Photochemical In-Flow Synthesis of 2,4-Methanopyrrolidines: Pyrrolidine Analogues with Improved Water Solubility and Reduced Lipophilicity

Article abstract of DOI:10.1021/acs.joc.8b02071

A practical synthesis of 2,4-methanopyrrolidines was elaborated. The key synthetic step was an intramolecular photochemical [2 + 2]-cycloaddition of an acrylic acid derivative in flow. In spite of a higher molecular weight, 2,4-methanopyrrolidines were shown to have higher solubility in water and lower lipophilicity than pyrrolidines, important characteristics of bioactive molecules in drug design.

Full text of DOI:10.1021/acs.joc.8b02071

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Article
Photochemical in flow synthesis of 2,4-methanopyrrolidines: pyrrolidine
analogues with improved water solubility and reduced lipophilicity
Vadym V. Levterov, Oleg Michurin, Petro O. Borysko, Sergey Zozulya,
Iryna V. Sadkova, Andrey A. Tolmachev, and Pavel K. Mykhailiuk
J. Org. Chem., Just Accepted Manuscript • DOI: 10.1021/acs.joc.8b02071 • Publication Date (Web): 25 Oct 2018
Downloaded from http://pubs.acs.org on October 27, 2018
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The Journal of Organic Chemistry
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Photochemical in flow synthesis of 2,4-methanopyrrolidines:
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pyrrolidine analogues with improved water solubility
reduced lipophilicity
and
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Vadym V. Levterov,† Oleg Michurin,† Petro O. Borysko,†† Sergey Zozulya,†† Iryna V. Sadkova,†
Andrey A. Tolmachev,†‡ and Pavel K. Mykhailiuk†‡*
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† Enamine Ltd., Chervonotkatska 78, Kyiv 02094 (Ukraine), www.enamine.net,
†† Bienta, Chervonotkatska 78, Kyiv 02094 (Ukraine), www.bienta.net,
‡
Department of Chemistry, Taras Shevchenko National University of Kyiv, Volodymyrska 64, Kyiv 01601, Ukraine
www.mykhailiukchem.org
Solub.
logP
366 nm
R
R
in flow
PhCOMe
[2+2]
N
N
N
CO2Me
H
H
Bz
Rigid Pyrrolidines
Pyrrolidines
ABSTRACT: A practical synthesis of 2,4-methanopyrrolidines was elaborated. The key synthetic step was an intramolecular
photochemical [2+2]-cycloaddition of an acrylic acid derivative in flow. In spite of higher molecular weight
a
2,4-methanopyrrolidines were shown to have higher solubility in water, and lower lipophilicity (logD) than pyrrolidines, -
important characteristics of bioactive molecules in drug design.
INTRODUCTION
Recent trends in drug discovery - Escape from Flatland1 and Conformational restriction2 - significantly changed the structural
requirements to bioactive compounds. In particular, medicinal chemists have been using now small saturated building blocks, rather than
the bulky aromatic compounds.3,4,5 On the other hand, at the early stages of drug discovery, scientists still pay much attention to
lipophilicity and water solubility of bioactive compounds.6 Tricks to fine-tune these characteristics during a hit-to-lead optimization
become therefore important.7 In particular, great progress in the area of bioisosteric replacements was achieved already.8,9
Pyrrolidine is among the most commonly used secondary amines in medicinal chemistry.10 Moreover, its motif appears in more
than 100 FDA-approved drugs.11 Indeed, development of novel bioisosteres for pyrrolidine with the known physico-chemical
characteristics is of interest to medicinal chemists. In this context, herein we report on the in flow photochemical synthesis of
conformationally rigid pyrrolidine analogues – 2,4-methanopyrrolidines. We also demonstrate here experimentally, that in spite of a
slightly higher molecular weight of 12 daltons compared to pyrrolidines, 2,4-methanopyrrolidines have higher solubility in water, and
lower lipophilicity (logD) - important characteristics of bioactive molecules in drug design.
In 1980, 2,4-methanopyrrolidine was isolated from the seeds of Ateleia Herbert smithii Pittier, a tree commonly growing on the
coast of Costa-Rica.12,13 Due to a stabilization of the N-trans amide bond,14 scientists used this conformationally restricted analogue of
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L-Proline in the preparation of peptidomimetics.15 Following these studies, diverse pharmaceutical companies employed
2,4-methanopyrrolidines as conformationally restricted surrogates of pyrrolidines (Figure 1). Moreover, in 2016, Siu and Huestis based on
calculations, suggested that 2,4-methanopyrrolidines might be slightly less lipophilic than pyrrolidines.16 The authors, however, did not
validate this hypothesis experimentally.
1
2
3
4
5
6
7
In spite of a high potential, 2,4-methanopyrrolidines are still rare today in drug discovery programs – only 117 hits in the
ChEMBL database (Figure 1).17 Presumably, this is due to a lack of practical approaches to them.
8
9
a)
Common
128623 hits (ChEMBL)
105 drugs (FDA)
Innovative
monocyclic
bicyclic
only 117 hits
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(ChEMBL)
conformational
restriction
R
R
N
N
21th century
b)
Ph
N
N
N
N
O
HN
N
N
N
N
CF3
N
Cl
N
N
O
O
NH
CF3
N
Antischizophrenia agent
Genenteck
Antibacterial agent
Sanofi
US2012/71536
DLK inhibitor
Hoffmann-La Roche
US2014/328805
WO2016/142310
O
O
NH2
N
NHR
N
N
N
O
HN
O
OH
PARP inhibitor
HIV inhibitor
Gilead Sciences
WO2015/6733
Lead Therapeutics
US2009/62268
Figure 1. a) Pyrrolidines and 2,4-methanopyrrolidines in drug discovery; b) Bioactive derivatives of 2,4-methanopyrrolidine.
Three different approaches to 2,4-methanopyrrolidines were described in the literature. In 1980, Pirrung18 and Clardy19
independently cyclized diene 1 into the bicyclic amine 2 (Scheme 1a). The key step was an intramolecular photochemical [2+2]-
cyclization.20 In 2003, Malpass repeated the synthesis of amino acid 3, and prepared conformationally restricted nicotinic acetylcholine
ligands.21 In 2010, Varnes and colleagues from AstraZeneca also used this strategy to obtain 20 g of amino acid 3.22 Subsequently, the
photochemical approach was acquired by other groups to synthesize the substituted analogues of 2,4-methanopyrrolidine 4. In particular,
Esslinger synthesized GABA analogue 4 (R=CO2H),23 while our group reported on fluoro- and methyl-substituted analogues 4 (R=H, F;
Figure 1a).24 In 1999, Piotrowski synthesized aromatic and heteroaromatic 2,4-methanopyrrolidines 5 using intramolecular photochemical
[2+2]-cyclization of acetophenone derivatives.25 Following this method, Elliott and Booker-Milburn in 2016 performed the photochemical
synthesis in flow of N-Bz product 5 (R=Ph) on a kilogram scale (Scheme 1a).26 A photochemical approach was also used by Winkler in
2001 to synthesize the 2-acetyl 2,4-methanopyrrolidine 6.27 Later, Krow with coworkers followed this transformation and performed the
subsequent transformations of compound 6.28
The second strategy to 2,4-methanopyrrolidines relies on an intramolecular cyclization of the substituted aminocyclobutanes
(Scheme 1b). In 1996, Stevens and De Kimpe reacted imine 7 with LiAlH4, and the intermediate amine 8 immediately underwent rapid
intramolecular cyclization into 2,4-methanopyrrolidine 9.29 Later, Siu and Huestis optimized this procedure to obtain 200 g of
unsubstituted 2,4-methanopyrrolidine 9 (R=H).16 Stevens used this tactic to develop an alternative synthesis of amino acid 3.30 Grygorenko
and Komarov used the same approach to synthesize nitrile 1031 and Gorichko – to prepare the substituted amino acid 11.32 Slightly
modified approaches to 2,4-methanopyrrolidine core by Gaoni33and Huet34 are also worth mentioning.
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The third approach to 2,4-methanopyrrolidines was elaborated in 1998 by Krow and co-workers: they reacted compound 12 with
Br2 to form the needed bicyclic molecule 13 (Scheme 1c).35
Although, several approaches to substituted 2,4-methanopyrrolidines already exist, only the synthesis of monofunctional
4
compound 5 by Elliott and Booker-Milburn in collaboration with scientists from GlaxoSmithKline and AstraZeneca was performed on a
5
6
large scale in flow.
Previous work
7
Photochemistry
a)
. Pirrung and Clardy (1980)
8
9
hv
PhCOMe
HCl
CO2Me
C6H6
87%
CO2H
N
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N
CO2Me
N
H
Bz
Bz
1
2
3
R
Ac
Het(Ar)
CO2H
N
N
N
Boc
6
H
H
4
5
R = CO2H, F, Me
Piotrowski (1999)
Winkler (2001)
Krow (2003)
Esslinger (1998)
Booker-Milburn (2016)
in flow
Intramolecular cyclization
b)
. Stevens, De Kimpe (1996)
Cl
Cl
LiAlH4
N
R
NR
NHR
7
9
8
HO
CO2H
N
CN
N
CO2H
N
H
H
Ph
3
10
11
Stevens (2002)
Komarov (2006)
Gorichko (2014)
Rearrangement
c)
. Krow (1998)
Br
Br
Br2
R
R
N
N
CO2Et
CO2Et
12
13
This work
366 nm
PhCOMe
CO2Me
R
in flow
C6H6
87%
N
H
N
N
CO2Me
Bz
Bz
Pyrrolidines with
improved solubility
1
2
Scheme 1. Approaches to substituted 2,4-methanopyrrolidines.
In this work, we report on an in batch and in flow photochemical synthesis of a bifunctional compound 2, and the subsequent
synthesis of 2,4-methanopyrrolidine-containing pharmaceutically-related building blocks. We also demonstrate here, that in spite of a
higher molecular weight, 2,4-methanopyrrolidines have slightly better solubility in water, and lower lipophilicity than pyrrolidines –
important characteristics in drug design.
RESULTS AND DISCUSSION
Optimization studies. Recently, we elaborated the photochemical synthesis of substituted analogues of 2,4-methanoproline, and
studied the role of an electronic effect on the cis-trans amide bond population. Herein, we applied this method for the synthesis of
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compound 2. First, we synthesized the starting material 1 in two steps from methyl pyruvate.21a Next, the photochemical transformation of
compound 1 into bicyclic compound 2 smoothly proceeded at room temperature, under irradiation at 366 nm with benzophenone as a
triplet sensitizer. We performed the photochemical step on a milligram to gram scale using general 10 mL – 1 L glass flasks (Scheme 2).
