Synthesis of Pyridopyrazine-1,6-dione γ-Secretase Modulators via Selective 4-Methylimidazole N1-Buchwald Arylation

Article abstract of DOI:10.1021/acs.joc.8b02953

An efficient synthesis of pyridopyrazine-1,6-dione γ-secretase modulators (GSMs) is described. Our route features the construction of a crystalline lactone intermediate via a selective palladium-catalyzed 4-methylimidazole N¹-arylation using the Buchwald Xantphos Pd G4 precatalyst, which does not require a preactivation step. The weak inorganic base KHCO₃ was employed to minimize saponification of a particularly sensitive lactone substrate. Additional key transformations include DABAL-Me₃-mediated lactone aminolysis and a mild TBD/ethyl trifluoroacetate mediated lactam ring closure to afford a representative GSM in high yield.

Full text of DOI:10.1021/acs.joc.8b02953

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Note
Synthesis of Pyridopyrazine-1,6-dione #-Secretase Modulators
via Selective 4-Methylimidazole N1- Buchwald Arylation
Longfei Xie, Christopher W. am Ende, Martin Pettersson, Danica
A Rankic, Neil Sach, Subas Sakya, and John M. Humphrey
J. Org. Chem., Just Accepted Manuscript • DOI: 10.1021/acs.joc.8b02953 • Publication Date (Web): 08 Jan 2019
Downloaded from http://pubs.acs.org on January 10, 2019
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Synthesis of Pyridopyrazine-1,6-dione γ-Secretase
Modulators via Selective 4-Methylimidazole N1-
Buchwald Arylation
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Longfei Xie, a Christopher W. am Ende, a Martin Pettersson,b Danica A. Rankic, a Neal Sach,c Subbas
Sakya,a John M. Humphreya*
aPfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, USA
bPfizer Worldwide Research and Development, 1 Portland Street, Cambridge, Massachusetts 02139,
USA
cPfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, CA, 92121,
USA.
TOC Graphic: for Table of Contents use only
NH
O
O
Xantphos Pd G4
N
toluene/dioxane
O
O
N
N
KHCO3
N
Br
O
4 Å mol seives
O
N
71%
sole regiomer
ABSTRACT
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An efficient synthesis of pyridopyrazine-1,6-dione -secretase modulators (GSMs) is described.
Our route features the construction of a crystalline lactone intermediate via a selective palladium-
catalyzed 4-methylimidazole N1- arylation using the Buchwald Xantphos Pd G4 precatalyst, which does
not require a pre-activation step. The weak inorganic base KHCO3 was employed to minimize
saponification of a particularly sensitive lactone substrate. Additional key transformations include
DABAL-Me3-mediated lactone aminolysis and a mild TBD/ethyl trifluoroacetate mediated lactam ring
closure to afford a representative GSM in high yield.
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Alzheimer’s disease (AD) is a fatal debilitative neurodegenerative disorder that is characterized
by progressive cognitive impairment and a loss of motor function.1 AD represents a significant unmet
medical need given the lack of therapeutic agents that can halt or slow progression of the disease. A
possible cause of AD is the aberrant accumulation of neurotoxic amyloid 42 (A42) peptides that
aggregate to form amyloid plaques. These A peptides are formed via sequential processing of the
amyloid precursor protein (APP) by the aspartyl protease enzymes β-secretase and γ-secretase.2 As a
result, suppression of amyloid plaque formation through inhibition or modulation of these enzymes is an
area of considerable interest in the search for effective AD therapies.
A promising therapeutic strategy for the treatment of AD involves modulation of γ-secretase
activity through the application of small molecule γ-secretase modulators (GSMs).3 Compounds of this
class do not inhibit γ-secretase but rather shift the cleavage site of APP to reduce formation of
neurotoxic Aβ42 peptide in favor of shorter, more benign species. Maintenance of γ-secretase activity
vs. total enzyme inhibition is critical to avoid serious side effects resulting from inhibition of Notch
signaling.4 Several classes of GSMs have emerged, with most being loosely derived from an A, B, C, D-
type ring framework as exemplified by compounds 1-4 (Figure 1).5 A key structural facet of these
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compounds is the presence of a 5-methyl-3-imidazolyl motif (ring A, structure 1), which plays a critical
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role in GSM activity.
