 with 3-morpholinopropionitrile in anhydrous DMSO containing a catalytic amount
of NaOCH3 led to a red oil, which on sequential refluxing with aniline hydrochloride in isopropanol solution afforded 3-
anilinoacrylonitrile 4. Condensation of 4 with guanidine hydrochloride in the presence of NaOCH3 in ethanol solution
afforded 5-substituted benzyl-2,4-diamino pyrimidine 5 [9].
Compounds 6–15 were synthesized according to the above method. The structure and analysis data of the
compounds shown in Table 1. Melting point was detected by YRT-3 Melting point apparatus made by Tianjing
Table 1
The structure of compounds 6–15.
ID
Structure
mp (8C)
Yield
(%)
FAB-MS
1H NMR (400 MHz, DMSO-d6, d, J Hz)
(m/z)
[TD$INLINE]
6
173.8–175.8
14.5
447.0a
3.56 (s, 2H), 3.76 (s, 3H), 3.83 (s, 3H), 4.84 (s, 2H),
5.74 (s, 2H), 6.15 (s, 2H), 6.92–6.94 (d, 2H, J = 8.7 Hz), 6.97
(d, J = 1.7 Hz, 1H), 7.01 (d, 1H, J = 1.7 Hz), 7.34–7.40
(d, 2H, J = 8.7 Hz), 7.57 (s,1H)
[TD$INLINE]
7
8
177.4–179.5
193 dec.
13.0
13.2
431.0a
417.0a
2.31 (s, 3H), 3.65 (s, 2H), 3.82 (s, 3H), 4.87 (s, 2H),
5.72 (s, 2H), 6.12 (s, 2H), 6.97 (d, 1H, J = 1.7 Hz),
7.00 (d, 1H, J = 1.7 Hz), 7.17–7.19 (d, J = 8.0 Hz, 1H),
7.35–7.37 (d, 2H, J = 8.0 Hz), 7.57(s, 1H)
[TD$INLINE]
3.53 (s, 2H), 3.75 (s, 3H), 5.07 (s, 2H), 5.74 (s, 2H),
6.12 (s, 2H), 6.94–6.96 (m, 2H), 7.11 (m, 2H),
7.37–7.45 (m, 3H), 7.53 (s, 1H)
[TD$INLINE]
9
177.9–179.6
187.6–189.3
14.5
13.7
399.0
2.30 (s, 3H), 3.53 (s, 2H), 5.11 (s, 2H), 5.73 (s, 2H),
6.11 (s, 2H), 7.09 (d, 2H, J = 8.4 Hz), 7.14–7.16 (dd 1H,
J1 = 8.4 Hz, J2 = 2.0 Hz), 7.33–7.35 (d, 2H, J = 8.4 Hz),
7.42–7.43 (d, 2H, J = 2.0 Hz), 7.53 (s, 1H)
10
418.0a
3.56 (s, 2H), 3.82 (s, 3H), 4.98 (s, 2H), 5.76 (s, 2H),
6.16 (s, 2H), 6.98 (d, 1H J = 1.7 Hz), 7.03 (d, 1H, J = 1.7Hz),
7.41–7.44 (dd, 1H, J1 = 7.8 Hz, J2 = 4.9 Hz), 7.58 (s, 1H),
7.88–7.90 (d, 2H, J = 7.8 Hz), 8.54 (dd, 1H, J1 = 4.9 Hz,
J2 = 1.7 Hz), 8.65 (d, 1H, J = 1.7 Hz)
[TD$INLINE]

1320
L.B. Xu et al. / Chinese Chemical Letters 21 (2010) 1318–1321
Table 1 (Continued )
ID
Structure
mp (8C)
Yield
(%)
FAB-MS
1H NMR (400 MHz, DMSO-d6, d, J Hz)
(m/z)
[TD$INLINE]
11
219.3–221.3
13.6
386.0
3.55 (s, 2H), 4.21 (s, 2H), 5.74 (s, 2H), 6.13 (s, 2H),
7.18 (m, 3H), 7.45 (m, 2H), 7.53 (s, 1H), 7.86–7.88 (m, 2H),
8.54 (dd, 1H, J1 = 4.8 Hz, J2 = 1.7 Hz), 8.68–8.68
(d, 1H, J = 1.7 Hz)
[TD$INLINE]
12
185.1–187.8
9.3
367.1b
3.52 (s, 2H), 3.71 (s, 3H), 3.76 (s, 3H), 4.93 (s, 2H), 6.14
(br s, 2H), 6.53 (br s, 2H), 6.73–6.76 (dd, 1H, J1 = 8.4 Hz,
J2 = 2.0 Hz), 6.86–6.88 (d, 1H, J = 8.4 Hz), 6.92–6.94
(d, 2H, J = 8.7 Hz), 6.97 (d, 1H, J = 2.0 Hz), 7.33–7.36
(d, 2H, J = 8.7 Hz), 7.45 (s, 1H)
[TD$INLINE]
13
14
172.8–174.8
184.5–186.5
11.5
9.6
351.1b
