3-((Hetera)cyclobutyl)azetidines, "stretched" Analogues of Piperidine, Piperazine, and Morpholine: Advanced Building Blocks for Drug Discovery

Article abstract of DOI:10.1021/acs.joc.8b02822

Four 3-((hetera)cyclobutyl)azetidine-based isosteres of piperidine, piperazine, and morpholine were designed and synthesized on up to gram scale. The key step of the synthetic sequence included cyclization of N-protected 2-(azetidin-3-yl)propane-1,3-diol

Full text of DOI:10.1021/acs.joc.8b02822

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Article
3-((Hetera)cyclobutyl)azetidines – “stretched” analogues of piperidine,
piperazine and morpholine: advanced building blocks for drug discovery
Illia O. Feskov, Anton V. Chernykh, Yuliya O. Kuchkovska, Constantin
G. Daniliuc, Ivan S. Kondratov, and Oleksandr O. Grygorenko
J. Org. Chem., Just Accepted Manuscript • DOI: 10.1021/acs.joc.8b02822 • Publication Date (Web): 24 Dec 2018
Downloaded from http://pubs.acs.org on December 25, 2018
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3-((Hetera)cyclobutyl)azetidines – “stretched”
analogues of piperidine, piperazine and morpholine:
advanced building blocks for drug discovery
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Illia O. Feskov,a,b Anton V. Chernykh,a Yuliya O. Kuchkovska,a,c Constantin G. Daniliuc,d Ivan S.
Kondratova,b* and Oleksandr O. Grygorenkoa,c*
a Enamine Ltd. (www.enamine.net) Chervonotkatska Street 78, Kyiv 02094, Ukraine
b Institute of Bioorganic Chemistry & Petrochemistry, NAS of Ukraine, Murmanska Street 1,
Kyiv 02660, Ukraine
c National Taras Shevchenko University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine
d Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstrasse 40,
48149 Münster, Germany
*E-mail: kondratov@mail.enamine.net (I.S.K.); gregor@univ.kiev.ua (O.O.G.)
KEYWORDS: Isosteres, Cyclization, Cyclobutanes, Oxetanes, Thietanes, Azetidines
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ABSTRACT. Four 3-((hetera)cyclobutyl)azetidine-based isosteres of piperidine, piperazine, and
morpholine were designed and synthesized on up to gram scale. The key step of the synthetic
sequence included cyclization of N-protected 2-(azetidin-3-yl)propane-1,3-diol or the correspon-
ding 1,3-dibromide. X-ray diffraction studies of the products obtained, followed by exit vector
plot analysis of their molecular geometry demonstrated their larger size and increased
conformational flexibility as compared to the parent heterocycles, and confirmed their potential
utility as building blocks for lead optimization programs.
INTRODUCTION
According to the recent extensive analysis of cyclic fragments in contemporary
pharmaceuticals, piperidine, piperazine and morpholine occurred among top 20 heterocycles1
and top 30 general ring systems2 that were found in small molecule FDA approved drugs. Many
efforts of current research have been put into design of structures that are topologically similar to
the aforementioned scaffolds, whilst have slightly different geometrical and/or electronic
parameters (i.e. bioiososteric replacements).3 In many cases, such little structural alternation
allowed to increase ligand selectivity and improve their pharmacokinetic properties.4,5
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R
(a)
O
S O
CO2H
Cl
N
O
O
N
N
N
N
N
S
R =
O
N
7
1a
1b
1c
1d
1e
8
9
N
1a 1b
97 136 10 10
18 14 >30 >30
1c 1d
1e
1
CF3
IC50(nM)
MLM t1/2 (min)
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F
R
(b)
(c)
O
S
F3C
O
R
N
S
O
HN
O
H2N
O
Cl
2
3
Cl
O
O
O
O
R =
R =
O
Cl
2a
N
N
2b
2b
3a
3b
3a
3c
3c
2a
3b
EC50 (nM)
HLM CLint (L/min/mg)
IC50 (nM)
HLM CLint (mL/min/kg)
33
17
12
9
45.2 8.58 16.9
156 114 28.6
Figure 1. Some bioisosteric replacements of saturated six-membered heterocycles which
resulted in improved potency and/or metabolic stability: (a) 11β-hydroxysteroid dehydrogenase
type I inhibitors; (b) serotonin receptor subtype 2C agonists; (c) γ-secretase inhibitors
Among numerous possibilities available for design of piperidine, piperazine and morpholine
bioisosteres, several approaches are worth mentioning here. In particular, extension of this
heterocycle series with derivatives bearing sulfone or carboxylic functional groups can be
suggested. Indeed, variation of the heteroaromatic side chain in a series of 11β-hydroxysteroid
dehydrogenase type I (11β-HSD1) inhibitors 1 revealed that improved potency and metabolic
stability in mouse liver microsomes (MLM) was observed for derivatives 1d and 1e as compared
to the parent piperidine 1a, piperazine 1b and morpholine 1c (Figure 1a).6 Variation of the ring
size is another possible option; in this view, four-membered carbo- and heterocycles have
attracted much attention.7–10 For example, replacement of the piperidine ring in the molecule of
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serotonin receptor subtype 2C (5-HT2C) agonist 2a with azetidine fragment resulted in improved
human liver microsomal (HLM) stability and lowered EC50 value (Figure 1b).11 Similar effect
was observed when tetrahydropyran was replaced by oxetane in a course of optimization of N-
arylsulfonamide-based γ-secretase inhibitors 3 (Figure 1c).12
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Being inspired by these successful examples, we have designed four novel piperidine,
piperazine and morpholine surrogates 4–7 which are based on the structural modifications
mentioned above (i.e. the use of four-membered rings and/or incorporation of sulfone and
carboxylic acid functionalities) (Figure 2). It should be noted that a number of fused, bridged and
spirocyclic analogues of the parent saturated six-membered heterocycles were described in the
literature.13–16 These bicyclic ring systems have already proven their value for medicinal
chemistry:17–26 some of them can be found in the structures of marketed drugs, e.g. boceprevir27,
gliclazide28, ledipasvir27 etc. Nevertheless, all these surrogates were obtained by introducing
additional conformational restriction to the piperidine, piperazine and morpholine rings; on the
contrary, the molecules of 4–7 are more flexible as compared to the parent structures due to the
presence of a rotatable bond.