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8
9
Figure 1. Representative heteroaryl GSMs.
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O
D
HN
N
N
C
S
N
F
N
B
F
O
N
N
A
2)
E2012 (
Eisai
1
NGP-555 ( )
Neurogenetics
CF3
CF3
O
N
N
N
N
N
O
N
N
H
N
N
O
N
O
3
E2212 ( )
Eisai
4
Pfizer ( )
We have recently reported on the discovery of compound 4 and related chromene derivatives,
that are structurally defined, in part, by a pyridopyrazine-1,6-dione bicyclic core that was critical for the
alignment of potency with metabolic stability and CNS exposure.6 The GSM 4 afforded robust reduction
of brain A42 when dosed orally in rat at 10 and 40 mg kg-1, thus establishing the series as a promising
direction for our research. As other members of this series progressed through preclinical studies, we
sought to streamline the synthetic route to support anticipated bulk demands.
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Our initial synthesis of the pyridopyrazine-1,6-dione GSMs featured a novel HATU-mediated
coupling/cyclization reaction to form the desired compounds (5) from the pyridone carboxylic acid (6)
and various substituted amino alcohols (7) (Figure 2A).7 This approach enabled early evaluation of
structure-activity relationships and provided material to support preclinical in vivo studies. However, the
synthesis had a number of drawbacks including the requirement for >2 equivalents of the high-energy
coupling reagent HATU (1-[Bis(dimethylamino)methylene]-1H-1,2,3-triazolo[4,5-b]pyridinium 3-oxide
hexafluorophosphate),8 low yields (20-30%) with sterically hindered amines,7a and challenging product
isolation. Furthermore, the poor solubility and amorphous nature of the solid pyridone carboxylic acid 6
made isolation, purification, and employment of this intermediate cumbersome. Each of these issues
were effectively addressed by preparation of the highly crystalline lactone intermediate 8 (Figure 2B),
and development of a facile amidation / lactamization sequence that was amenable to the incorporation
of hindered amines.9 One notable challenge in each of these approaches centered on differentiation
between the two nitrogen atoms (N1/N3) of the asymmetrical 4-methylimidazole substituent.
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Figure 2. Original and revised lactam strategies
R
CO2H
HN
(2A) Original Approach: 1-Pot
HATU-mediated
coupling/cyclization.
NH
HCl
N
+
N
7
OH
O
6
O
amorphous, poor
organic solubility
R
N
N
N
N
O
O
O
5
R
H2N
+
N
N
N
9
(2B) Revised Approach:
Amidation followed by alcohol
activation and cyclization.
O
8
crystalline, moderate
organic solubility
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Our first route to the key lactone 8 is illustrated in Scheme 1 and has been reported.10 The simple
structure of the starting 3-aminopyridine (10) vs. the relatively complex product 8 necessitated a number
of functionalization steps. Imidazole N1/N3 differentiation was achieved through stepwise construction
of the imidazole by elaboration of the pyridyl 3-amino group, which further added to the length of the
sequence.
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Scheme 1. Original route to pyridone carboxylic acid 6 and lactone 8.
Br
Br
Br
Ac2O
NBS
Na
N
N
N
N
H2N
H2N
H2N
HN
HCOOH
MeOH, dioxane
DMSO H2O
Br
11
O
O
O
12
13
10
O
CO2Me
Br
Br
O
Pd(dppf)Cl2, DCM
TEA, CO, MeOH
Cl
NH4OAc
AcOH
N
N
O
N
N
N
N
O
N
N
KI,Cs2CO3,DMF
O
O
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14
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O
O
CO2H
NH
Br
Br
HCl, dioxane
150 °C, quant
N
N
N
Cs2CO3, DMF
90 o
N
N
.