No special quartz glassware was required, as common glass transmits the light with the wavelength of 366 nm very efficiently.5a,36
Subsequently, we performed the photochemical step in flow to obtain kilogram quantities of compound 2 in one run (Scheme 2).
1
2
3
4
5
6
7
8
9
1)
NH2
366 nm
CO2Me
N
N
CO2Me
PhCOMe
C6H6
[2+2]
O
CO2Me
2)
PhCOCl
NEt3
65%
10
11
12
13
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Ph
O
Ph
O
Methyl pyruvate
1
2
20 mg
(5 mL flask)
10 g
(1 L flask)
1000 g
in flow
Scheme 2. [2+2]-Photochemical synthesis of compound 2 at different scale.
Synthesis of building blocks. Having synthesized intermediate 2 on a large scale, we next used it to obtain
the appropriately substituted 2,4-methanopyrrolidines for the direct use in drug discovery projects.
R
N
1. Fluorinated amines. Fluorinated amines play an important role in medicinal chemistry due to a unique
impact of the fluorine atom on physico-chemical properties of organic molecules. In particular, placing fluorine atoms
close to a nitrogen atom, makes amines less basic and more metabolically stable.37,38 Therefore, we demonstrated the
Monofunctional
synthetic utility of compound 2 by synthesizing three fluorinated amines – monofluoromethyl, difluoromethyl and trifluoromethyl-
substituted 2,4-methanopyrrolidines. In particular, simultaneous reduction of the ester and benzoyl groups in 2 with LiAlH4, followed by a
standard tosylation of alcohol 14, and treatment of the intermediate tosylate 15 with Bu4NF in THF at room temperature gave compound
16 in 92% yield. Hydrogenation of the N-Bn bond in 16 over Pd/C as a catalyst and acidic work-up provided the needed
monofluoromethyl-pyrrolidine 17*HCl in 95% yield (Scheme 3). The structure of compound 17*HCl was confirmed by an X-Ray analysis
(Figure 2). It is worth mentioning that the applications of analogous monofluoromethyl-substituted pyrrolidine is reported in more than 30
patents by diverse pharmaceutical companies.39
LiAlH4
1) TosCl
CO2Me
N
N
N
THF
96%
2) 15, Bu4NF
THF
96%
OH
F
Ph
O
Ph
Ph
2
14
16
1.H2/Pd
2. HCl
95%
X-Ray
N
N
H
H
F
F
>30 patents by
pharm. companies
*HCl
17
*HCl
Scheme 3. Synthesis of monofluoromethyl-substituted amine 17*HCl.
Hydrogenation of the N-Bn bond in compound 14 over Pd/C as a catalysis smoothly gave amino alcohol 18. Treatment of
compound 18 with TosCl in dichloromethane in the presence of triethylamine as a base afforded the N-Tos derivative of substituted
alcohol 19. Swern oxidation of the alcohol group and treatment of the intermediate aldehyde with Morpho-DAST gave difluoromethyl-
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substituted compound 20 in 88% yield. Subsequent cleavage of N-Tos group in product 20 with sodium amalgam in methanol provided the
needed difluoromethyl-substituted amine 21*HCl in 58% yield (Scheme 4). The structure of compound 21*HCl was confirmed by an X-
Ray analysis (Figure 2). In the crystal structure of amine 17*HCl the F-C-C-N+ gauche effect was present. It is also interesting to mention
that in the crystal structure of amine 21*HCl only one fluorine atom was involved in the F-C-C-N+ gauche effect.40
1
2
3
4
5
6
7
TosCl
N
S
H2/Pd
NEt3
8
9
OH
O
N
O
CH2Cl2
98%
N
MeOH
96%
OH
H
OH
Ph
10
11
12
13
14
15
16
17
18
19
20
21
22
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14
18
19
F
1) Swern
oxidation
X-Ray
N
Na/Hg
F
F
O
S O
MeOH
58%
2)
N
O
N SF3
H
F
CH2Cl2
88%
*HCl
21
*HCl
20
Scheme 4. Synthesis of difluoromethyl-substituted amine 21*HCl.
Reaction of amino acid derivative 22 with sulfur tetrafluoride in anhydrous liquid hydrogen fluoride resulted in the
trifluoromethylated product 23 in 88% yield. Hydrogenation of compound 23 over Pd/C cleaved the N-Bn bond to give the target
trifluoromethyl-substituted amine 24*HCl in 96% yield (Scheme 5). The structure of compound 24*HCl was also confirmed by an X-Ray
analysis (Figure 2). It is also important to note that the application of trifluoromethyl-substituted pyrrolidine is mentioned in more than 150
patents by diverse pharmaceutical companies.41
X-Ray
SF4/HF
H2/Pd
CO2H
CF3
N
N
CF3
*HCl
MeOH
96%
88%
N
H
Ph
Ph
22
23
24
*HCl
CF3
N
H
>150 patents by
pharm. companies
Scheme 5. Synthesis of trifluoromethyl-substituted amine 24*HCl.
2. Heterocycles. Hydrogenation of amino alcohol 14 using Pd/C as a catalyst in methanol in the presence of Boc2O, followed by
Swern oxidation of the intermediate N-Boc alcohol gave aldehyde 25. Treatment of the latter with 10 M aqueous NH4OH and an aqueous
solution of 40% glyoxal at room temperature gave compound 26 in 75% yield. Acidic cleavage of the N-Boc protecting group finalized the
synthesis of imidazole 27*HCl in 93% yield (Scheme 6).
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NH4OH
C2H2O2
1) H2/Pd
Boc2O
1
2
3
4
N
N
MeOH
75%
MeOH
2) Swern
oxidation
84%
N
N
OH
HN
O
Boc
Boc
Ph
14
25
26
5
6
7
8
*HCl
HCl
N
dioxane
93%
N
H
HN
9
27
*HCl
10
11
12
13
14
15
16
17
18
19
20
21
22
23
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Scheme 6. Synthesis of substituted imidazole 27*HCl.
Next, the N-Bn protected amino acid 22 was treated first with sulfuric acid in methanol, and the formed methyl ester was reacted
with hydrazine hydrate to give hydrazide 28 in 90% yield. Compound 28 was treated first with N,N-dimethylformamide dimethyl acetal
under reflux in acetonitrile, and triethylamine was added. Under these conditions compound 29 underwent the cyclization into
1,2,4-oxadiazole 30. Hydrogenation of the N-Bn bond in compound 30 over Pd/C as a catalyst in methanol furnished the synthesis of the
heterocyclic compound 31 in 93% yield (Scheme 7).
NMe2
1) MeOH
H2SO4
MeO
MeO
O
O
NMe2
CO2H
N
N
2) N2H4
MeOH
90%
MeCN
N
HN
NHNH2
N
Ph
O
Ph
Ph
22
28
29
O
N
H2/Pd
Et3N
N
MeOH
93%
THF
70%
N
N
H
N
N
Ph
30
31
Scheme 7. Synthesis of substituted 1,2,4-oxadiazole 31.
Treatment of compound 3 with SOCl2 in MeOH under reflux resulted in the corresponding amino ester that was protected with
BnBr to give 32. The N-Bn protected ester 32 was treated with N-hydroxyacetimidamide in the presence of sodium methoxide as a base in
THF gave the cyclized product 33 in 30% yield. Hydrogenation of the N-Bn bond in compound 33 over Pd/C as a catalyst in methanol led
to the desired oxadiazole 34*HCl in 89% yield (Scheme 8).
HO
N
1) SOCl2
MeOH, 90%
H2N
NaOMe
CO2H
CO2Me
N
N
2) BnBr, Et3N
CH2Cl2, 89%
THF, 30%
H
Ph
32
3
*HCl
N
H2/Pd
O
O
N
N
MeOH
89%
N
N
H
N
Ph
33
34
*HCl
Scheme 8. Synthesis of substituted 1,3,4,-oxadiazole 34*HCl.
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3.Tricyclic building blocks. Next, we synthesized several 2,4-methanopyrrolidine-containing building blocks. In particular,
treatment of amino alcohol 18 with 2-chloroacrylonitrile in toluene at room temperature gave compound 35. Addition of t-BuOK in
toluene led to the cyclization of compound 35 into the tricyclic nitrile 36 in 54% yield. Hydrolysis of the nitrile 36 under the acidic
conditions to acid 37*HCl followed by reduction with LiAlH4 in THF at room temperature provided alcohol 38 in 85% yield. Finally,
treatment of compound 36 with Ni-Raney alloy afforded amine 39 in 75% yield. (Scheme 9).
7
8
CN
t-BuOK
Cl
N
9
toluene
54%
toluene
96%
N
H
OH
Cl
OH
10
11
12
13
14
15
16
17
18
19
20
21
22
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CN
18
35
HCl
O
1) H2SO4
MeOH
N
N
2) HCl
90%
O
CN
CO2H
36
37
*HCl
Ni/Raney
40 atm
MeOH
LiAlH4
THF
75%
85%
N
N
O
O
NH2
OH
39
38
Scheme 9. Synthesis of tricyclic building blocks 37-39.
Reductive amination of aldehyde 25 with methyl ester of glycine gave compound 40. Acidic cleavage of N-Boc group, followed
by an addition of aqueous ammonia as a base, gave piperazinone 41 in 20% yield (Scheme 10).
1) TFA
CH2Cl2
H2N CO2Me
NaBH(OAc)3
N
N
N
2) NH4OH
20%
CH2Cl2
50%
NH
NH
Boc
O
Boc
O
CO2Me
25
40
41
Scheme 10. Synthesis of the tricyclic compound 41.
4. Functional building blocks. Next, we examined the synthesis of bifunctional 2,4-methanoproline-
containing building blocks. In particular, alcohol 14 was reacted with TosCl in pyridine to form tosylate 15. Reaction
with NaN3, followed by reduction of the intermediate azide with PPh3 in ethyl acetate at room temperature gave N-Bn
diamine 42 in 90% yield. Next, we synthesized two isomeric N-Boc substituted diamines. In particular, amine 42 was
treated with (CF3CO2)2O in dichloromethane to give compound 43. Hydrogenation of compound 43 over Pd/C as a
N
Bifunctional
catalyst in the presence of Boc2O, followed by cleavage of N-TFA group with potassium carbonate gave the target N-Boc diamine 44.
Alternatively, N-Boc protection of compound 42, followed by hydrogenative cleavage of N-Bn bond in intermediate 45, gave an isomeric
N-Boc diamine 46 in 92% yield (Scheme 11).