previous works
this work
X
X
X NR1
N
CO2H
O O
S
R1
Boc
N
O
N
O
N
R1
R1
(88/562)
(101/532)
(173/473)
N
R1
N
H
R1N
(27/289)
X
N
H
N
N
H
1N
X
R2
N
R1N
X
R
Boc
4
5
6
7
(26/438)
(135/1100)
N
X = O, NR2, S (in any state), CR2R3
R1
Figure 2. Surrogates of piperidine, piperazine and morpholine (values in brackets correspond to
numbers of papers/patents reporting biological activity according to Reaxys® database29)
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In this work, we have developed an approach to the synthesis of all four building blocks 4–7
which allowed for their preparation on up to gram scale. In addition to that, structural
characterization of these novel scaffolds was performed using an exit vector plot (EVP) tool,
which was applied to the data of X-Ray diffraction studies.
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RESULTS AND DISCUSSION
Synthesis. Previously, nucleophilic substitution of 1,3-dielectrophiles by electron-rich carbon-
or heteroatom-containing reagents has proven itself as an efficient approach towards four-
membered ring construction.8,30,31 This method was successfully applied for similar
spiro[3.3]heptane synthesis;32–36 therefore, it was envisaged for the key retrosynthetic
disconnection of 4–7 (Scheme 1). Since all our target structures contained azetidine fragment, N-
protected azetidin-3-ol derivative 8 was used as a starting material. The choice of the benzhydryl
protecting group was guided by its stability towards LiAlH4 reduction implied by the developed
synthetic strategy, as well as increase in lipophilicity of the intermediates involved into the
synthetic scheme, which should facilitate their isolation and purification.
O
O
Z
Z
X
EtO
OEt
+
OH
N
N
R1
R1
N
R1
X = NH, O, SO2, CHCOOH
1  protecting group or H
Z  good leaving group
R
Scheme 1. Retrosynthetic analysis of the compounds 4–7
The synthesis commenced with preparation of diester 10 using a slightly modified literature
method,37 i.e. mesylation of alcohol 8, followed by nucleophilic substitution in the intermediate
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mesylate 9 with diethyl malonate sodium salt (75% yield for two steps) (Scheme 2). The
subsequent reduction of 10 with LiAlH4 gave diol 11 (78% yield). The compound 11 was
subjected to the protecting group replacement (i.e. benzhydryl to Boc), which was achieved by
hydrogenolysis of 11 using 10% Pd-C as the catalyst in presence of Boc2O and led to diol 12
(69% yield). Notably, hydrogenolysis of 11 using Pd(OH)2 as the catalyst under similar
conditions resulted in a mixture of the target compound 12 with unidentified by-products.
The next steps required transformation of the hydroxyl moieties in the molecule of the diol 12
into good nucleofuges. Our preliminary attempts relied on the use of sulfonates as the leaving
groups; however, transformation of 12 into the corresponding 1,3-ditriflate or 1,3-dimesylate,
followed by reaction with benzylamine or tosylamine appeared to be unfruitful. In the latter case,
removal of the tosyl group could not be achieved with satisfactory yield using neither Na–Hg nor
Mg in MeOH as the reducing reagents. Therefore, we have switched to 1,3-dibromide 13, which
appeared to be relatively stable and could be obtained by Appel reaction in 81% yield.
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EtOOC
COOEt
OH
N
OMs
N
MsCl
Et3N
CH2(CO2Et)2
NaH, DMF
LiAlH4
THF
78%
CH2Cl2
98%
77%
N
Ph
Ph
Ph
Ph
Ph
Ph
8
9
10
OH OH
H2, 1 atm
10% Pd-C
Boc2O
OH OH
Br Br
Br2, PPh3
Et3N
CH2Cl2
EtOAc
N
69%
81%
N
N
Boc
Boc
Ph
Ph
11
12
13
Scheme 2. Synthesis of the intermediate dibromide 13
Reaction of the dibromide 13 with benzylamine gave the corresponding N-benzyl derivative 14
(83% yield), which was subjected to hydrogenolysis using 10% Pd-C as a catalyst.
Unfortunately, the product 4 obtained as a free base decomposed slowly upon standing.
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Therefore, isolation of the 3,3-biazeditine derivative 4 as an oxalate salt32 was envisaged to
improve stability of this compound. Thus, hydrogenolysis of intermediate 14 using 10% Pd-C as
the catalyst in the presence of oxalic acid gave oxalate 40.5H2C2O4 in good yield (91%)
(Scheme 3).
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CF3COO-
O O
S
O O
S
S
TFA
CH2Cl2
m-CPBA
CH2Cl2
90%
85%
N
N
N
Boc
H2
Boc
15
16
5·
CF3COOH
Na2S·5H2O
2-
99%
0.5 C2O4
CH3CN, 50 °C
H2
N
Bn
N
Br Br
H2,1 atm
10% Pd-C
H2C2O4
BnNH2
i-Pr2NEt
91%
83%
N
N
N
Boc
Boc
Boc
13
14
4·
0.5H2C2O4
CH2(CO2Et)2
86%
NaH, DMF, 75 °C
HO
O
EtO2C CO2Et
HO2C CO2H
LiOH
pyridine
reflux
THFH2O
89%
99%
N
N
N
Boc
Boc
Boc
17
18
6
Scheme 3. Synthesis of the building blocks 4–6
Synthesis of sulfone-containing building block 5 commenced with reaction of 13 and Na2S,
which gave thietane 15 in nearly quantitative yield. Subsequent oxidation of 15 with m-CPBA,
followed by deprotection of 16 with TFA gave 5 as a trifluoroacetate salt (76% yield over two
steps). Analogously, the amino acid 6 was synthesized in three steps including reaction of 13
with malonic ester sodium salt, alkaline hydrolysis of diester 17, and decarboxylation of the
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corresponding dicarboxylic acid 18 in pyridine (76% yield from 13, ca. 1:1 mixture of
diastereomers).