HCl
O
O
C
6
8
For a more direct path we chose the commercial pyridone carboxylic acid 17 as an ideally
functionalized feedstock for conversion into 8 through a bromination/N1-arylation strategy (Scheme 2).
This tactic would require exquisite regioselectivity in the N1-arylation reaction to avoid trace isomeric
contaminants in the final active substance – a problem that plagued us previously in a related system.11
As detailed in a report by Buchwald et al., high selectivity is not generally achievable through SNAr or
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Ullmann-type arylation but can be obtained through a pre-activated Me4tBuXPhos palladium catalyst
system. According to Buchwald et al., steric hindrance induced by the imidazole methyl substituent
within the palladium complex strongly favors reaction intermediates leading to the desired N1-arylation
product.12
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The pyridone acid 17 can be brominated regioselectively, but the product of the reaction is an
intractable amorphous solid with poor organic solubility. In a more scalable process, initial bis-
alkylation with 1,2-dibromoethane gave the crystalline lactone 18,13 and subsequent bromination
afforded the crystalline aryl bromide 19 in two steps without chromatography (Scheme 2). Isomeric
bromine derivatives were not observed. Application of the Buchwald procedure,12 employing
Me4tBuXPhos palladium and potassium phosphate in toluene-dioxane, afforded complete imidazole N1-
arylation selectivity for the conversion of the bromide 19 into the target lactone 8 in 76% crystallized
yield. Consistent with the Buchwald report, this transformation was best achieved through a 120 °C pre-
activation of the catalyst and ligand prior to imidazole introduction.
Subsequent to this result, our internal reaction screening and optimization efforts (See
Supporting Information) revealed that commercially available Xantphos Pd G4 precatalyst gave the
target lactone in comparable yield (71%). Employment of the G4 precatalyst system is operationally
simpler with no need for preactivation vs. the reported method.12 In subsequent optimization work with
the G4 precatalyst system, we found that KHCO3 provided superior results to other bases (e.g. K2CO3,
K3PO4) in minimizing saponification of the lactone 8 to the corresponding hydroxy-acid. Molecular
sieves were essential in maintaining an anhydrous environment to further minimize hydrolysis of this
particularly susceptible lactone.
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Scheme 2. Improved route to the key lactone template 8.
5
6
7
8
9
O
O
Br
Br
OH
O
NH
N
Cs2CO3
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O
DMSO, 85 °C
85%
O
17
18
O
NH
N
Xantphos Pd G4
Br2/MeOH
91%
O
N
toluene/dioxane
8
Br
KHCO3
O
4 Å mol seives
19
71%
Conversion of the lactone 8 into the representative GSM 22 was accomplished via lactone
amidation with the requisite amine 20, followed by activation of the resultant primary alcohol
intermediate 21, and base catalyzed intramolecular SN2 cyclization (Scheme 3). The amidation could be
accomplished via direct amine addition in a polar solvent such as methanol or DMF, but this
transformation required a large excess of the amine component to drive the reaction beyond ~60%
conversion. To incorporate the complex, precious amines present in our most advanced GSMs, we
turned instead to the air-stable Lewis acid DABAL-Me3 (bis(trimethylaluminum)-1,4-
diazabicyclo[2.2.2]octane adduct),14 which provided yields in excess of 90% utilizing only
stoichiometric amine.
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Scheme 3. DABAL-Me3 amidation and TBD/ethyl trifluoroacetate cyclization sequence.