It is important to mention that proline analogues of diamines 44 and 46 are very common in drug design – they occur in more
than 2000 patents by diverse pharmaceutical companies (Scheme 11).41
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TsCl
NEt3
1) NaN3
DMF
1
2
3
4
5
6
7
8
N
N
N
2) PPh3
EtOAc
90%
CH2Cl2
98%
OH
OTs
NH2
Ph
Ph
Ph
14
15
42
1) Pd/H2
Boc2O
MeOH
(CF3CO)2O
N
N
CH2Cl2
90%
2) K2CO3
90%
NHCOCF3
43
NH2
Boc
44
Ph
9
Boc2O
DMAP
H2/Pd
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
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N
CH2Cl2
95%
MeOH
92%
N
NHBoc
H
NHBoc
46
Ph
45
N
H
NH2
>2000 patents by
pharm. companies
Scheme 11. Synthesis of isomeric N-Boc-protected diamines 44 and 46.
The Horner–Wadsworth–Emmons reaction of aldehyde 25, followed by hydrogenation of C=C double bond over Pd/C as a
catalyst in the intermediate alkene 47 afforded ester 48 in 87% yield. Hydrolysis of the ester group 48 under the basic conditions resulted
in 49, followed by an acidic cleavage of the N-Boc group gave amino acid 50*HCl - a conformationally restricted analogue of γ -
aminobutyric acid (GABA) - the chief inhibitory neurotransmitter in the mammalian central nervous system (Scheme 12). The structure of
compound 50*HCl was confirmed by an X-Ray analysis (Figure 2). The Ohira-Bestmann reaction of aldehyde 25 gave alkyne 51 in 92%
yield. Cleavage of N-Boc group under acidic conditions gave amino alkyne 52 – a small bifunctional linker useful for click-reactions with
azides. Finally, an addition of PhMgBr followed by acidic cleavage of N-Boc group in 25 provided amino alcohol 54*HCl - a
conformationally restricted analogue of Ephedrine – a medication used to prevent low blood pressure (Scheme 12).
CO2Et
1)
X-Ray
CO2Et
20% NaOH
1) EtOH
PO(OEt)2
CO2H
NaH/THF
N
N
49
2) , 5 N HCl
47
MeOH
87%
2)
, Pd/H2
H
dioxane
95%
Boc
GABA-analogue
48
50
*HCl
*HCl
X-Ray
COMe
N2
HCl
PO(OEt)2
N
N
Boc
51
N
H
MeOH
94%
K2CO3
MeOH
92%
O
Boc
52
*HCl
*HCl
25
*HCl
HCl
PhMgBr
Ph
Ph
OH
dioxane
96%
THF
91%
N
Boc
53
N
H
OH
Ephedrine-analogue
54
*HCl
Scheme 12. Synthesis of compounds 50*HCl, 52*HCl and 54*HCl.
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1
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17*HCl
21*HCl
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24*HCl
50*HCl
52*HCl
Figure 2. X-Ray crystal structure of compounds 17*HCl, 21*HCl, 24*HCl, 50*HCl, 52*HCl.41 The N, C, F, O-atoms are shown
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at 30% thermal ellipsoid % probability.
Physico-chemical properties. After the synthesis, we wanted to experimentally validate the hypothesis of Siu and Huestis that
2,4-methanopyrrolidines were less lipophilic than pyrrolidines. Therefore, we prepared first the N-Bn model compounds 55-58, and
measured experimentally their logD values. The measurement was performed in n-octanol / 100 mM sodium carbonate-sodium bicarbonate
buffer at pH 10 to avoid the reversible protonation of the basic nitrogen atom (Table 1). Indeed, compound 56 was significantly less
lipophilic than pyrrolidine 55 (logD = 2.4 vs 3.0; ΔlogD = -0.6) in spite of the higher molecular weight (187 vs 175). In larger compounds
57, 58 this effect was less prominent (logD = 2.6 vs 2.5; ΔlogD = -0.1). Indeed, the higher the molecular weight, the smaller the input of
intrinsic lipophilicity of 2,4-methanopyrrolidine/pyrrolidine units onto the overall lipophilicity.42
Next, we measured the thermodynamic solubility of molecules 55-58 in an aqueous buffer at pH = 10 (sodium carbonate -
sodium bicarbonate buffer), again to avoid the partial protonation of the basic nitrogen atom. Incredibly, compound 56 had more than three
times higher aqueous solubility than pyrrolidine 55 (Solubility = 25.1 vs 7.2)! As expected, in larger molecules 57, 58 this effect was less
profound (10.9 vs 8.4).
We think that the compact conformationally rigid structure of 2,4-methanopyrrolidines makes the lone pair of a nitrogen atom
more accessible to the water solvent. This leads to reduced lipophilicity and better water solubility of compounds 56, 58 compared to
pyrrolidines 55, 57. Moreover, this effect is strong enough to override the higher molecular weight of 2,4-methanopyrrolidines compared
to pyrrolidines.
It is important to mention, that both models 55 and 56 had similar metabolic stability, as measured by clearance rate in mouse
liver microsomes. Compounds 57 and 58 were unstable metabolically due to a fast hydrolysis of the ester group.
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1
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Table 1. Experimental ADME-parameters.
3
c
Compound
LogD(10.0)a Sol(10.0)b CLint
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6
7
8
9
N
55
3.0
2.4
2.6
7.2
25.1
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3.9
2.6
Ph
N
56
57
58
Ph
O
O
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n.d.d
N
N
Ph
O
2.5
10.9
n.d.d
O
Ph
aExperimental n-octanol/water (100 mM sodium carbonate - sodium bicarbonate buffer) distribution coefficient at pH 10.0 (log); bThermodynamic aqueous solubility at pH =
10 in 100 mM sodium carbonate - sodium bicarbonate buffer (mM). cIntrinsic clearance rate CLint (mg/(min·μL)) measured in mouse liver microsomes; d Very fast decomposition.
In short summary, 2,4-methanopyrrolidines possess an interesting ADME-profile for drug discovery. They have similar
metabolic stability; possess lower lipophilicity, and higher water solubility than pyrrolidines.
CONCLUSIONS
Herein we developed a photochemical synthesis of compound 3 in batch on a milligram to gram scale, and in flow on a on kilogram
scale. From compound 3, several novel 2,4-methanopyrrolidine-containing building blocks were synthesized: amino acids, diamines,
fluorinated amines, amino alcohols, amino alkynes, etc. We also showed experimentally that 2,4-methanopyrrolidines have similar
metabolic stability to that of pyrrolidines. Importantly, in spite of a higher molecular weight of 12 daltons due to one additional carbon
atom, 2,4-methanopyrrolidines they have better solubility in water and lower lipophilicity than pyrrolidines – important characteristics in
drug design.
Given the rapid synthetic access to 2,4-methanopyrrolidines, and their interesting physico-chemical profile, we believe that medicinal
chemists will soon start to use them as “water-soluble” bioisosteres of pyrrolidines in drug discovery projects.
EXPERIMENTAL SECTION
General methods
All chemicals were provided by Enamine Ltd (www.enamine.net). High pressure reactors were provided by UOSlab (en.uoslab.com). All
solvents were treated according using standard methods. All reactions were monitored by thin-layer chromatography (TLC) and were
visualized using UV light. Product purification was performed using silica gel column chromatography. TLC-characterization was
performed with pre-coated silica gel GF254 (0.2 mm), while column chromatography characterization was performed with silica gel (100-
200 mesh).1H-NMR, 19F-NMR, 13C-NMR spectra were recorded with tetramethylsilane (TMS, δ = 0.00 ppm) as the internal standard. 1H-
NMR spectra were recorded at 400 or 500 MHz (Varian); 19F-NMR spectra were recorded at 376 MHz (Varian), 13C NMR spectra were
recorded at 100 or 126 MHz (Varian). 1H-NMR chemical shifts are reported downfield from CDCl3 (δ = 7.26 ppm), D2O (δ = 4.79 ppm) or
DMSO-d6 (δ = 2.50 ppm). 13C-NMR chemical shifts for 13C-NMR are reported relative to the central CDCl3 (δ = 77.16 ppm) or DMSO-d6
(δ = 39.52 ppm). Coupling constants are given in Hz. MS analysis was performed on an LCMS instrument with chemical ionization or
GCMS with electrospray ionization. Melting points are reported for recrystallized and pure compounds.
Methyl 2-(N-allylbenzamido)acrylate (1)
To a solution of methyl pyruvate (1236.4 g, 12.19 mol, 1 equiv) in 8 L of toluene allylamine (695.2 g, 12.19 mol, 1 equiv) was added, and
the mixture was stirred for 12 h at RT under argon. After stirring, the reaction mixture was poured into water and the organic layer was
separated, washed with brine, dried over Na2SO4 and filtered. The filtrate was cooled to -10-0 ºC and triethylamine (1355.2 g, 13.42 mol,
1.1 equiv) was added followed by benzoyl chloride (1713.8 g, 12.19 mol, 1 equiv) maintaining the temperature. The resulting mixture was
allowed to warm to RT and left overnight. The precipitate of triethyamine hydrochloride was filtered off and washed with toluene. The
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filtrate was concentrated under reduced pressure and purified by flash chromatography (hexanes/ethyl acetate, 4:1) to afford the final
compound as a yellow oil. Yield (1940.4 g, 7.92 mol, 65%). The product is relatively unstable and can be polymerized very quickly;
therefore, it should be used immediately for the next step. All analytical data are consistent with the literature.21
Methyl (1s,4s)-2-benzoyl-2-azabicyclo[2.1.1]hexane-1-carboxylate (2)
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8
The compound 1 (23.5 g, 0.096 mol) was dissolved in distilled acetonitrile (1 L) and acetophenone (2.5 g, 0.021 mol) was added. The
reaction was irradiated at 366 nm, and reaction progress was monitored by NMR. After the reaction completeness, the mixture was
concentrated under reduced pressure and the residue was purified by flash column chromatography using hexane/EtOAc = 3/2 as an eluent
to give the desired product 2 as a white solid. Yield (20.5 g, 0.0837 mol, 87% yield), m. p. = 123-125 ºC.
1H NMR (400 MHz, CDCl3) δ: 1.78-1.75 (2H, m), 2.11-2.28 (2H, m), 2.73-2.87 (1H, m), 3.55 (2H, s), 7.79-7.86 (5H, m). 13C NMR (126
MHz, CDC13) δ: 35.2, 41.6, 51.9, 54.9, 69.9, 128.1, 128.3, 131.2, 134.2, 168.7, 173.6.
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Methyl (1s,4s)-2-benzoyl-2-azabicyclo[2.1.1]hexane-1-carboxylate (2), 1 kg scale.