2.30 (s, 3H), 3.49 (s, 2H), 3.71 (s, 3H), 4.96 (s, 2H),
5.69 (s, 2H), 6.05 (s, 2H), 6.72–6.74 (dd, 1H, J1 = 8.1 Hz,
J2 = 1.7 Hz), 6.85–6.87 (d, 1H, J = 8.1 Hz), 6.95–6.96
(d, 1H, J = 1.7 Hz), 7.17–7.19 (d, 2H, J = 7.8 Hz),
7.30–7.32 (d, 2H, J = 7.8 Hz), 7.46 (s, 1H)
[TD$INLINE]
338.1b
3.51 (s, 2H), 3.72 (s, 3H), 5.07 (s, 2H), 5.69 (s, 2H),
6.05 (s, 2H), 6.76–6.78 (d, 1H, J = 8.0 Hz), 6.88–6.90
(d, 1H, J = 8.0 Hz), 6.994 (s, 1H), 7.40–7.45 (m, 2H),
7.47 (s, 1H), 7.84–7.86 (d, 1H, J = 7.8 Hz), 8.54–8.55
(d, 1H, J = 4.6 Hz), 8.650 (s, 1H)
[TD$INLINE]
15
181.0–183.0
12.6
338.1b
3.52 (s, 2H), 3.73 (s, 3H), 5.07 (s, 2H), 5.66 (br s, 2H),
6.03 (br s, 2H), 6.70 (dd, 1H, J1 = 8.1 Hz, J2 = 2.0 Hz),
6.89 (d, 1H, J = 2.0 Hz), 6.94–6.96 (d, 1H, J = 8.1 Hz),
7.40–7.43 (dd, 1H, J1 = 7.6 Hz, J2 = 4.8 Hz), 7.47 (s, 1H),
7.83–7.85 (d, 1H, J = 7.6 Hz), 8.52 (dd, 1H, J1 = 4.8 Hz,
J2 = 1.6 Hz), 8.63–8.64 (d, 1H, J = 1.6 Hz)
a
[M + 2]+
[M + 1]+
.
.
b
China. MS spectra were recorded on a Micromass Zabspec spectrophotometer. NMR spectra were recorded on a
JEOL JNM-ECA-400 (400 MHZ) spectrophotometer. The inhibitory c-Fms kinase activities of compounds were
evaluated by inhibiting M-CSF-dependent M-NFS-60 tumor cell proliferation effect [8]. The test cells also
included a normal cell (HLF). The 50% inhibitory concentration (IC50) mean values and selective index are
summarized in Table 2.
Table 2
Inhibition of cell proliferation effect by GW2580, compound 6–15.
Compound ID
HLFa
M-NFS-60a
SIb
11.48
6
32.96
2.87
3.68
6.56
16.56
2.57
1.13
3.29
5.20
5.49
1.45
0.69
7
15.64
14.06
9.24
4.25
2.14
8
9
10
0.56
40.19
35.17
172.33
58.91
176.70
15.64
31.12
52.38
11.33
32.17
206.70
228.98
11
12
13
14
15
GW2580
ꢀ300
158.00
a
The test concentration ranges were from 0.1 to 300 mmol/L. The given data are mean values of three parallel experiments.
SI is the mean of the ratio of IC50 of Inhibition of HLF and IC50 of Inhibition of M-NFS-60.
b

L.B. Xu et al. / Chinese Chemical Letters 21 (2010) 1318–1321
1321
As shown in Table 2, compound 15, 5-[3-methoxy-4-(pyridine-3-yl) benzyl]-2,4-diamino pyrimidine, had an IC50
of 1.45 mmol/L in inhibiting the proliferation of M-CSF-dependent myeloid leukemia cells in mice (NFS-60) and SI of
206.70, both are similar with GW2580. These results are of great significance for the design of news compounds with
higher activity and drug likeness. Further studies on the mechanism of action of these compounds are in progress.
Acknowledgments
This work was financially supported by the National High-Tech Research and Development Program of China (863
Program) (No. 2006AA10A201) and National Natural Science Foundation (No. 30472093).
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