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CF3
CF3
O
9
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8
N
H
N
H2N
O
N
N
DABAL-Me3
93%
O
O
OH
21
20
CF3
TBD
O
CF3CO2Et
N
N
N
H
N
THF, 93%
(or DMF)
N
O
N
N
TBD
O
22
The intermediate 21 afforded us with numerous opportunities for activation and SN2 ring closure,
some of which we have reported previously.6, 9, 13 In order to achieve improved and more consistent
yields we initiated a base / solvent screen on a related chloride intermediate utilizing the 3-aminopentane
derived amide as a relatively hindered amide nucleophile (see Supporting Information). In this study,
the strong organic bases TBD (1,5,7-Triazabicyclo[4.4.0]dec-5-ene) and BEMP (2-tert-Butylimino-2-
diethylamino-1,3-dimethylperhydro-1,3,2-diazaphosphorine) provided superior results vs. both
inorganic and weaker tertiary amine bases, and DMF provided faster reaction rates over THF. We also
examined a variety of activation methods including Mitsunobu, sulfonate, and trifluoroacetic anhydride
activations. Each of these methods suffered from drawbacks ranging from by-product generation,
imidate formation, elimination reaction, and the need for careful attention to stoichiometry during the
activation step. We ultimately developed a remarkably mild in situ activation system comprised of ethyl
trifluoroacetate and TBD,13 the latter of which provided superior results to DBU with respect to rate of
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reaction and purity profile. The reaction catalyzed by TBD could be conducted in THF or DMF, with the
latter solvent providing significantly faster reactions. For the specific case of intermediate 21, treatment
with 5 equivalents of ethyl trifluoroacetate and 2.2 equivalents of TBD in THF provided complete
conversion to the target 22 within 4 h at room temperature in 93% crystallized yield after aqueous
workup. The moderate excess of ethyl trifluoroacetate conveniently acted as a water scavenger such that
strictly anhydrous conditions were unnecessary.
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In conclusion, we have demonstrated a succinct synthetic route to the pyridone-1,6-dione class of
GSMs, represented by the chromene derivative 22. The method features a selective N1-imidazole
arylation with the commercially available Xantphos Pd G4 Buchwald precatalyst performed on the key
crystalline lactone intermediate 8. Catalyst pre-activation is not necessary for this system, which
presents an ease-of-use advantage over the literature method. We have optimized conditions for the
mild, room temperature conversion of this lactone into target - secretase modulators via DABAL-Me3
mediated amidation and subsequent base catalyzed ring closure with TBD and ethyl trifluoroacetate. All
products depicted in Schemes 2 and 3 were isolated as crystalline solids without chromatography, which
facilitated work on multi-gram quantities.
EXPERIMENTAL SECTION
Reagents and starting materials were obtained from commercial sources and used without
purification unless otherwise indicated. The Xantphos Pd G4 precatalyst was obtained from Sigma-
Aldrich. Potassium bicarbonate was dried under vacuum overnight at 130 °C. All products were isolated
and purified as crystalline solids. Silica gel chromatography, used in one instance to assess the amount
of product 8 remaining in the mother liquor after crystallization, was performed via through a glass
1
13
column hand-packed with JT Baker 40 µM flash silica gel. H and C NMR spectra are presented as
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chemical shifts (ppm) relative to the solvent with multiplicities reported as s (singlet), bs (broad singlet),
d (doublet), t (triplet), q (quartet), m (multiplet), comp (complicated pattern of overlapping resonances),
app (apparent), and obsc (obscured peaks). Fluorine NMR spectral data are presented as chemical shifts
relative to trifluoroacetic acid (-75.4 ppm). Products were shown to be >97% by 1H NMR analysis and
by HPLC (Waters Acuity instrumentation, CSH C18 1.7 µM 2.1 x 50 mm column, mobile phase A: 99.9
acetonitrile/ 0.1 formic acid; mobile phase B: 99.9 water/0.1 formic acid. Elutions were effective via a
1.5 min gradient beginning at 5:95 A/B and ending with 100% B) with compound identified by UV =
215 nM and ESI positive ion mass spectrometry.
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7-bromo-3,4-dihydropyrido[2,1-c][1,4]oxazine-1,6-dione (19).