The compound 1 (1110 g, 4.53 mol) was dissolved in dry acetonitrile (5 L) and acetophenone (185 g, 1.54 mol) was added under argon.
The reaction was irradiated at 366 nm for 1 d in a flow reactor (flow rate = 20 mL/min, tube diameter = 8 mm, material - fluorinated
ethylene propylene, power = 4 × 600 W). After the reaction completeness, the mixture was concentrated under reduced pressure. The crude
product was washed with a cold mixture of MTBE/EtOAc (1st portion). The resulted solution was concentrated under reduced pressure,
and the solid residue washed again with a cold mixture of MTBE/EtOAc (2nd portion). Acetophenone was removed from the residue by
distillation (1 mm Hg). The residue containing the desired product was washed with a cold mixture of MTBE/EtOAc (3rd portion). Yield
(1000 g, 4.08 mol, 90%).
All procedures for 3, 14, 18, 22, 25, 32 were taken from the literature.21
(2-Benzyl-2-azabicyclo[2.1.1]hexan-1-yl)methyl 4-methylbenzenesulfonate (15)
p-Toluenesulfonyl chloride (68.6 g, 0.36 mol, 1.2 equiv) was added to a solution of 14 (84.3 g, 0.3 mol, 1 equiv) and Et3N (45.5 g, 0.45
mol, 1.5 equiv) in CH2Cl2 (1 L) dropwise at 0 °C. The mixture was stirred at RT overnight. Water was added, and the mixture was
partitioned. The organic layer was washed with brine, dried over Na2SO4, and concentrated under reduced pressure. The crude product was
used for the next step without further purification (126.1 g, 0.35 mol, 98%).
1H NMR (400 MHz, CDCl3) δ: 1.58 – 1.49 (m, 2H), 1.73 – 1.62 (m, 2H), 2.41 (s, 3H), 2.63 (s, 3H), 3.54 (s, 2H), 4.17 (s, 2H), 7.36 – 7.19
(m, 7H), 7.75 (d, J = 8.2 Hz, 2H). m/z (APCI): 358.1 (M+H). Anal. calcd. for C20H23NO3S: C, 67.20; H, 6.49; N, 3.92. Found: C, 67.45; H,
6.63; N, 3.70.
2-Benzyl-1-(fluoromethyl)-2-azabicyclo[2.1.1]hexane (16)
The tosylated compound 15 (20.0 g, 0.1 mol, 1 equiv) was dissolved in THF (300 mL), and Bu4NF (41.2 g, 0.14 mol, 1.4 equiv) was
added. The mixture was stirred at RT overnight. The reaction mixture was partially concentrated under reduced pressure, diluted with
distilled water and CH2Cl2. The organic layer was separated, washed with brine, dried over Na2SO4, and concentrated under reduced
pressure. The desired product was purified by column chromatography (gradient, hexanes/MTBE) to give a white solid. Yield (18.9 g, 0.09
mol, 92%).
1H NMR (400 MHz, CDCl3) δ: 1.75 – 1.71 (m, 2H), 1.67 – 1.62 (m, 2H), 2.73 – 2.67 (m, 3H), 3.73 (s, 2H), 4.53 (s, 1H), 4.65 (s, 1H), 7.24
(t, J = 7.1 Hz, 1H), 7.32 (t, J = 7.4 Hz, 2H), 7.41 (d, J = 7.3 Hz, 2H). 19F NMR (376 MHz, CDCl3) δ: -225.0 (s). Anal. calcd. for C13H16FN:
C, 76.06; H, 7.86; N, 6.82. Found: C, 75.93; H, 7.75; N, 6.99.
1-(Fluoromethyl)-2-azabicyclo[2.1.1]hexane hydrochloride (17)
The compound 16 (30.0 g, 0.147 mol) was dissolved in 300 mL of MeOH and 2 g of 10% Pd/C was added to the mixture. The mixture was
hydrogenated at 10 atm at RT overnight. Pd/C was filtered out, and the reaction mixture was concentrated under reduced pressure. The
residue was dissolved in a 5 M HCl solution in MeOH and concentrated under reduced pressure to afford the final compound as a white
powder. Yield (21.1 g, 0.14 mol, 95%), mp 182-183 ºC.
1H NMR (400 MHz, DMSO-d6) δ: 1.68 – 1.49 (m, 2H), 2.01 (s, 2H), 2.86 (s, 2H), 3.27 (s, 2H), 4.83 (d, J = 46.9 Hz, 2H), 9.83 (br s, 2H).
19F NMR (376 MHz, DMSO-d6) δ: -227.2 (s). 13C NMR (126 MHz, DMSO-d6) δ: 27.0 (d, JCF = 7.5 Hz), 27.4 (d, JCF = 18.0 Hz), 32.3 (d,
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JCF = 7.0 Hz), 37.5 (d, JCF = 16.4 Hz), 50.2, 111.8 (d, 1JCF = 242.5 Hz). m/z (APCI): 116.2 (M+H). Anal. calcd. for C6H11ClFN: C, 47.53;
H, 7.31; N, 9.24. Found: C, 47.23; H, 7.49; N, 9.41.
1
2
3
(2-Tosyl-2-azabicyclo[2.1.1]hexan-1-yl)methanol (19)
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8
9
p-Toluenesulfonyl chloride (51.9 g, 0.27 mol, 1 equiv) was added in portions to a stirring solution of 18 (30.85 g, 0.27 mol, 1 equiv) and
Et3N (80 mL, 0.57 mol, 2.1 equiv) in CH2Cl2 (900 mL) to keep the temperature below 10 °C (water +ice bath). The reaction mixture was
allowed to warm to RT and stirred for 12 h. The mixture was washed with a solution of 0.5 M HCl (2 × 500 mL) and brine (1 × 500 mL).
The organic layer was separated, dried over Na2SO4, filtered and concentrated in vacuo to give the desired product as a white crystalline
solid. Yield (71.2 g, 0.27 mol, 98 %), mp 134-136 °C.
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1H NMR (500 MHz, CDCl3) δ: 1.28 (dd, 2H, J = 5.0, 1.9 Hz), 1.62 – 1.60 (m, 2H), 2.42 (s, 3H), 2.67 (t, 1H, J = 3.0 Hz), 3.14 (t, 1H, J =
6.9 Hz), 3.38 (s, 2H), 4.01 (d, 2H, J = 6.3 Hz), 7.32 (d, 2H, 3JHH = 8.1 Hz), 7.76 (d, 2H, 3JHH = 8.2 Hz). 13C NMR (101 MHz, CDCl3) δ:
21.6, 35.0, 40.1, 54.0, 61.9, 128.1, 130.0, 135.2, 144.0. m/z (APCI): 268 (M+H). Anal. calcd. for C13H17NO3S: C, 58.41; H, 6.41; N, 5.24;
S, 11.99. Found: C, 58.25; H, 6.20; N, 5.45; S, 11.78.
1-(Difluoromethyl)-2-tosyl-2-azabicyclo[2.1.1]hexane (20)
To a stirred solution of oxalyl chloride (34.4 mL, 0.393 mol, 1.5 equiv) in dry CH2Cl2 (800 mL) was added DMSO (26 mL, 0.393 mol, 1.5
equiv) dropwise at -78 °C under argon atmosphere. The mixture was stirred 10 min at -78 °C, then a solution of compound 19 (70 g, 0.262
mol, 1 equiv) in CH2Cl2 (500 mL) was added dropwise. The resulting mixture was stirred for 30 min at -78 °C, and Et3N (110 mL, 0.786
mol, 3 equiv) was added keeping the temperature below -60 °C. The mixture was allowed to warm to RT. The resulting solution was
poured into water (700 mL), the organic layer was separated and washed with a solution of 0.5 M HCl (2 × 500 mL) and brine (500 mL).
The organic layer was dried over anhydrous Na2SO4, filtered, and concentrated under reduced pressure to give crude aldehyde. The
aldehyde was dissolved in dry CH2Cl2 (1000 mL) and morpholinosulfur trifluoride (137 g, 0.786 mol, 3 equiv) was added to the resulting
solution over 20 min at temperature below 10 °C. The reaction was stirred overnight at RT, then poured onto ice and slowly neutralized
with a 10% solution of K2CO3. The layers were separated, the organic layer was washed sequentially with a 0.5 M solution of HCl (2 ×
500 mL) and brine (2 × 500 mL). The organic layer was dried over anhydrous Na2SO4, filtered and concentrated under reduced pressure.
The residue was purified by silica gel flash column chromatography (5% EtOAc in hexanes), affording 20 as a white solid. Yield (71.2 g,
0.25 mol, 98 %), mp 137-139 °C.
1H NMR (500 MHz, CDCl3) δ: 1.41 – 1.34 (m, 2H), 1.99 – 1.92 (m, 2H), 2.43 (s, 3H), 2.72 (t, 1H, J = 3.1 Hz), 3.45 (s, 2H), 6.53 (t, 1H,
2JHF = 55.1 Hz), 7.32 (d, 2H, 3JHH = 8.2 Hz), 7.76 (d, 2H, 3JHH = 8.3 Hz). 19F NMR (376 MHz, CDCl3) δ: -122.3 (s).13C NMR (101 MHz,
CDCl3) δ: 21.7, 34.1, 38.3 (t, 3JCF= 3.5 Hz), 53.8, 74.8 (t, 2JCF= 31.5 Hz), 111.7 (t, 1JCF = 237.6 Hz, CF2), 128.3, 129.9, 135.4, 144.1. m/z
(APCI): 288 (M+H). Anal. calcd. for C13H15F2NO2S: C, 54.34; H, 5.26; N, 4.87. Found: C, 54.14; H, 5.50; N, 4.99.
1-(Difluoromethyl)-2-azabicyclo[2.1.1]hexane hydrochloride (21)
Compound 20 (50 g, 6.96 mmol), solid sodium amalgam (2000 g) and CH3OH (800 mL) were heated in 2 L round bottom flask at reflux
for 12 h. The reaction mixture was allowed to cool to RT and decanted from the amalgam. pH of the mixture was adjusted to ~1 with 6 M
HCl. The resulting mixture was concentrated under reduced pressure. The residue was dissolved in water (500 mL), and the resulting
aqueous solution was extracted with EtOAc (5 × 400 mL). The aqueous layer was separated and basified to pH ~10 by a 10% solution of
K2CO3. The resulting mixture was extracted with Et2O (4 × 300 mL). The ethereal fractions were combined, dried over MgSO4 and
filtered. A solution of 2 M HCl in diethyl ether was added to the obtained organic solution, and then the precipitate was filtered, washed
with diethyl ether and dried to give 21*HCl as a yellow crystalline solid. Yield (17 g, 58%), mp 181-182 ºC.