7
8
9
Initially, we tried to synthesize 3-(oxetan-3-yl)azetidine (7) by intramolecular cyclization of
the diol 12. However, the subsequent removal of the N-Boc protective group in acidic medium
using either HCl – Et2O or TFA – CH2Cl2 was accompanied by partial oxetane ring opening. In
order to avoid the use of strong acids at the deprotection step, intramolecular cyclization with the
benzhydryl protected compound 11 was performed. The oxetane-containing intermediate 19 was
synthesized using the method of Moulines et al.,38 namely, one-pot sequential treatment of a 1,3-
diol with n-BuLi, TsCl, and another equivalent of n-BuLi. In the case of 11, this reaction
sequence gave the target product 19 in 42% yield (Scheme 4). Finally, hydrogenolysis of 19 in
the presence of oxalic acid resulted in the formation of 7, which was isolated as an oxalate salt in
86% yield.
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2
0.5 C2O4
OH OH
H2 (1 atm)
10% Pd-C
H2C2O4
O
O
1. n-BuLi
TsCl
2. n-BuLi
42%
86%
N
N
N
H2
Ph
Ph
Ph
Ph
19
7·
0.5H2C2O4
11
Scheme 4. Synthesis of the building block 7
EVP analysis. To validate the anticipated isosterism of 4–7 with saturated six-membered
heterocycles, we have compared their three-dimensional structure using the exit vector plot
(EVP) tool.39,40 One of the main features of this method is visualization of the bifunctional
scaffolds in the chemical space, which can be used to discuss the molecular geometry of diverse
compounds classes. To generate the EVPs, exit vectors n1 and n2 are introduced simulating the
functional groups (or any substituents) attached to the scaffold (Figure 3). The distance r
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between the two variation points of the scaffold (X1 and X2) is used to assess the size of the
scaffold, whereas two plane angles φ1 (between vectors n1 and X1X2) and φ2 (between vectors n2
and X2X1), as well as the dihedral angle θ defined by vectors n1, X1X2, and n2 describe its three-
dimensionality. Depiction of these parameters in r – θ and θ – φ1/φ2 coordinates introduces the
background for EVP-based chemical space analysis and provides a straightforward tool for
rational scaffold replacement.
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Figure 3. (a) Definition of exit vectors n1 and n2. (b) Definition of geometric parameters r, φ1, φ2
and θ.
Figure 4. ORTEP diagram for compounds 4–7 (only cations are shown for the compounds
4·0.5H2C2O4 (two independent cations in the asymmetric unit), 5·CF3COOH and
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7·0.5H2C2O4; for cis-6, only position A with the main occupancy (60%) is presented). Thermal
5
6
ellipsoids are shown at 50% probability level
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X-Ray single crystal diffraction studies of the compounds 4–7 revealed that in the case of 4,
two crystallographically independent cations (A and B) with similar molecular geometry were
found in the asymmetric unit (Figure 4). In the case of 6, the crystals which were subjected to the
X-Ray analysis contained only cis-isomer (cis-6); the two four-membered rings were disordered
over two positions (A and B) with 60% and 40% occupancies, respectively (see the SI for more
details).
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Table 1. Geometric parameters r, φ1, φ2, and θ for 4–7.
compound
r (Å) φ1 (°) φ2 (°) |θ| (°)a
b
4·0.5H2C2O4
cation A
5.301 25.1 17.0 169.2
cation B
5.317 27.4 6.4
171.7
5·CF3COOH
5.371 47.4 7.0
4.8
cis-6c
position A
position B
5.459 49.6 20.6 166.7
5.459 45.0 5.5 159.5
7·0.5H2C2O4
4.229 56.7 54.5 40.9
a Since the signs of θ angle are opposite for different enantiomeric conformations, only
absolute values of θ are considered. b Two independent cations in the asymmetric unit. c The two
four-membered rings were disordered over two positions (A and B) with 60% and 40%
occupancies, respectively
These data were used to calculate the values of the aforementioned geometrical parameters r,
φ1, φ2 and θ for the compounds 4, 5, cis-6, and 7 were calculated from the X-ray diffraction data
(Table 1). When assigning the plane angles φ1 and φ2, we let φ1 > φ2 (as it was done in the
previous works39,41). The size of the scaffolds 4–7 is varied in a relatively wide range (r = 4.23–
5.46 Å) depending on the conformation of the molecule (Figure 5). Expectedly, they are
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significantly larger as compared to the 1,4-disubstituted six-membered saturated heterocycles
(r = 2.43–3.22 Å39,40) and get close to 2,6-disubstituted (aza)spiro[3.3]heptanes (r ~ 4.13 Å42).
The building blocks 4 and 6 adopt extended conformation which can be described as a “stretched
chair”, which correspond to larger values of r (5.30 Å (4A), 5.32 Å (4B), and 5.46 Å (6)). In the
θ – φ1/φ2 plot, these molecules are located in the  region (|θ| = 160–172, φ1 = 25–50, φ2 = 6–
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21), which is characteristic for the typical chair conformations of 1,4-disubstituted six-
membered saturated heterocycles with equatorial position of the substitutent(s).
Figure 5. Geometric parameters of 4·0.5H2C2O4, 5·CF3COOH, cis-6 and 7·0.5H2C2O4 shown in
the (a) r – θ plot (polar coordinates), and (b) θ – φ1/φ2 plot.
In the case of 5, the corresponding data point is located in the  region of the θ – φ1/φ2 plot
(|θ| = 5, φ1 = 47, φ2 = 7). The molecular conformation of 5 can be described as a “stretched
boat”, which is characterized by r = 5.37 Å, which is close to that of 4 and 6. Such angle values
are characteristic for cis-1,4-disubstituted cyclohexanes, and are encountered for less common
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conformations of 1,4-disubstituted six-membered saturated heterocycles with axial position of
one of the substituents. The molecule of 7 adopts a “stretched twist” conformation, which results
in the lowest r value (4.23 Å) in a series studied. In the θ – φ1/φ2 plot, the corresponding data
point is shifted towards “three-dimensional” area which is remote from the θ = 0/180 and
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φ1/φ2 = 0 lines (|θ| = 41, φ1 = 57, φ2 = 54).
