Synthesis of macrocycles containing 1,3,4-oxadiazole and pyridine moieties

Article abstract of DOI:10.1016/j.tetlet.2013.08.099

A series of peptide-like 25-28 membered macrocycles containing 1,3,4-oxadiazoles and pyridines bearing a chiral center scaffold have been synthesized by using known coupling reagents and common protecting groups. The yield of the purified macrocycles was poor on an average, yet it seems to be independent of amino acid substitution or stereochemistry. These macrocycles represent a new class of structures for further development and for future application in high-throughput screening against a variety of biological targets.

Full text of DOI:10.1016/j.tetlet.2013.08.099

Tetrahedron Letters 55 (2014) 305–309
Contents lists available at ScienceDirect
Tetrahedron Letters
journal homepage: www.elsevier.com/locate/tetlet
Synthesis of macrocycles containing 1,3,4-oxadiazole and pyridine
moieties
b
Subba Poojari a, P. Parameshwar Naik b, , G. Krishnamurthy
⇑
a Syngene International Ltd, Biocon Park, Plot Nos. 2 & 3, Bommasandra IV Phase, Jigani Link Road, Bangalore 560 099, India
b Department of P.G. Studies and Research in Chemistry, Sahyadri Science College (Autonomous), Shimoga 577 203, India
a r t i c l e i n f o
a b s t r a c t
Article history:
A series of peptide-like 25–28 membered macrocycles containing 1,3,4-oxadiazoles and pyridines bear-
ing a chiral center scaffold have been synthesized by using known coupling reagents and common pro-
tecting groups. The yield of the purified macrocycles was poor on an average, yet it seems to be
independent of amino acid substitution or stereochemistry. These macrocycles represent a new class
of structures for further development and for future application in high-throughput screening against
a variety of biological targets.
Received 26 June 2013
Revised 22 August 2013
Accepted 24 August 2013
Available online 31 August 2013
Keywords:
Macrocycles
Oxadiazoles
Pyridine
Ó 2013 Elsevier Ltd. All rights reserved.
Aminoacids
Medium and large-sized ring compounds have always been
considered by medicinal chemists as a stand-alone class of mole-
cules, not only due to their interesting physico-chemical and bio-
logical properties, but also due to the challenge of their
synthesis.1 Natural products contain a wide variety of conforma-
tionally constrained, macrocyclic, peptide based rings that present
both as backbone and side chain pharmacophoric groups for inter-
acting with biological targets.2 Such biologically active compounds
are generally used by plants and animals in chemical warfare in or-
der to gain an advantage against competitors or assaults.3 Peptide
based macrocycles from marine sources continue to be investi-
gated for their biological activity,3,4 as are similar compounds from
plants.5
Medicinal chemists have long used macrocyclization as a tool in
drug discovery. A classic illustration of this technique was the dis-
covery of potent cyclic peptide somatostatin mimics three decades
ago.6,7 The method of cyclization since then developed into a gen-
eral paradigm in peptidomimetic drug design that has been widely
used in the discovery of biologically-active compounds for study-
ing the cell.8 Indeed, there are both natural product and synthetic
macrocyclic peptides with known anticancer use or potential9
thereby illustrating their functional similarity.
peptides, cyclic peptides also resist proteolytic degradation and
other metabolisms.
In view of the above aspects of cyclization of peptides, we re-
port the synthesis and characterization of peptide-like macrocyclic
compounds that contain oxadiazoles and pyridine, thereby yield-
ing a unique compound class from macrocyclic natural products
and known paradigms in drug discovery. The final compounds
are 25–28 membered macrocycles with variations in stereochem-
istry and amino acid side chains. Indeed, macrocycles are under-
represented in screening libraries due in part to their synthetic
challenge14,15 and some biologically active compounds as shown
in Figure 1.
It is important to note that these macrocycles represent a new
class of compounds. Their features mimic those of known bioactive
natural products, and we anticipate that such compounds would
have reasonable pharmacokinetic properties. The presence of
intrinsic points of diversity allows for the introduction of addi-
tional pharmacophores into the periphery, which has been selected
by comparing known drugs and natural products.
The synthetic plan for the macrocyclic construction is summa-
rized in Scheme 1. The core intermediate 7 was prepared from
methyl 5-(4-aminophenyl)pyridine-3-carboxylate 6 by reacting
with 4-carboxybenzaldehyde under reductive amination condi-
tions.16 Introduction of pinacolborane moiety by Miyaura–Ishiy-
ama protocol afforded 4 in good yield.17 Boronate 4 was coupled
with commercially available amino protected bromo compound 2
under Suzuki coupling conditions to afford pyridine biphenyl 5 in
81%.18 Deprotection of tert-butyl carbamate in acidic media gave
6 in good yield.
Several research groups have reported the synthesis of macro-
cyclic peptides containing heterocyclic amino acids.10–13 In addi-
tion to the potency and selectivity gained by macrocyclization of
⇑
Corresponding author. Tel.: +91 9448158393; +91 8182240435.
E-mail address: parashchem@gmail.com (P. Parameshwar Naik).
0040-4039/$ - see front matter Ó 2013 Elsevier Ltd. All rights reserved.
http://dx.doi.org/10.1016/j.tetlet.2013.08.099