1H NMR (400 MHz, DMSO-d6) δ: 1.66 (br s, 2H), 2.14 (br s, 2H), 2.89 (br s, 1H), 3.34 (br s, 2H), 6.55 (t, 1H, 2JHF = 54.1 Hz), 10.26 (br s,
3
2
2H). 19F NMR (376 MHz, DMSO-d6) δ: -125.6 (s). 13C NMR (101 MHz, DMSO-d6) δ: 35.4, 36.4 (t, JCF = 2.8 Hz), 48.4, 69.8 (t, JCF
=
27.7 Hz), 111.6 (t, 1JCF = 239.7 Hz). m/z (APCI): 134.2 (M+H). Anal. calcd. for C6H10ClF2N: C, 42.49; H, 5.94; N, 8.26. Found: C, 42.61;
H, 5.78; N, 8.11.
2-Benzyl-1-(trifluoromethyl)-2-azabicyclo[2.1.1]hexane (23)
Hydrogen fluoride (HF) and sulfur tetrafluoride SF4 are toxic compounds! Special care must be taken when working with them.
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The compound 22 (15.0 g, 0.069 mol, 1 equiv), anhydrous liquid HF (13.8 mL, 0.69 mol, 10 equiv) and SF4 (0.207 mol, 3 equiv) were
heated in a stainless steel autoclave at 70 °C for 12 h. After completion of the reaction, the gaseous products were vented off, the reaction
mixture was poured onto ice and neutralized with a 10% aqueous solution of K2CO3. The product was extracted with MTBE (3 × 100 mL).
Combined organic extracts were washed with brine, dried over Na2SO4, and concentrated under reduced pressure to give the pure 23 as a
yellowish oil. Yield (14.6 g, 0.061 mol, 88%).
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8
1H NMR (400 MHz, CDCl3) δ: 1.83 (dd, 2H, J = 4.5, 1.8 Hz), 1.99 (br s, 2H), 2.70 (br s, 3H), 3.81 (s, 2H), 7.27 (t, 3JHH = 7.2 Hz, 1H), 7.34
(t, 2H, 3JHH = 7.4 Hz), 7.43 (d, 2H, 3JHH = 7.3 Hz). 19F NMR (376 MHz, CDCl3) δ: -71.1 (s). 13C NMR (101 MHz, CDCl3) δ: 36.2, 37.4 (d,
2
1
9
J = 1.9 Hz), 56.9 (d, J = 1.3 Hz), 57.2, 70.7 (q, JCF = 32.5 Hz), 124.3 (q, JCF = 276.8 Hz), 127.1, 128.4, 128.9, 139.1. m/z (APCI): 242
(M+H). Anal. calcd. for C13H14F3N: C, 64.72; H, 5.85; N, 5.81. Found: C, 64.47; H, 5.83; N, 5.84.
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1-(Trifluoromethyl)-2-azabicyclo[2.1.1]hexane hydrochloride (24)
The compound 23 (14.0 g, 0.058 mol, 1 equiv) was dissolved in CH3OH (500 mL) and 10% Pd/C (1.0 g) was added to the solution. The
mixture was hydrogenated at RT under hydrogen pressure of 20 atm. for 10 h. The catalyst was filtered through a pad of Celite (ca. 1 cm),
which was washed with CH3OH (2 × 100 mL). A 2 M solution of HCl in CH3OH (35 mL, 1.2 equiv) was added to the obtained solution,
and the solvents were evaporated under reduced pressure to afford compound pure 24*HCl as a white powder. Yield (10.5 g, 0.056 mol,
96%), mp 176-177 ºC.
1H NMR (400 MHz, DMSO-d6) δ: 1.89 – 1.77 (m, 2H), 2.33 (br s, 2H), 2.95 (br s, 1H), 3.43 (br s, 2H), 10.92 (br s, 2H). 19F NMR (376
MHz, DMSO-d6) δ: -71.3 (s). 13C NMR (126 MHz, DMSO-d6) δ: 35.2, 37.1, 49.0, 67.9 (q, 2JCF = 37.0 Hz), 121.8 (q, 1JCF = 277.3 Hz). m/z
(APCI): 152.2 (M+H). Anal. calcd. for C6H9ClF3N: C, 38.42; H, 4.84; N, 7.47. Found: C, 38.12; H, 5.16; N, 7.31.
tert-Butyl 1-(1H-imidazol-2-yl)-2-azabicyclo[2.1.1]hexane-2-carboxylate (26)
Compound 25 (20.0 g, 0.1 mol, 1 equiv) was dissolved in a mixture of 50 mL of CH3OH and 75 mL of 10 M NH4OH (Exothermic!). The
resulting mixture was stirred for 30 min; then an aqueous solution of 40% glyoxal (20.0 g, 0.13 mol, 1.3 equiv) was added, and the solution
was stirred at RT overnight. The mixture was concentrated under reduced pressure; the residue was dissolved in water and extracted with
CH2Cl2. The organic layers were dried over Na2SO4 and concentrated under reduced pressure to give a light brown solid. The crude
product was washed with a mixture of MTBE with 5% of MeOH to afford the pure desired product. Yield (18.7 g, 0.075 mol, 75%).
1H NMR (400 MHz, CDCl3) δ: 1.28 (s, 9H), 1.84 (d, J = 2.6 Hz, 2H), 2.26 (s, 2H), 2.75 (s, 1H), 3.50 (s, 2H), 6.95 (s, 2H), 10.62 (br s, 1H).
13C NMR (101 MHz, CDCl3) δ: 28.4, 34.7, 44.7, 53.2, 68.8, 79.7, 121.8, 144.9, 157.2. m/z (APEI): 249 (M). Anal. calcd. C13H19N3O2: C,
62.63; H, 7.68; N, 16.85. Found: C, 62.44; H, 7.86; N, 16.67.
1-(1H-imidazol-2-yl)-2-azabicyclo[2.1.1]hexane dihydrochloride (27)
Compound 26 (15.7 g, 0.063 mol, 1 equiv) was dissolved in 100 mL of a solution of 5 M HCl in dioxane at RT. The mixture was stirred
overnight. The resulting precipitate was filtered, dried to afford the desired product as a white solid. Yield (13.0 g, 0.059 mol, 93%), mp
208-210 ºC.
1H NMR (400 MHz, D2O) δ: 2.25 – 2.12 (m, 2H), 2.67 (br s, 2H), 3.20 (br s, 1H), 3.69 (br s, 2H) 3.74 (br s, 2H), 7.57 (s, 2H). 13C NMR
(126 MHz, D2O) δ: 37.1, 40.8, 50.2, 63.3, 66.6, 120.9, 137.3. m/z (APCI): 150.2 (M+H). Anal. calcd. C8H13Cl2N3: C, 43.26; H, 5.90; N,
18.92. Found: C, 43.09; H, 6.12; N, 18.75.
2-Benzyl-2-azabicyclo[2.1.1]hexane-1-carbohydrazide (28)
To a solution of 22 (69.3 g, 0.3 mol, 1 equiv) in MeOH (500 mL) was added NH2NH2*H2O (32.0 g, 0.6 mol, 2 equiv). The mixture was
refluxed for 4 h, and then stirred for 16 h at RT. The solvent was evaporated under reduced pressure. The residue was dissolved in CH2Cl2
(1 L), washed with water, brine, dried over Na2SO4, and concentrated under reduced pressure. The highly pure product 27 obtained was
analyzed without further purification. Yield (62.4 g, 0.27 mol, 90%), pale yellow oil.
1H NMR (400 MHz, DMSO-d6) δ: 1.82 – 1.73 (m, 2H), 2.01 (br s, 2H), 2.68 (br s, 1H), 2.75 (s, 2H), 3.66 (s, 2H), 7.24 (t, 1H, 3J = 6.5 Hz),
7.41 – 7.27 (m, 4H), 7.61 (br s, 1H). Anal. calcd. for C13H17N3O: C, 67.51; H, 7.41; N, 18.17. Found: C, 67.41; H, 7.18; N, 18.43.
N'-(2-benzyl-2-azabicyclo[2.1.1]hexane-1-carbonyl)-N,N-dimethylacetohydrazonamide (29)
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To a solution of 28 (23.1 g, 0.1 mol, 1 equiv) in CH3CN (150 mL) was added DMFDMA (52.4 g, 0.44 mol, 4.4 equiv). The mixture was
refluxed for 6 h. The reaction mixture was allowed to cool to ambient temperature, and the resultant precipitate was filtered off, washed
several times with Et2O, and used for the next step without any purification.
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To a stirred solution of 29 (18.0 g, 0.06 mmol, 1 equiv) in THF (200 mL) was added triethylamine (18.2 g, 0.18 mol, 3 equiv), and the
reaction was stirred for 10 min at RT. p-Toluenesulfonyl chloride (17.2 g, 0.09 mol, 1.5 equiv) was added, and the stirring was continued
for 15 h. The mixture was concentrated, diluted with CH2Cl2, washed with water, brine, dried over Na2SO4 and concentrated under reduced
pressure. The residue was purified by flash chromatography to give the final product as a yellow viscous oil. Yield (10.7 g, 0.042 mol,
70%).
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1H NMR (400 MHz, CDCl3) δ: 2.14 – 1.99 (m, 4H), 2.33 (s, 3H), 2.79 (br s, 1H), 2.87 (s, 2H), 3.65 (br s, 2H), 7.19 – 7.12 (m, 1H), 7.22 (t,
J = 7.3 Hz, 2H), 7.27 (d, J = 7.2 Hz, 2H). 13C NMR (101 MHz, CDCl3) δ: 10.9, 38.2, 40.8, 57.4, 57.8, 66.4, 126.9, 128.2, 128.8, 139.2,
164.1, 164.7. m/z (APEI): 255 (M). Anal. calcd. for C15H17N3O: C, 70.56; H, 6.71; N, 16.46. Found: C, 70.80; H, 6.98; N, 16.21.
2-(2-Azabicyclo[2.1.1]hexan-1-yl)-5-methyl-1,3,4-oxadiazole (31)
Compound 30 (10.0 g, 0.04 mol, 1 equiv) was dissolved in 100 mL of MeOH and 1 g of 10%-Pd/C was added to the mixture. The mixture
was hydrogenated at 10 atm at RT overnight. Then Pd/C was filtered out, and the reaction mixture was concentrated under reduced
pressure to afford the desired compound as a pink oil. Yield (6.1 g, 0.024 mol, 93%).