A round bottom flask
equipped with an over-sized stir bar was charged with 3,4-dihydropyrido[2,1-c][1,4]oxazine-1,6-dione
(18) (2.00 g, 14.4 mmol)13 and the solid was dissolved by the addition of hot methanol (30 mL). The
solution was allowed to cool slightly. Prior to commencement of starting material precipitation, bromine
1
(4.22 g, 26.4 mmol) was added rapidly dropwise (exothermic). Analysis by H NMR indicated that the
reaction was complete within 45 min. Near the end of the addition, a thick flocculent precipitate formed.
The amorphous solid was stirred vigorously overnight to afford a granular slurry. The slurry was cooled
in an ice bath for 30 min, and the precipitate was collected via filtration and rinsed with ether to afford
2.57 g (87%) of the title compound as a white powder. The mother liquor was concentrated and
partitioned between 1 M sodium thiosulfate (1x) and ethyl acetate (3x). The organic portion was washed
with brine, dried over MgSO4, and concentrated to afford an additional 96 mg for a combined yield of
2.67 g (91%). Mp 200.9-204.4 °C (dec); IR (thin film) 1727, 1244, 1051, 742 cm-1; 1H NMR (400 MHz,
DMSO-d6)  8.11 (d, J = 7.8 Hz, 1H), 7.00 (d, J = 7.4 Hz, 1H), 4.66 (t, J = 5.7 Hz, 2H), 4.22 (t, J = 5.7
Hz, 2H); 13C{1H} NMR (100 MHz, DMSO-d6) 158.8, 155.9, 140.6, 132.8, 121.2, 110.7, 65.6, 40.1); MS
m/z (ion) 244 (M + 1); HRMS (ESI-TOF) m/z: [M + H]+ calcd for C8H6BrNO3, 243.9604; found,
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243.9603; Analysis calcd. for C8H6BrNO3: C, 39.37; H, 2.48; N, 5.74; Found: C, 39.38; H, 2.33; N,
5.65.
6
7
8
9
7-(4-methyl-1H-imidazol-1-yl)-3,4-dihydropyrido[2,1-c][1,4]oxazine-1,6-dione (8). To 7-
bromo-3,4-dihydropyrido[2,1-c][1,4]oxazine-1,6-dione (19) (5.00 g, 20.5 mmol), 4-methylimidazole
(3.36 g, 41.0 mmol) potassium bicarbonate (4.10 g, 41.0 mmol) and activated 4 Å molecular sieves (40
g) in toluene (100 mL) and dioxane (33 mL) under a nitrogen atmosphere was added Xantphos Pd G4
precatalyst (304 mg, 0.31 mmol). The mixture was heated at reflux for 16 h, at which point it was cooled
to rt and filtered through a silica gel pad, rinsing with 1:9 MeOH/CH2Cl2 (200 mL). The solvent was
removed under vacuum and the residue was partitioned between EtOAc (50 mL) and 1 N HCl (100 mL).
The organic layer was extracted with water (1 x 10 mL). The combined aqueous material was basified
with saturated NaHCO3 and extracted with CH2Cl2 (3 x 50 mL). The combined extracts were dried over
anhydrous Na2SO4 and concentrated to afford 3.69 g of the title compound as a yellow solid. The
material was recrystallized from a solution of methyl tert-butyl ether (50 mL) and CH2Cl2 (30 mL) to
afford 3.51 g (70%) of the title compound as a pale yellow solid. Silica gel chromatography of the
mother liquor, eluting with a 0 – 10% gradient of methanol in CH2Cl2, afforded an additional 46 mg for
a combined yield of 3.56 g (71%). Spectral and physical data for this compound are consistent with that
previously reported.9
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N-((2,2-dimethyl-6-(trifluoromethyl)-2H-chromen-4-yl)methyl)-1-(2-hydroxyethyl)-5-(4-
methyl-1H-imidazol-1-yl)-6-oxo-1,6-dihydropyridine-2-carboxamide (21). To 7-(4-methyl-1H-