These data show that the scaffolds of 4–7 can adopt a number of conformations, both similar to
that of the parent six-membered saturated heterocycles (with |θ| close to 0 or 180) and more
“three-dimensional” (with |θ| being far from these boundary values). Therefore, the building
blocks developed in this work can be used as “stretched” analogues of piperidine, piperazine and
morpholine with slightly enhanced conformational flexibility.
CONCLUSIONS
Cyclization of N-protected 2-(azetidin-3-yl)propane-1,3-diol or the corresponding 1,3-dibro-
mide is a convenient method for the preparation of 3-((hetera)cyclobutyl)azetidines, in particular,
3-(oxetan-3-yl)- and 3-(thietan-3-yl)azetidine, 3,3'-biazetidine, as well as 3-(azetidin-3-yl)cyclo-
butanecarboxylic acid derivatives (compounds 4–7). The target compounds were prepared in 5–8
steps from the commercially available materials in 21–25% overall yields on up to 24 g scale.
Analysis of molecular geometry of the compounds described in this paper using exit vector plot
(EVP) tool shows that their scaffolds can be considered “stretched” analogues of piperidine,
piperazine and morpholine with diminished conformational restriction, which provides access
not only to the molecular geometries covered by the parent heterocycles, but also to “three-
dimensional” areas of chemical space. Therefore, the azetidine derivatives obtained in this work
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are promising advanced building blocks for extensive application in drug discovery programs, in
particular, for the isosteric replacement of saturated six-membered heteroaliphatic rings.
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EXPERIMENTAL SECTION
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General Methods. The solvents were purified according to the standard procedures.43 All
starting materials were purchased from commercial sources. Melting points were measured on
automated melting point system. Column chromatography was performed using Kieselgel Merck
1
60 (230–400 mesh) as the stationary phase. H and 13C NMR spectra were recorded at
499.9 MHz or 400.4 MHz and 124.9 MHz or 100.7 MHz, respectively. Chemical shifts are
reported in ppm downfield from TMS as an internal standard. Elemental analyses were
performed at the Laboratory of Organic Analysis, Department of Chemistry, National Taras
Shevchenko University of Kyiv. Mass spectra were recorded on an Agilent 1100 LCMSD SL
instrument (chemical ionization (APCI), electrospray ionization (ESI)) and Agilent 5890 Series
II 5972 GCMS instrument (electron impact ionization (EI)). The X-Ray diffraction data sets
were collected with a CMOS diffractometer for the compounds 40.5H2C2O4, cis-6 and
70.5H2C2O4 and with a CCD diffractometer for the compound 5CF3COOH. Single crystals
were obtained by slow evaporation of the compound solutions in MeCN (40.5H2C2O4 and
5CF3COOH), hexane (cis-6) or MeOH (70.5H2C2O4). Programs used in the X-Ray diffraction
studies: data collection: APEX3 V2016.1-0;44 cell refinement and data reduction: SAINT
V8.37A;45 absorption correction, SADABS V2014/7;46 structure solution and structure
refinement, SHELXT-2015.47 R-values are given for observed reflections, and wR2 values are
given for all reflections. CCDC-1868836 (40.5H2C2O4), CCDC-1868837 (5CF3COOH),
CCDC-1868838 (cis-6) and CCDC-1868839 (70.5H2C2O4) contain the supplementary
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crystallographic data for this paper. These data can be obtained free of charge from The
Cambridge Crystallographic Data Centre via www.ccdc.cam.ac.uk/data_request/cif.
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1-Benzhydrylazetidin-3-yl methanesulfonate (9).48,49 Et3N (13.1 mL, 94.0 mmol) was added
to a solution of 1-benzhydrylazetidin-3-ol (8) (15.0 g, 62.7 mmol) in CH2Cl2 (150 mL) and
reaction mixture was cooled to –20 °C. Methanesulfonyl chloride (8.61 g, 75.2 mmol) was added
dropwise maintaining the temperature below –20 °C. When addition was completed the reaction
mixture was allowed to warm to rt and then poured into H2O (100 mL). The organic layer was
separated, washed with 10% aq NaHCO3 (350 mL), dried over anhydrous Na2SO4 and
concentrated under reduced pressure to give the title compound. White solid, mp 114–116 °C
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(lit.48 mp 115–116 °C); 98% yield (19.5 g). H NMR (400 MHz, CDCl3): δ 7.40 (d, J = 7.4 Hz,
4H), 7.28 (t, J = 7.4 Hz, 4H), 7.20 (t, J = 7.2 Hz, 2H), 5.10 (quint, J = 5.8 Hz, 1H), 4.42 (s, 1H),
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3.68 – 3.59 (m, 2H), 3.24 – 3.16 (m, 2H), 2.94 (s, 3H). C{1H} NMR (101 MHz, CDCl3): δ
141.4, 128.7, 127.5, 127.4, 78.2, 68.0, 60.2, 38.1. LCMS (m/z): 318 (M+H+). Anal. Calcd for
C17H19NO3S: C, 64.33; H, 6.03; N, 4.41; S, 10.10. Found: C, 64.42; H, 5.88; N, 4.21; S, 10.12.