1H NMR (400 MHz, CDCl3) δ: 1.71 – 1.55 (m, 2H), 2.14 (br s, 2H), 2.18 (br s, 1H), 2.45 (s, 3H), 2.86 (br s, 1H), 3.08 (br s, 2H). 13C NMR
(126 MHz, CDCl3) δ: 10.9, 38.5, 43.8, 48.5, 62.4, 163.8, 165.3. m/z (APCI): 166.2 (M+H). Anal. calcd. for C8H11N3O: C, 58.17; H, 6.71;
N, 25.44. Found: C, 58.44; H, 6.84; N, 25.61.
5-(2-Benzyl-2-azabicyclo[2.1.1]hexan-1-yl)-3-methyl-1,2,4-oxadiazole (33)
Compound 32 (69.3 g, 0.3 mol, 1 equiv) was dissolved in 800 mL of THF and sodium methoxide (48.6 g, 0.9 mol, 3 equiv) was added.
The resulting mixture was stirred for 30 min; then N-hydroxyacetimidamide (24.4 g, 0.33 mol, 1.1 equiv) was added, and the reaction was
heated to 40 °C and stirred for 12 h. The mixture was cooled to RT and filtered; the filtrate was dissolved in water and extracted with
EtOAc. The combined organic layers were dried over Na2SO4, filtered and concentrated under reduced pressure to give a brown solid. The
crude product was washed with a mixture of MTBE with 5% of MeOH to afford the pure final product. Yield (23.2 g, 0.091 mol, 30%).
1H NMR (400 MHz, CDCl3) δ: 2.09 – 2.05 (m, 2H), 2.13 (s, 2H), 2.34 (s, 3H), 2.79 (s, 1H), 2.80 (s, 2H), 3.68 (s, 2H), 7.18 (t, J = 7.0 Hz,
1H), 7.27 (t, J = 7.2 Hz, 2H), 7.35 (d, J = 6.9 Hz, 2H). 13C NMR (101 MHz, CDCl3) δ: 11.6, 38.1, 41.2, 56.8, 57.4, 67.1, 126.9, 128.2,
128.6, 139.0, 167.1, 176.8. m/z (APEI): 255 (M). Anal. calcd. for C15H17N3O: C, 70.56; H, 6.71; N, 16.46. Found: C, 70.88; H, 6.95; N,
16.29.
5-(2-Azabicyclo[2.1.1]hexan-1-yl)-3-methyl-1,2,4-oxadiazole hydrochloride (34)
Compound 33 (20.8 g, 0.078 mol) was dissolved in 200 mL of MeOH and 2 g of 10%-Pd/C was added to the mixture. The mixture was
hydrogenated at 10 atm at RT overnight. Then Pd/C was filtered out, and the reaction mixture was concentrated under reduced pressure to
afford the desired compound as a white powder, mp 222-223 ºC. Yield (14.0 g, 0.07 mol, 89%).
1H NMR (400 MHz, D2O) δ: 2.15 – 1.99 (m, 2H), 2.46 (s, 3H), 2.72 (br s, 2H), 3.18 (br s, 1H), 3.68 (br s, 2H). 13C NMR (126 MHz, D2O)
δ: 10.5, 37.1, 41.7, 49.8, 64.8, 168.1, 171.6. m/z (APEI): 165 (M). Anal. calcd. for C8H12ClN3O: C, 47.65; H, 6.00; N, 20.84. Found: C,
47.49; H, 5.81; N, 20.99.
2-Chloro-3-(1-(hydroxymethyl)-2-azabicyclo[2.1.1]hexan-2-yl)propanenitrile (35)
To a solution of 18 (33.9 g, 0.3 mol, 1 equiv) in toluene (300 mL) was added 2-chloroacrylonitrile (29.0 g, 0.32 mol, 1.05 equiv) at RT.
The reaction mixture was diluted with water, the organic layer was separated, and aqueous layer was additionally washed with EtOAc. The
combined organic layers were washed with brine and dried over Na2SO4. The solvent was removed under reduced pressure to give the
desired product as a yellow oil. The compound is relatively unstable and should be immediately used for the next step. Yield (57.7 g, 0.29
mol, 96%).
1H NMR (500 MHz, CDCl3) δ: 1.55 – 1.46 (m, 2H), 1.65 – 1.59 (m, 2H), 2.75 (s, 1H), 3.00 (s, 2H), 3.10 (dd, J = 13.1, 5.9 Hz, 1H), 3.19
(dd, J = 13.1, 8.4 Hz, 1H), 3.82 (d, J = 2.8 Hz, 2H), 4.49 (dd, J = 8.2, 6.0 Hz, 1H). m/z (APEI): 200 (M).
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Tetrahydro-1H,6H-7,8a-methanopyrrolo[2,1-c][1,4]oxazine-3-carbonitrile (36)
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To a solution of 35 (40.1 g, 0.2 mol, 1 equiv) in toluene (300 mL) was added potassium tert-butoxide (23.5 g, 0.21 mol, 1.05 equiv) at -30
°C. The reaction mixture was warmed to RT, and diluted with water, the organic layer was separated, and aqueous layer was additionally
washed with EtOAc. The combined organic layers were washed with brine and dried over Na2SO4. The solvent was removed under
reduced pressure to give the desired product as a yellow solid. Yield (17.7 g, 0.1 mol, 54%), mp 43-44 °C.
1H NMR (400 MHz, CDCl3) δ: 1.54 (m, 4H), 2.61 – 2.26 (m, 1H), 2.70 (s, 1H), 2.93 (br s, 2H), 3.79 (d, J = 11.5 Hz, 1H), 4.01 (d, J = 12.0
Hz, 1H), 4.58 (br s, 1H). 13C NMR (101 MHz, CDCl3) δ: 37.6, 53.2, 56.5, 64.7, 66.4, 68.1 (br s), 117.0. m/z (APEI): 164 (M). Anal. calcd.
for C9H12N2O: C, 65.83; H, 7.37; N, 17.06. Found: C, 65.61; H, 7.16; N, 17.31.
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Tetrahydro-1H,6H-7,8a-methanopyrrolo[2,1-c][1,4]oxazine-3-carboxylic acid hydrochloride (37)
To a solution of 36 (32.8 g, 0.2 mol, 1 equiv) in MeOH (300 mL) was added H2SO4 (21.3 mL, 0.4 mol, 2 equiv). The mixture was brought
to reflux for 2 d. The cold mixture was treated with a solution of NaHCO3 to neutralize the solution, and then concentrated under reduced
pressure. The residue was dissolved in water and extracted with CH2Cl2. The organic layer was washed with brine, dried over Na2SO4, and
concentrated under reduced pressure to give the desired product as a yellow oil. The crude product was treated with concd. HCl and
brought to reflux for 2 h. The precipitate was filtered, washed with Et2O, and dried to give the desired product as a beige solid (39.5 g,
90%), mp 206-208 °C.
1H NMR (400 MHz, D2O) δ: 1.62 (t, J = 9.9 Hz, 1H), 2.03 (t, J = 10.1 Hz, 1H), 2.12 (br s, 1H), 2.27 (d, J = 8.9 Hz, 1H), 3.03 (s, 1H), 3.27
(d, J = 9.8 Hz, 1H), 3.38 (t, J = 12.2 Hz, 1H), 3.82 (t, J = 9.0 Hz, 1H), 4.04 (dd, J = 13.0, 5.0 Hz, 2H), 4.37 (d, J = 13.5 Hz, 1H), 4.50 (d, J
= 11.0 Hz, 1H). 13C NMR (126 MHz, D2O) δ: 35.7, 36.2, 37.7, 49.4, 57.8, 65.7, 71.2, 72.1, 169.8. m/z (APCI): 184.2 (M+H). Anal. calcd.
for C9H13NO3: C, 59.00; H, 7.15; N, 7.65. Found: C, 59.25; H, 7.32; N, 7.47.
(Tetrahydro-1H,6H-7,8a-methanopyrrolo[2,1-c][1,4]oxazin-3-yl)methanol (38)
LiAlH4 (1.2 g, 0.03 mol, 0.65 equiv) was dissolved in dry THF and cooled to 0 °C. Compound 37-CO2Me (9.5 g, 0.048 mol, 1 equiv) was
added in small portions. The mixture was stirred overnight at RT. The excess of LiAlH4 was quenched with a 40% NaOH solution.
Inorganic precipitates were filtered off, and the solution was concentrated under reduced pressure to afford the final compound as a white
solid (6.9 g, 0.04 mol, 85%), mp 98-99 °C.
1H NMR (400 MHz, CDCl3) δ: 1.47 – 1.32 (m, 2H), 1.77 – 1.58 (m, 2H), 2.33 (d, J = 7.8 Hz, 1H), 2.43 (t, J = 10.4 Hz, 1H), 2.71 (s, 1H),
2.90 (d, J = 10.2 Hz, 1H), 3.18 (d, J = 7.3 Hz, 1H), 3.69 – 3.52 (m, 2H), 3.75 – 3.73 (m, 1H), 3.74 (d, J = 11.8 Hz, 1H), 3.97 (d, J = 11.8
Hz, 1H). 13C NMR (126 MHz, CDCl3) δ: 35.0, 37.6, 40.5, 52.8, 57.1, 64.1, 67.2, 69.3. m/z (APEI): 169 (M). Anal. calcd. for C9H15NO2: C,
63.88; H, 8.93; N, 8.28. Found: C, 64.08; H, 8.70; N, 8.54.
{3-Oxa-6-azatricyclo[6.1.1.0,1,6]decan-4-yl}methanamine (39)
Compound 36 (14.7 g, 0.09 mol) was dissolved in 200 mL of CH3OH followed by the addition of Raney nickel (3 g), filled with hydrogen
two times and the resulting solution was stirred for 12 h, filtered. The filtrate was concentrated under reduced pressure to obtain as a
colorless oil. Yield (11.3 g, 0.067 mol, 75%).
1H NMR (400 MHz, DMSO-d6) δ: 1.55 – 0.96 (m, 6H), 2.08-1.96 (m, 2H), 2.48 – 2.20 (m, 3H), 2.71 (d, 1H, J = 10.6 Hz), 2.87 (d, 1H, J =
7.8 Hz), 3.29 – 3.13 (m, 1H), 3.35 (d, 1H, J = 11.4 Hz), 3.70 (d, 1H, J = 11.4 Hz). 13C NMR (126 MHz, DMSO-d6) δ: 34.3, 37.0, 44.6,
54.0, 56.2, 66.7, 68.4, 78.3. m/z (APEI): 168.1 (M). Anal. calcd. for C9H16N2O: C, 64.25; H, 9.59; N, 16.65. Found: C, 64.03; H, 9.57; N,
16.67.
tert-Butyl 1-(((2-methoxy-2-oxoethyl)amino)methyl)-2-azabicyclo[2.1.1]hexane-2-carboxylate (40)
The compound 25 (20.0 g, 0.1 mol, 1 equiv) was dissolved in CH2Cl2, and glycine methyl ester hydrochloride (18.8 g, 0.15 mol, 1.5 equiv)
was added. The mixture was stirred for 30 min at RT, and sodium triacetoxyborohydride (42.4 g, 0.2 mol, 2 equiv) was added. The
resulting mixture was stirred overnight. The precipitate was filtered out, and the filtrate was washed with water, dried over Na2SO4, and
concentrated under reduced pressure. The crude product was purified by column chromatography (gradient, hexanes/EtOAc) to give a
yellow oil. Yield (14.2 g, 0.05 mol, 50%).