imidazol-1-yl)-3,4-dihydropyrido[2,1-c][1,4]oxazine-1,6-dione (8) (2.65 g, 10.8 mmol) and (2,2-
dimethyl-6-(trifluoromethyl)-2H-chromen-4-yl)methanamine (20) (2.25 g, 8.73 mmol), in THF (20 mL)
at rt was added DABAL-Me3 (2.68 g, 10.5 mmol). The mixture was stirred at rt for 18 h, and was then
cooled in an ice bath and quenched via the dropwise addition of water (10 mL) followed by 5 N NaOH
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(10 mL). The mixture was partitioned between 1 N NaOH (1 x 300 mL) and EtOAc (2 x 300 mL). The
combined organic extracts were washed with brine, dried over MgSO4, and concentrated to a thick
slurry. The slurry was stirred overnight, and then cooled for 20 min in an ice bath. The solids were
collected via filtration and rinsed with ethyl ether to afford 4.07 g (93%) the title compound as a white
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powder: mp 200.8 - 201.4 C; IR (thin film) 3224 (br), 2980, 2923, 1644, 1280 cm-1; H NMR (400
MHz, DMSO-d6)  9.26 (t, J = 5.6 Hz, 1H), 8.15 (s, 1 H), 7.70 (d, J = 7.4 Hz, 1H), 7.58 (s, 1H), 7.51 (d,
J = 8.6 Hz, 1H), 7.34 (s, 1H), 6.97 (d, J = 8.2 Hz, 1H), 6.41 (d, J = 7.8 Hz, 1H), 5.93 (s, 1H), 4.90 (t, J =
5.1 Hz, 1H), 4.27 (comp, 6.2 Hz, 4H), 3.60 (q, 2 H), 2.14 (s, 3H), 1.41 (s, 6 H); C{1H} NMR (100
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MHz, DMSO-d6)  163.0, 156.9, 155.6 (app d, JCF = 1.5 Hz), 142.0, 136.9, 136.3, 129.3, 128.5, 127.6,
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126.5, 126.4 (q, JCF = 3.7 Hz), 124.5 (q, JCF = 270.7 Hz), 121.4 (q, JCF = 32.3 Hz), 120.7, 120.2 (q,
3JCF = 3.7 Hz), 116.8, 115.2, 105.4, 77.2, 58.2, 47.6, 39.3, 27.7, 13.5; F NMR (376 MHz, CDCl3) 
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61.3 (s). HRMS (ESI-TOF) m/z: [M + H]+ calcd for C25H25F3N4O4, 503.1901; found, 503.1892.
2-((2,2-dimethyl-6-(trifluoromethyl)-2H-chromen-4-yl)methyl)-7-(4-methyl-1H-imidazol-1-
yl)-3,4-dihydro-2H-pyrido[1,2-a]pyrazine-1,6-dione (22). To a slurry of N-((2,2-dimethyl-6-
(trifluoromethyl)-2H-chromen-4-yl)methyl)-1-(2-hydroxyethyl)-5-(4-methyl-1H-imidazol-1-yl)-6-oxo-
1,6-dihydropyridine-2-carboxamide (21) (1.66 g, 2.30 mmol) in THF (13 mL) was added ethyl
trifluoroacetate (2.34 g, 16.5 mmol) followed by 1,5,7-triazabicyclo[4.4.0]dec-5-ene (TBD) (964 mg,
6.92 mmol). The white slurry turned yellow and dissolved within a few minutes. After 4.5 h, the solution
was diluted with water and extracted twice with ethyl acetate. The combined extracts were washed with
brine, dried over MgSO4, and concentrated. The residue was recrystallized from EtOAc/heptane with
cooling in an ice bath for 1 h to afford 1.48 g (93%) of the title compound. Mp 198.0-198.5 °C (Lit.
196.5-197.0 °C6); 19F NMR (76 MHz, CDCl3)  61.6 (s). Other spectral and physical data for this
compound are consistent with that previously reported.6
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Supporting Information: Experimental procedures for Buchwald reaction conditions screening;
solvent and base screening methods for optimization of the SN2 cyclization;
1H, 13C, and 19F NMR spectra.
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