Diethyl 2-(1-benzhydrylazetidin-3-yl)malonate (10).37 Diethylmalonate (14.4 g, 89.9 mmol)
was added dropwise to a suspension of NaH (60% in mineral oil, 3.27 g, 81.8 mmol) in DMF (90
mL) while the temperature of the reaction mixture was maintained below 25 °C. After stirring for
additional 1 h, a solution of 1-benzhydrylazetidin-3-yl methanesulfonate (9) (13.0 g, 41.0 mmol)
in DMF (20 mL) was added. The reaction mixture was stirred at 70 °C for 2 d, then cooled to rt,
poured into H2O (200 mL) and extracted with EtOAc (2200 mL). The combined organic layers
were washed with H2O (3150 mL), brine (100 mL), dried over Na2SO4 and concentrated under
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reduced pressure. An excess of diethylmalonate was distilled off (1 mmHg, 50–60 °C), and the
residue was purified by column chromatography on silica gel (hexanes – EtOAc – Et3N (8:1:0.5)
as eluent, Rf = 0.4) to afford the title product. White solid, mp 72–74 °C; 77% yield (12.0 g). 1H
NMR (400 MHz, CDCl3): δ 7.38 (d, J = 7.3 Hz, 4H), 7.25 (t, J = 7.4 Hz, 4H), 7.17 (t, J = 7.2 Hz,
2H), 4.32 (s, 1H), 4.21 – 4.09 (m, 4H), 3.64 (d, J = 10.5 Hz, 1H), 3.37 (t, J = 7.1 Hz, 2H), 3.07 –
2.96 (m, 1H), 2.90 (t, J = 6.5 Hz, 2H), 1.23 (t, J = 7.1 Hz, 6H). 13C{1H} NMR (101 MHz,
CDCl3): δ 168.4, 142.1, 128.5, 127.5, 127.2, 78.1, 61.5, 57.8, 55.9, 29.5, 14.2. LCMS (m/z): 382
(M+H+), 380 (M–H+). Anal. Calcd for C23H27NO4: C, 72.42; H, 7.13; N, 3.67. Found: C, 72.68;
H, 6.98; N, 3.53.
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2-(1-Benzhydrylazetidin-3-yl)propane-1,3-diol (11). To a suspension of LiAlH4 (2.87 g,
75.5 mmol) in THF (150 mL), diethyl 2-(1-benzhydrylazetidin-3-yl)malonate (10) (12.0 g, 31.4
mmol) was added dropwise at rt, and the reaction mixture was stirred overnight. The reaction
mixture was cooled to 0 °C and H2O (3 mL) was added carefully, followed by 50% aq NaOH (3
mL) and H2O (15 mL). The suspension was stirred for additional 30 min and then filtered. The
solids were washed with THF (2100 mL) and the combined filtrates were evaporated under
reduced pressure. The residue was dissolved in CH2Cl2 (200 mL), dried over anhydrous Na2SO4,
and concentrated under reduced pressure. The crude product was purified by column
chromatography (CH2Cl2 – MeOH – Et3N (92:3:5) as eluent, Rf = 0.35) to give 11. Amorphous
white solid, mp 112–115 °C; 78% yield (7.27 g). 1H NMR (500 MHz, CDCl3): δ 7.38 (d, J = 7.4
Hz, 4H), 7.27 (t, J = 7.5 Hz, 4H), 7.19 (t, J = 7.3 Hz, 2H), 4.37 (s, 1H), 3.92 (br s, 2H), 3.71 –
3.56 (m, 4H), 3.33 (t, J = 7.6 Hz, 2H), 2.98 (t, J = 6.6 Hz, 2H), 2.51 – 2.41 (m, 1H), 2.01 – 1.88
(m, 1H). 13C{1H} NMR (126 MHz, CDCl3): δ 141.5, 128.7, 127.5, 127.4, 78.2, 63.3, 58.0, 46.2,
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29.1. LCMS (m/z): 298 (M+H+). Anal. Calcd for C19H23NO2: C, 76.74; H, 7.80; N, 4.71. Found:
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C, 76.65; H, 8.16; N, 4.34.
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tert-Butyl 3-(1,3-dihydroxypropan-2-yl)azetidine-1-carboxylate (12). 10% Pd-C (1.50 g)
was added to a solution of 2-(1-benzhydrylazetidin-3-yl)propane-1,3-diol (11) (15.0 g, 50.4
mmol) and Boc2O (16.5 g, 75.6 mmol) in EtOAc (200 mL). The resulting mixture was
hydrogenated at 1 atm and rt for 3 d. The catalyst was filtered off, the solvent was evaporated
under reduced pressure, and the residue was purified by column chromatography (CH2Cl2 –
MeOH (10:1) as eluent, Rf= 0.36) to give the title product. Amorphous white solid, mp 79–
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81 °C; 69% yield (8.03 g). H NMR (400 MHz, CDCl3): δ 3.95 (t, J = 8.5 Hz, 2H), 3.72 – 3.63
(m, 4H), 3.56 (dd, J = 10.7, 6.5 Hz, 2H), 3.49 (s, 2H), 2.62 – 2.47 (m, 1H), 1.91 – 1.79 (m, 1H),
1.38 (s, 9H). 13C{1H} NMR (101 MHz, CDCl3): δ 156.5, 79.7, 62.5, 52.8, 46.2, 28.4, 27.4.
LCMS (m/z): 132 (M+H+–CO2–C4H9). Anal. Calcd for C11H21NO4: C, 57.12; H, 9.15; N, 6.06.
Found: C, 57.23; H, 8.85; N, 6.12.
tert-Butyl 3-(1,3-dibromopropan-2-yl)azetidine-1-carboxylate (13). To a solution of PPh3
(82.6 g, 315 mmol) in CH2Cl2 (450 mL), Br2 (50.4 g, 315 mmol) was added dropwise at 0 °C,
and the reaction mixture was stirred at the same temperature for 1 h. Then Et3N (43.9 mL, 315
mmol) was added dropwise while the temperature was maintained below 5 °C, and the reaction
mixture was stirred for additional 1 h. A solution of tert-butyl 3-(1,3-dihydroxypropan-2-
yl)azetidine-1-carboxylate (12) (24.3 g, 105 mmol) in CH2Cl2 (100 mL) was added dropwise at
0 °C. When the addition was complete, the reaction mixture was allowed to warm to rt and
stirred overnight. The resulting light brown suspension was poured into H2O (500 mL), and the
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organic layer was separated. The aqueous layer was extracted with CH2Cl2 (2250 mL), and the
combined organic layers were washed with saturated aq NaHCO3 (250 mL), dried over
anhydrous Na2SO4, and concentrated under vacuum. The residue was washed with petroleum
ether (500 mL), the solids were filtered off, and the filtrate was evaporated under reduced
pressure. The crude product was purified by flash column chromatography (hexanes – EtOAc
(7:1) as eluent, Rf = 0.25) to give the title product. White solid, mp 107–109 °C; 81% yield (30.4
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g). H NMR (500 MHz CDCl3): δ 4.03 (t, J = 8.4 Hz, 2H), 3.79 – 3.64 (m, 2H), 3.57 (dd, J =
10.5, 3.0 Hz, 2H), 3.41 (dd, J = 10.4, 6.6 Hz, 2H), 2.71 – 2.59 (m, 1H), 2.27 – 2.18 (m, 1H), 1.43
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(s, 9H). C{1H} NMR (126 MHz, CDCl3): δ 156.2, 79.8, 52.8, 45.7, 32.9, 31.0, 28.5. LCMS
(m/z): 258 (M+H+–CO2–C4H9). Anal. Calcd for C11H19Br2NO2: C, 37.00; H, 5.36; N, 3.92; Br,