1H NMR (400 MHz, CDCl3) δ: 1.40 (s, 9H), 1.54 – 1.44 (m, 2H), 1.77 (s, 2H), 2.21 (br s, 1H), 2.66 (s, 1H), 3.14 (s, 2H), 3.32 (s, 2H), 3.41
(s, 2H), 3.66 (s, 3H).
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Tetrahydro-6H-7,8a-methanopyrrolo[1,2-a]pyrazin-4(1H)-one (41)
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Compound 40 (10.0 g, 0.035 mol) was dissolved in 50 mL of CH2Cl2 and 10 mL of TFA. The resulting mixture was stirred for 2 h at RT,
and then concentrated under reduced pressure. The residue was dissolved in 100 mL of CH3OH and 50 mL of aq. NH4OH. The mixture
was concentrated under reduced pressure. The desired product was separated by extraction with CH2Cl2. Yield (1.0 g, 0.007 mol, 20%),
yellow oil.
1H NMR (400 MHz, CDCl3) δ: 1.58 – 1.49 (m, 2H), 1.84 (br s, 2H), 2.85 (br s, 1H), 3.14 (br s, 2H), 3.38 (br s, 2H), 3.45 (br s, 2H), 5.44
(br s, 1H). 13C NMR (126 MHz, CDCl3) δ: 34.3, 42.6, 46.7, 48.4, 49.9, 70.0, 168.1. m/z (APCI): 153.2 (M+H). Anal. calcd. for C8H12N2O:
C, 63.13; H, 7.95; N, 18.41. Found: C, 62.87; H, 7.93; N, 18.45.
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(2-Benzyl-2-azabicyclo[2.1.1]hexan-1-yl)methanamine (42)
A mixture of compound 15 (107.3 g, 0.30 mol, 1 equiv) and NaN3 (29.3 g, 0.45 mol, 1.5 equiv) in DMF (1.5 L) was heated, and stirred at
40 °C for 10 h until TLC-analysis indicated the reaction to be complete. The reaction mixture was cooled to RT and poured into cold water
(2 L). The mixture was extracted with EtOAc (3 × 700 mL). The organic extract was back-washed with water (3 × 500 mL), brine, dried
over Na2SO4, and the solvent was partially evaporated under reduced pressure to give a solution of the desired compound. The solution of
the azide approximately (68.4 g, 0.3 mol, 1 equiv) in EtOAc (1.5 L) was poured into a round bottomed flask equipped with magnetic
stirring, mixed with PPh3 (86.5 g, 0.33 mol, 1.1 equiv), and left for 14 h at RT. The reaction was monitored by TLC. Upon completion of
the reaction, the reaction mixture was acidified with a 5 M HCl solution. The layers were separated, and the aqueous layer was additionally
washed with EtOAc, then basified with K2CO3, extracted with CH2Cl2 several times. The combined organic layers were washed with
brine, dried over Na2SO4, and concentrated under reduced pressure. The resulting oil was solidified in hexanes to give a yellow solid of the
desired product. Yield (54.5 g, 0.27 mol, 90%).
1H NMR (400 MHz, DMSO-d6) δ: 1.34 (br s, 2H), 1.49 (br s, 2H), 2.43 (br s, 1H), 2.46 (br s, 2H), 2.68 (s, 2H), 3.51 (s, 2H), 7.15 (t, 1H,
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3JHH = 6.8 Hz), 7.23 (t, 2H, JHH = 6.8 Hz), 7.32 (d, 2H, JHH = 6.9 Hz). 13C NMR (126 MHz, DMSO-d6) δ: 35.7, 36.9, 41.8, 55.0, 57.5,
74.8, 126.3, 128.0, 128.3, 140.5. m/z (APCI): 203.1 (M+H). Anal. calcd. for C13H18N2: C, 77.18; H, 8.97; N, 13.85. Found: C, 77.39; H,
9.09; N, 13.71.
tert-Butyl 1-(aminomethyl)-2-azabicyclo[2.1.1]hexane-2-carboxylate (44)
Compound 42 (47.9 g, 0.258 mol, 1 equiv) was dissolved in a mixture of CH2Cl2 (1.5 L) and Et3N (141.4 g, 1.4 mol, 5 equiv). The mixture
was cooled to 0 °C, and TFAA (59.6 g, 0.28 mol, 1.1 equiv) was added. The ice-bath was removed after the addition was complete, and the
reaction stirred for 16 h at RT. The mixture was poured into cold water and layers were separated. The organic layer was washed with
brine, dried over Na2SO4, filtered, and concentrated under reduced pressure to afford crude compound 43 as a yellow oil. The compound
43 (77.1 g, 0.259 mol, 1 equiv) was stirred in dry CH3OH (1.5 L) with 10% Pd/C (8 g) and Boc2O (39.5 g, 0.181 mol, 0.7 equiv) under 10
atm of H2 at RT overnight. Then Pd/C was filtered out, and the reaction mixture was concentrated under reduced pressure. The residue was
dissolved in water and extracted with CH2Cl2 several times. The combined layers were washed with brine, dried over Na2SO4, filtered, and
concentrated under reduced pressure. The residue was dissolved in MeOH and K2CO3 (107.2 g, 0.78 mol, 3 equiv) was added at 0 °C. The
mixture was sitter at RT for 4 h, then filtered and concentrated under reduced pressure. Finally, the product was purified by distillation to
give a colorless oil. Yield (38.4 g, 0.18 mol, 70%).
1H NMR (400 MHz, CDCl3) δ: 1.44 (s, 9H). 1.50 (d, 2H, J = 4.4 Hz), 1.68 (br s, 2H), 1.78 (br s, 2H), 2.69 (br s, 1H), 3.19 (br s, 2H), 3.34
(br s, 2H). 13C NMR (126 MHz, CDCl3) δ: 28.7, 33.8, 41.9, 43.6, 52.6, 75.3, 79.3, 155.2. m/z (APEI): 212.2 (M). Anal. calcd. for
C11H20N2O2: C, 62.24; H, 9.50; N, 13.20. Found: C, 62.40; H, 9.77; N, 13.04.
tert-Butyl ((2-benzyl-2-azabicyclo[2.1.1]hexan-1-yl)methyl)carbamate (45)
To a stirred solution of 42 (54.0 g, 0.267 mol, 1 equiv) in CH2Cl2 (1.5 L) at 0 °C were added Boc2O (61.2 g, 0.28 mol, 1.05 equiv), DMAP
(3.3 g, 0.1 equiv), and Et3N (28.3 g, 0.28 mol, 1.05 equiv). After stirring at RT overnight, the mixture was diluted with EtOAc and poured
into a saturated aqueous solution of NH4Cl (30 mL). The aqueous layer was separated and extracted with EtOAc. The combined extracts
were washed with brine, dried over Na2SO4, and concentrated under reduced pressure to give a yellow oil. Yield (76.6 g, 0.25 mol, 95%).
The crude product was sufficiently pure to be used for the next step.
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1H NMR (400 MHz, CDCl3) δ: 0.86 – 0.71 (m, 2H), 1.18 (br s, 2H), 1.35 (s, 9H), 2.61 – 2.57 (m, 3H), 3.33 (br s, 2H), 3.54 (d, 2H, J = 3.8
Hz), 4.75 (br s, 1H), 7.16 (t, 1H, J = 6.6 Hz), 7.24 (t, 2H, J = 5.7 Hz), 7.31 (d, 2H, J = 5.8 Hz). Anal. calcd. for C18H26N2O2: C, 71.49; H,
8.67; N, 9.26. Found: C, 71.31; H, 8.89; N, 9.14.
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Compound 45 (76.0 g, 0.25 mol) was dissolved in 500 mL of MeOH, and 7 g of 10%-Pd/C was added to the mixture. The mixture was
hydrogenated at 10 atm at RT overnight. Then Pd/C was filtered out, and the reaction mixture was concentrated under reduced pressure to
afford the final compound as a white powder. Yield (48.7 g, 0.23 mol, 92%), mp 65-67 ºC.
1H NMR (400 MHz, DMSO-d6) δ: 1.06 (br s, 2H, CH2). 1.37 (s, 9H), 1.49 (br s, 2H), 1.43 (br s, 1H), 2.59 (br s, 1H), 2.77 (br s, 2H), 3.13
(d, 2H, J = 5.3 Hz), 6.75 (br s, 1H). 13C NMR (126 MHz, DMSO-d6) δ: 28.2, 36.4, 40.2, 42.3, 48.3, 69.5, 77.6, 155.7. Anal. calcd. for
C11H20N2O2: C, 62.24; H, 9.50; N, 13.20. Found: C, 62.45; H, 9.74; N, 13.04.
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tert-Butyl-1-(3-ethoxy-3-oxoprop-1-en-1-yl)-2-azabicyclo[2.1.1]hexane-2-carboxylate (47)
To a suspension of NaH (5.50 g, 0.125 mol, 1.2 equiv) in 150 mL of dry THF was added dropwise ethyl 2-(diethyl phosphono)acetate
(27.0 g, 0.12 mol, 1.2 equiv) with rapid stirring under atmosphere of argon at RT. At the end of the addition, the mixture was stirred for 1 h
at RT. The aldehyde 25 (20.0 g, 0.10 mol, 1 equiv) was dissolved in 50 mL of THF and added dropwise to the reaction. The reaction
mixture was stirred at RT until TLC-analysis showed complete consumption of starting material (~ 1 h). The reaction was quenched with
water, diluted with EtOAc, and washed with brine. The organic layer was separated and washed with 1 M HCl, dried over Na2SO4, filtered,
and concentrated under reduced pressure to afford the desired compound as a yellow oil. Yield (24 g, 0.09 mol, 90%). The crude
compound was sufficiently pure to be used directly in the next step. All analytical data are consistent with the literature.21
tert-Butyl 1-(3-ethoxy-3-oxopropyl)-2-azabicyclo[2.1.1]hexane-2-carboxylate (48)
Compound 47 (23.0 g, 0.086 mol, 1 equiv) was dissolved in 150 mL of MeOH and 4 g of 10%-Pd/C was added to the mixture. The
mixture was hydrogenated at RT overnight. Then Pd/C was filtered out, and the reaction mixture was concentrated under reduced pressure
to afford the final compound as a yellow oil. Yield (22.4 g, 0.083 mol, 97%).
1H NMR (400 MHz, CDCl3) δ: 1.23 (t, J = 7.0 Hz, 3H), 1.44 (s, 11H), 1.68 (br s, 2H), 2.42 (br s, 4H), 2.67 (s, 1H), 3.35 (s, 2H), 4.10 (q,
6.7 Hz, 2H). Anal. calcd. for C15H25NO4: C, 63.58; H, 8.89; N, 4.94. Found: C, 63.82; H, 8.69; N, 5.12.
3-(2-(tert-Butoxycarbonyl)-2-azabicyclo[2.1.1]hexan-1-yl)propanoic acid (49)
The crude compound 48 (20.0 g, 0.078 mol, 1 equiv) was dissolved in EtOH, and a 20% solution of NaOH (6.3 g, 0.157 mol, 2 equiv) was
added at RT. The resulting mixture was stirred overnight, and then concentrated to dryness under reduced pressure. The residue was
dissolved in cold water, acidified with 0.1 M HCl, diluted with CHCl3 and partitioned. The organic layer was dried over Na2SO4, filtered
and concentrated under reduced pressure. The crude product was solidified in pentane, filtered, dried to afford the final product as a white
powder. Yield (18.9 g, 0.074 mol, 95%), mp 77-78 ºC.
1H NMR (400 MHz, CDCl3) δ: 1.46 (s, 9H), 1.51-1.43 (m, 2H), 1.71 (br s, 2H), 2.53 – 2.40 (m, 4H), 2.71 (br s, 1H), 3.37 (br s, 2H), 10.98
(br s, 1H). 13C NMR (126 MHz, CDCl3) δ: 27.3, 28.7, 30.8, 33.9, 43.2, 52.9, 73.3, 79.7, 155.9, 178.8. m/z (APCI): 256.0 (M+H). Anal.
calcd. for C13H21NO4: C, 61.16; H, 8.29; N, 5.49. Found: C, 61.29; H, 8.52; N, 5.32.
3-(2-Azabicyclo[2.1.1]hexan-1-yl)propanoic acid hydrochloride (50)
Compound 49 (18.5 g, 0.073 mol, 1 equiv) was dissolved in 50 mL of MeOH, and a solution of 5 M HCl in MeOH (150 mL) was added at
RT. The mixture was stirred overnight, and then concentrated to dryness under reduced pressure. The crude product was washed with
Et2O, and dried to afford the desired product as a white solid. Yield (13.3 g, 0.07 mol, 96%), mp 189-190 ºC.
1H NMR (400 MHz, DMSO-d6) δ: 1.50 – 1.42 (m, 2H), 1.86 (br s, 2H), 2.07 (t, 2H, 3JHH = 7.7 Hz), 2.41 (t, 2H, 3JHH = 7.7 Hz), 2.73 (br s,
1H), 3.18 (br s, 2H), 9.43 (br s, 2H), 12.28 (br s, 1H). 13C NMR (126 MHz, CDCl3) δ: 24.7, 29.5, 35.1, 38.6, 47.9, 72.9, 173.6. m/z (APCI):
156.2 (M+H). Anal. calcd. for C8H14ClNO2: C, 50.14; H, 7.36; N, 7.31. Found: C, 50.31; H, 7.52; N, 7.05.
tert-Butyl 1-ethynyl-2-azabicyclo[2.1.1]hexane-2-carboxylate (51)
To a solution of 25 (11.2 g, 0.053 mol, 1.0 equiv) and dimethyl-1-diazo-2-oxopropylphosphonate (15.3 g, 0.079 mol, 1.5 equiv) in MeOH
(200 mL) was added K2CO3 (14.6 g, 0.106 mol, 2.0 equiv) in portions at 0 °C. After stirring for 1 h at 0 °C, then for 2 h at RT, the mixture
was diluted with EtOAc, quenched with a saturated NH4Cl solution. The aqueous layer was then extracted with EtOAc. The combined
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organic layers were washed with brine, dried over Na2SO4, and concentrated in vacuo. Purification on silica gel column chromatography
(hexane/EtOAc) afforded 51 as a colorless oil (10.1 g, 0.049 mol, 92%).
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1H NMR (400 MHz, CDCl3) δ: 1.49 (s, 9H), 1.76 (br s, 2H), 2.11 (br s, 2H), 2.63 (br s, 1H), 2.68 (br s, 1H), 3.38 (br s, 2H). m/z (APEI):
207 (M). Anal. calcd. for C12H17NO2: C, 69.54; H, 8.27; N, 6.76. Found: C, 69.82; H, 8.50; N, 6.49.
1-Ethynyl-2-azabicyclo[2.1.1]hexane hydrochloride (52)
The compound 51 (6.8 g, 0.033 mol) was dissolved in 100 mL of MeOH-HCl at RT. The mixture was stirred at RT overnight. The
resulting precipitate was filtered, dried to afford the final compound as a beige powder, mp 194-195 ºC. Yield (4.4 g, 0.03 mol, 94%).
1H NMR (400 MHz, DMSO-d6) δ: 1.93 – 1.66 (m, 2H), 2.21 (s, 2H), 2.75 (s, 1H), 3.22 (s, 3H), 4.03 (s, 1H), 10.14 (br s, 2H). 13C NMR
(126 MHz, DMSO-d6) δ: 36.3, 42.3, 47.2, 59.0, 76.4, 80.6. m/z (APCI): 109.2 (M+H). Anal. calcd. for C7H10ClN: C, 58.54; H, 7.02; N,
9.75. Found: C, 58.78; H, 7.22; N, 9.51.
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tert-Butyl 1-(hydroxy(phenyl)methyl)-2-azabicyclo[2.1.1]hexane-2-carboxylate (53)
PhMgBr (1 M in THF, 95 mL, 0.095 mol, 1 equiv) was added to a solution of 25 (20.0 g, 0.095 mol, 1 equiv) in THF (200 mL). The
resulting mixture was stirred at RT and the reaction was monitored by TLC. After complete conversion, saturated NH4Cl solution (100
mL) was poured into the mixture. The mixture was extracted with EtOAc, and the organic layer was separated, dried over anhydrous
MgSO4, and evaporated under reduced pressure. Yield (17.9 g, 0.086 mol, 91%).
1H NMR (400 MHz, CDCl3) δ: 1.34 – 1.16 (m, 1H), 1.54 – 1.40 (m, 2H), 1.49 (s, 9H), 1.70 – 1.58 (m, 1H), 2.56 (s, 1H), 3.37 (q, J = 8.7
Hz, 2H), 5.27 (s, 1H), 7.40 – 7.18 (m, 5H). m/z (APCI): 290.2 (M+H). Anal. calcd. for C17H23NO3: C, 70.56; H, 8.01; N, 4.84. Found: C,
70.38; H, 8.32; N, 4.71.
(2-Azabicyclo[2.1.1]hexan-1-yl)(phenyl)methanol hydrochloride (54)
The compound 53 (7.8 g, 0.027 mol) was dissolved in 100 mL of a 4 M solution of dioxane-HCl at RT. The mixture was stirred at RT
overnight. The resulting precipitate was filtered, dried to afford the final compound as a white powder, mp 224-225 ºC. Yield (5.4 g, 0.024
mol, 89%).
1H NMR (500 MHz, D2O) δ: 1.51 (t, J = 9.8 Hz, 1H), 1.64 (t, J = 9.8 Hz, 1H), 2.02 (d, J = 8.4 Hz, 1H), 2.13 (d, J = 8.3 Hz, 1H), 2.93 (s,
1H), 3.38 (q, J = 9.6 Hz, 2H), 5.19 (s, 1H), 7.70 – 7.30 (m, 5H). 13C NMR (126 MHz, D2O) δ: 34.9, 36.4, 37.2, 49.0, 70.1, 76.7, 125.8,
128.3, 128.5, 137.6. m/z (APCI): 190.2 (M+H). Anal. calcd. for C12H16ClNO: C, 63.86; H, 7.15; N, 6.21. Found: C, 63.99; H, 7.36; N,
6.01.
“ADME parameters of the compounds (aqueous solubility, logD, hepatic microsomal stability) were determined at Bienta (Enamine
Biology Services) bioanalytical lab accordingly to the experimental protocols published elsewhere.43
ASSOCIATED CONTENT
Supporting Information
Experimental copies of NMR spectra and X-ray crystallography data. This material is available free of charge via the Internet at
http://pubs.acs.org.
AUTHOR INFORMATION
Corresponding Author
* E-mail: Pavel.Mykhailiuk@gmail.com
Homepage: www.mykhailiukchem.org
Notes
The authors declare no competing financial interest.
ACKNOWLEDGMENT
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The Journal of Organic Chemistry
Authors are very grateful to Dr. E. Rusanov for X-Ray analysis of compounds 17*HCl, 21*HCl, 24*HCl, 50*HCl, 52*HCl.
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38 Our previous interest in fluorinated alicyclic amines: (a) Kubyshkin, V. S.; Afonin, S.; Kara, S.; Budisa, N.; Mykhailiuk, P. K.; Ulrich,
A. S. γ-(S)-Trifluoromethyl proline: evaluation as a structural substitute of proline for solid state 19F-NMR peptide studies. Org. Biomol.
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39 The search was performed in August 2018 on Reaxys DB database.
40
Briggs, C. R. S.; Allen, M. J.; O'Hagan, D.; Tozer, D. J.; Slawin, A. M. Z.; Goet, A. E.; Howard, J. A. K. The observation of a large
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41 CCDC numbers: 1859863 (17*HCl), 1859075 (21*HCl), 1859076 (24*HCl), 1859077 (50*HCl), 1859078 (52*HCl).
42
While this manuscript was under revision, a related effect on morpholine and piperazine derivatives was observed: Degorce, S. L.;
Bodnarchuk, M. S.; Cumming, I. A.; Scott, J. S. Lowering lipophilicity by adding carbon: one-carbon bridges of morpholines and
piperazines. J. Med. Chem. 2018, in press (DOI: 10.1021/acs.jmedchem.8b01148).
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based on 3-(1,3,4-thiadiazol-2yl) propanoic acid scaffold. J. Enzyme Inhib. Med. Chem. 2016, 24, 2954–2963.
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