44.75. Found: C, 36.66; H, 5.45; N, 3.57; Br, 44.59.
tert-Butyl 1'-benzyl-[3,3'-biazetidine]-1-carboxylate (14). Benzylamine (15.0 g, 0.140 mol)
and i-Pr2NEt (61.1 mL, 0.350 mol) were added to a solution of tert-butyl 3-(1,3-dibromopropan-
2-yl)azetidine-1-carboxylate (13) (25.0 g, 70.0 mmol) in CH3CN (400 mL), and the reaction
mixture was heated at reflux overnight. The solution was cooled to rt and concentrated to about
1/6 of the initial volume. The residue was dissolved in EtOAc (500 mL) and washed with H2O
(300 mL). The aqueous layer was separated and extracted with EtOAc (2250 mL). The
combined organic layers were washed with saturated aq NaHCO3 (2300 mL), dried over
anhydrous Na2SO4 and concentrated under reduced pressure. The crude product was purified by
flash column chromatography (hexanes – EtOAc – Et3N (2:1:0.2) as eluent, Rf = 0.32) to give
the title compound. Light-yellow oil; 83% yield (17.6 g). 1H NMR (500 MHz, CDCl3): δ 7.34 –
7.27 (m, 2H), 7.27 – 7.19 (m, 3H), 3.98 (t, J = 8.3 Hz, 2H), 3.64 – 3.54 (m, 4H), 3.39 – 3.32 (m,
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2H), 2.92 – 2.85 (m, 2H), 2.80 – 2.64 (m, 2H), 1.43 (s, 9H). 13C{1H} NMR (126 MHz, CDCl3): δ
186.7, 156.2, 138.0, 128.3, 128.2, 126.9, 79.2, 63.4, 57.3, 33.5, 31.1, 28.3. LCMS (m/z): 303
(M+H+). Anal. Calcd for C18H26N2O2: C, 71.49; H, 8.67; N, 9.26. Found: C, 71.52; H, 8.94; N,
9.52.
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tert-Butyl [3,3'-biazetidine]-1-carboxylate (4·0.5H2C2O4). To a solution of tert-butyl 1'-
benzyl-[3,3'-biazetidine]-1-carboxylate (14) (17.0 g, 56.2 mmol) and H2C2O4 (2.53 g, 28.1
mmol) in MeOH (300 mL), 10% Pd–C (2.00 g) was added, and the mixture was hydrogenated at
1 atm and rt for 4 d until full conversion of the starting material was observed by TLC. Then the
catalyst was filtered off and washed with MeOH (100 mL), the filtrate was evaporated under
reduced pressure to yield the title compound. White solid, mp = 169–171 °C; 91% yield (10.9 g).
1H NMR (400 MHz, D2O): δ 4.10 – 4.01 (m, 2H), 3.96 (t, J = 8.8 Hz, 2H), 3.81 – 3.71 (m, 2H),
3.50 (dd, J = 9.2, 5.2 Hz, 2H), 3.16 (sext, J = 8.4 Hz, 1H), 2.85 – 2.73 (m, 1H), 1.29 (s, 9H).
13C{1H} NMR (126 MHz, D2O): δ 171.6, 157.9, 81.8, 51.6, 49.2, 34.0, 29.9, 27.6. GCMS (m/z):
212 (M+). Anal. Calcd for C24H42N4O8: C, 56.01; H, 8.23; N, 10.89. Found: C, 55.76; H, 8.54; N,
11.20.
tert-Butyl 3-(thietan-3-yl)azetidine-1-carboxylate (15). To a solution of tert-butyl 3-(1,3-
dibromopropan-2-yl)azetidine-1-carboxylate (13) (41.1 g, 115 mmol) in a mixture of CH3CN (1
L) and H2O (100 mL), Na2S·5H2O (38.6 g, 230 mmol) was added and the reaction mixture was
stirred at 50 °C for 12 h. Then it was allowed to cool to rt and was concentrated under vacuum.
The residue was diluted with EtOAc (1 L) and washed with H2O (2500 mL). The aqueous
phase was extracted with EtOAc (2500 mL). The combined organic layers were washed with
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brine (500 mL), dried over anhydrous Na2SO4 and concentrated under reduced pressure to give
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the title compound. Crystalline white solid, mp = 76–78 °C; 99% yield (26.2 g). H NMR (400
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8.9 Hz, 2H), 2.95 – 2.87 (m, 2H), 2.82 – 2.69 (m, 1H), 1.40 (s, 9H). C{1H} NMR (101 MHz,
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CDCl3): δ 156.3, 79.5, 51.7, 42.3, 33.1, 28.4, 28.1. LCMS (m/z): 130 (M+H+–CO2–C4H9) Anal.
Calcd for C11H19NO2S: C, 57.61; H, 8.35; N, 6.11; S, 13.98. Found: C, 57.51; H, 8.66; N, 6.17;
S, 13.74.
tert-Butyl 3-(1,1-dioxidothietan-3-yl)azetidine-1-carboxylate (16). A solution of tert-butyl
3-(thietan-3-yl)azetidine-1-carboxylate (15) (26.2 g, 114 mmol) in CH2Cl2 (250 mL) was treated
with m-chloroperoxybenzoic acid (85%, 70.0 g, 239 mmol) in CH2Cl2 (700 mL) at 0 °C. The
reaction mixture was allowed to warm to rt and stirred overnight, then the solids were filtered off
and filtrate was washed with saturated aq. Na2S2O3 (400 mL), 10% aq. Na2CO3 (400 mL) and
H2O (400 mL). The organic layer was dried over anhydrous Na2SO4 and concentrated under
vacuum to give the title compound. Amorphous beige solid, mp = 177–179 °C dec.; 90% yield
(26.8 g). 1H NMR (500 MHz, CDCl3): δ 4.24 (dd, J = 14.2, 9.1 Hz, 2H), 4.07 (t, J = 8.3 Hz, 2H),
3.79 (dd, J = 13.7, 5.1 Hz, 2H), 3.57 (dd, J = 8.6, 3.8 Hz, 2H), 2.93 – 2.76 (m, 2H), 1.42 (s, 9H).
13C{1H} NMR (126 MHz, CDCl3): δ 156.0, 79.9, 67.5, 52.1, 31.8, 28.2, 22.3. LCMS (m/z): 162
(M+H+–CO2–C4H9). Anal. Calcd for C11H19NO4S: C, 50.56; H, 7.33; N, 5.36; S, 12.27. Found:
C, 50.29; H, 7.16; N, 5.38; S, 11.88.
3-(1,1-Dioxidothietan-3-yl)azetidin-1-ium 2,2,2-trifluoroacetate (5·CF3COOH). To a
solution of tert-butyl 3-(1,1-dioxidothietan-3-yl)azetidine-1-carboxylate (16) (26.8 g, 103 mmol)
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in CH2Cl2 (270 mL), TFA (135 mL) was added dropwise at 0 °C. The resulting solution was
slowly warmed to rt and left to stir overnight. CH2Cl2 and TFA were distilled off under vacuum,
the residue was dissolved in H2O, solids were filtered off and filtrate was evaporated under
reduced pressure. Drying over P2O5 in desiccator gave the title product. White solid, mp = 110–
112 °C; 85% yield (24.3 g). 1H NMR (500 MHz, D2O): δ 4.41 – 4.30 (m, 2H), 4.17 (t, J = 10.0
Hz, 2H), 3.98 – 3.90 (m, 2H), 3.90 – 3.81 (m, 2H), 3.36 – 3.20 (m, 1H), 3.07 – 2.91 (m, 1H).
13C{1H} NMR (126 MHz, DMSO): δ 158.6 (q, J = 32.1 Hz), 117.00 (q, J = 298.0 Hz), 67.1,
48.8, 34.7, 21.3. LCMS (m/z): 162 (M+H+) Anal. Calcd for C8H12F3NO4S: C, 34.91; H, 4.39; N,
5.09; S, 11.65. Found: C, 34.89; H, 4.37; N, 4.90; S, 11.95.
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Diethyl 3-(1-(tert-butoxycarbonyl)azetidin-3-yl)cyclobutane-1,1-dicarboxylate (17). To a
suspension of NaH (6.05 g of 60% dispersion in mineral oil, 151 mmol) in DMF (270 mL),
diethylmalonate (26.7 g, 166 mmol) was added dropwise maintaining the temperature below 25
°C, and the resulting mixture was stirred for additional hour. A solution of tert-butyl 3-(1,3-
dibromopropan-2-yl)azetidine-1-carboxylate (13) (27.0 g, 75.6 mmol) in DMF (50 mL) was
added and the reaction mixture was stirred at 70 °C overnight, then cooled to rt, poured into H2O
(450 mL) and extracted with EtOAc (2400 mL). The combined organic layers were washed
with H2O (3250 mL), brine (250 mL), dried over anhydrous Na2SO4 and concentrated in
vacuum. The residue was purified by column chromatography (hexanes – EtOAc (3:1),
1
Rf = 0.33) to give the title product. Colorless oil; 86% yield (23.3 g). H NMR (400 MHz,
CDCl3): δ 4.20 – 4.05 (m, 4H), 3.86 (t, J = 8.2 Hz, 2H), 3.45 (dd, J = 8.2, 5.1 Hz, 2H), 2.63 –
2.39 (m, 4H), 2.25 – 2.06 (m, 2H), 1.35 (s, 9H), 1.21 – 1.16 (m, 6H). 13C{1H} NMR (101 MHz,
CDCl3): δ 171.6, 171.3, 156.3, 79.2, 61.5, 61.4, 52.0, 48.8, 32.6, 32.0, 31.6, 28.3, 14.0. LCMS
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(m/z): 256 (M+H+–CO2–C4H9). Anal. Calcd for C18H29NO6: C, 60.83; H, 8.22; N, 3.94. Found:
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C, 61.01; H, 7.89; N, 4.03.
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3-(1-(tert-Butoxycarbonyl)azetidin-3-yl)cyclobutane-1,1-dicarboxylic acid (18). To a
solution of diethyl 3-(1-(tert-butoxycarbonyl)azetidin-3-yl)cyclobutane-1,1-dicarboxylate (17)
(22.0 g, 61.9 mmol) in THF (120 mL), a solution of LiOH·H2O (13.0 g, 310 mmol) in H2O (360
mL) was added. The resulting solution was stirred overnight, diluted with H2O (200 mL),
washed with t-BuOMe (250 mL), and acidified to pH = 3 using 10% aq NaHSO4. The mixture
was extracted with EtOAc (2300 mL), dried over anhydrous Na2SO4 and evaporated under
reduced pressure to give the title product. White solid, mp 160–163 °C dec.; 99% yield (18.5 g).
1H NMR (500 MHz, CDCl3): δ 10.94 – 10.75 (br s, 2H), 3.95 (t, J = 8.3 Hz, 2H), 3.55 (dd, J =
8.2, 5.2 Hz, 2H), 2.77 – 2.62 (m, 3H), 2.62 – 2.52 (m, 1H), 2.35 – 2.25 (m, 2H), 1.40 (s, 9H).
13C{1H} NMR (126 MHz, CDCl3): δ 175.9, 175.4, 157.0, 80.4, 52.34 – 51.27 (br s), 48.6, 32.6,
31.9(2C), 28.3. LCMS (m/z): 200 (M+H+–CO2–C4H9), 298 (M–H+). Anal. Calcd for C14H21NO6:
C, 56.18; H, 7.07; N, 4.68. Found: C, 56.36; H, 6.80; N, 4.53.
3-(1-(tert-Butoxycarbonyl)azetidin-3-yl)cyclobutanecarboxylic acid (6). A solution of 3-(1-
(tert-butoxycarbonyl)azetidin-3-yl)cyclobutane-1,1-dicarboxylic acid (18) (18.2 g, 60.1 mmol)
in pyridine (200 mL) was heated to reflux overnight. After cooling to rt, pyridine was evaporated
under reduced pressure. The residue was diluted with H2O (250 mL), acidified with aq. NaHSO4
to pH~3 and extracted with EtOAc (2250 mL). The combined organic layers were dried over
anhydrous Na2SO4 and concentrated in vacuum. The product was obtained by crystallization
from hexanes – EtOAc (5:1). White solid, mp 103–105 °C; 89% yield (13.6 g). The compound
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was obtained as ca. 1:1 mixture of stereoisomers. 1H NMR (500 MHz, CDCl3): δ 11.31 – 10.67
(br s, 1H), 3.96 (t, J = 8.4 Hz, 1H) , 3.92 (t, J = 8.2 Hz, 1H), 3.61 – 3.46 (m, 2H), 3.12 – 3.05 (m,
0.5H), 3.01 (quint, J = 9.0 Hz, 0.5H), 2.71 – 2.63 (m, 0.5H), 2.63 – 2.56 (m, 0.5H), 2.56 – 2.45
13
(m, 1H), 2.44 – 2.35 (m, 1H), 2.35 – 2.24 (m, 1H), 2.02 – 1.88 (m, 2H), 1.41 (s, 9H). C{1H}
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NMR (126 MHz, CDCl3): δ 181.1 and 180.2, 156.49 and 156.46, 79.51 and 79.48, 52.1 (2C),
34.8 and 34.2, 33.8 and 33.6, 32.8 and 32.7, 28.4, 28.0, 27.5. LCMS (m/z): 254 (M–H+). Anal.
Calcd for C13H21NO4: C, 61.16; H, 8.29; N, 5.49. Found: C, 60.95; H, 8.60; N, 5.44.
1-Benzhydryl-3-(oxetan-3-yl)azetidine (19). To a solution of 2-(1-benzhydrylazetidin-3-
yl)propane-1,3-diol (11) (3.54 g, 11.9 mmol) in THF (70 mL), n-BuLi (2.5 M in hexanes, 4.76
mL, 11.9 mmol) was added slowly at –30 °C and stirred for 15 min. Then p-toluenesulfonyl
chloride (2.27 g, 11.9 mmol) was added and reaction mixture was warmed to rt and stirred for
additional 1 hour. Then reaction mixture was cooled to –30 °C and n-BuLi (2.5 M in hexanes,
4.76 mL, 11.9 mmol) was added and the resulting solution was left to stir at rt for 12 h. The
solution was diluted with H2O (120 mL) and extracted with EtOAc (350 mL). The combined
organic layers were dried over anhydrous Na2SO4 and concentrated under reduced pressure. The
residue was purified by column chromatography (EtOAc:hexanes:Et3N = 1:3:0.5, Rf= 0.53) to
give the title product. Colorless oil; 42% yield (1.39 g). 1H NMR (500 MHz, CDCl3): δ 7.45 (d, J
= 7.7 Hz, 4H), 7.30 (t, J = 7.0 Hz, 4H), 7.21 (t, J = 6.8 Hz, 2H), 4.84 (t, J = 6.3 Hz, 2H), 4.50 (t,
J = 5.4 Hz, 2H), 4.38 (s, 1H), 3.33 (t, J = 7.2 Hz, 2H), 3.30 – 3.22 (m, 1H), 2.93 (t, J = 6.2 Hz,
2H), 2.84 – 2.74 (m, 1H). 13C{1H} NMR (126 MHz, CDCl3): δ 142.2, 128.3, 127.4, 127.0, 77.9,
75.4, 56.4, 37.6, 31.7. LCMS (m/z): 280 (M+H+) Anal. Calcd for C19H21NO: C, 81.68; H, 7.58;
N, 5.01. Found: C, 81.53; H, 7.37; N, 4.85.
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3-(Oxetan-3-yl)azetidin-1-ium oxalate (7·0.5H2C2O4). To a solution of 1-benzhydryl-3-
(oxetan-3-yl)azetidine (19) (1.20 g, 4.29 mmol) and oxalic acid (195 mg, 2.16 mmol) in mixture
EtOAc–THF (3:1) (120 mL), Pd–C (200 mg, 10% on activated coal) was added and the mixture
was stirred under H2 atmosphere (1 atm) for 48 h. Then Pd–C was filtered off and washed with
THF (50 mL), the filtrate was evaporated under reduced pressure to yield the title compound.
Crystalline white solid, mp 148–150 °C dec.; 86% yield (420 mg). 1H NMR (500 MHz, D2O): δ
4.81 (t, J = 7.2 Hz, 2H), 4.35 (t, J = 6.2 Hz, 2H), 4.12 (t, J = 10.0 Hz, 2H), 3.88 – 3.77 (m, 2H),
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3.41 – 3.22 (m, 2H). C{1H} NMR (126 MHz, D2O): δ 173.4, 75.1, 49.3, 36.1, 33.4. GCMS
(m/z): 113 (M+). Anal. Calcd for C14H24N2O6: C, 53.15; H, 7.65; N, 8.86. Found: C, 53.45; H,
7.75; N, 8.59.
ASSOCIATED CONTENT
Supporting Information. The following files are available free of charge:
copies of NMR spectra and results of X-Ray diffraction studies (PDF)
crystallographic information files (CIF)
AUTHOR INFORMATION
Corresponding Author
* E-mail: kondratov@mail.enamine.net (I.S.K.); gregor@univ.kiev.ua (O.O.G.).
Author Contributions
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The manuscript was written through contributions of all authors. All authors have given approval
to the final version of the manuscript.
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ACKNOWLEDGMENT
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The work was funded by Enamine Ltd. The authors thank Prof. Andrey A. Tolmachev for his
encouragement and support.
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