306
S. Poojari et al. / Tetrahedron Letters 55 (2014) 305–309
OH
O
H
N
CH3
O
O
CH3
O
S
O
NH
NH
H3C
CH3
CH3
NH
N
NH
O
NH
O
N
CH3
O
NH
H3C
O
O
O
N
O
NH
O
H3C
N
CH3
CH3
OH
O
H3C
N
CH3
CH3
CH3
H3C
Argifin
(E)-Dehydroapratoxin A 6
Figure 1. Bioactive macrocycles.
O
H
NH2
N
O
HN
O
a
O
O
Br
B
1
2
O
c
O
O
N
O
Br
Br
OH
b
O
O
5
N
N
4
3
HN
NH2
OH
O
e
d
N
O
N
O
7
O
6
O
Scheme 1. Reagents and conditions: (a) (i) ditert-butylcarbamate (1.5 equiv), TEA (triethylamine) (3 equiv), THF, 80 °C, 8 h; (ii) bis(pinacolate)diboron (1.5 equiv),
PdCl2(dppf) (0.05 equiv), KOAc, dioxane–H2O, 90 °C, 16 h (b) thionyl chloride (4 equiv), MeOH, 80 °C, 4 h; (c) bis(triphenylphosphine) palladium(II) chloride, Na2CO3, DMF–
H2O (9:1), 10 h; (d) dioxane in HCl (4 M), rt, 2 h; (e) 4-carboxybenzaldehyde (1.5 equiv), acetic acid (5 equiv), sodium triacetoxyborohydride (3 equiv), DMF–THF, rt, 16 h.
The second challenge in the present synthetic method was the
preparation of oxadiazole intermediates. The synthesis was
achieved from commercially available amino acids as outlined in
Scheme 2. The treatment of amino acids with thionyl chloride in
the presence of methanol gave the substituted amino acid ester
products in good yield. Subsequent protection of amino group with
ditert-butyl carbamate provided compounds 8–11 in 80–92% yield.
The intermediate thus obtained was treated with hydrazine mono-
hydrate at reflux temperature to afford the substituted hydrazides
(12–15) in excellent yield. The hydrazides were reacted with
substituted isothiocyanate to form thiourea intermediates and
subsequently the resulting reaction mixture was treated with
EDCÁHCl at reflux temperature to afford the oxadiazole19,20 prod-
ucts (16–19) in one-pot. Further the deprotection tert-butyl carba-
mate or reduction of nitro group gave the corresponding amines
(20–23) in 92–97% overall yield (Table 1).
All reactions were carried out under inert atmosphere. The
crude reaction products were purified by column chromatography.
The fragments 20–23 were easily synthesized by a known
method. Then, condensation between amines and carboxylic acid
7 as described in the Schemes 1 and 2 in the presence of EDCÁHCl
and HOBT21 to afford corresponding amide derivatives in 60–80%
overall yield. Removal of tert-butyl carbamate protecting groups
with a solution of 4 M HCl in dioxane produced primary amines/
reduction of nitro group using Pd/C (10%) in DMSO at room tem-
perature gave amines. Then, hydrolysis of ester with LiOH/H2O
gave the corresponding free carboxylic acids in 85–94% excellent
yield.
The amine 20 synthesized (as shown in Scheme 2) was coupled
with an acid 7 to afford the amide derivatives 24 in good yield.
Hydrolysis of ester under basic medium gave the acid intermediate
25 in excellent yield. Hydrogenation of nitro group of 25 gave the
amine 26 in 85%. The critical macrocyclization was achieved after
optimization of the conditions.22 The optimum conditions pre-
sented in Table 2, entry 5, result in the cyclized compound in
65% yield. The same macrocyclization conditions was used for
the synthesis of 39.
The synthetic route has been simplified by using a common
intermediate and, in addition to this, alternative conditions were
developed for the synthesis of amine derivatives. To overcome
the solubility problem of compound 25, DMSO and methanol mix-
ture have been used as solvents but the removal of DMSO from the
mixture posed a major problem. Similarly to overcome the solubil-
ity issue of other two compounds such as 31 and 35, the synthetic
stratagies were changed. The nitro groups at the oxadiazoles were
reduced to amine derivatives by protecting the other side amino

S. Poojari et al. / Tetrahedron Letters 55 (2014) 305–309
307
O
O
O
H
N
H
O
O
N
a
b
R
R
R
H2N
O
HN
NH2
O
O
O
R=12, 13, 14, 15
R=8, 9, 10, 11
H
N
O
H
N
O
R
H
N
O
d
R
NO2
c
N
N
O
R1
Y
N
N
R=16, 17, 18, 19
R= 20, 21, 22, 23
R=
Y= -H, -CH3
O
Scheme 2. Reagents and conditions: (a) ditert-butylcarbamate (1.5 equiv), TEA (3 equiv), THF, 80 °C, 8 h; (b) hydrazinemonohydrate(2 equiv), methanol, 70 °C, 16 h; (c)
isothiocyantes, TEA (3 equiv), EDCÁHCl (1-ethyl-3-(3-diethylaminopropyl)carbodiimide) (2 equiv), DMF, 10 h; (d) HCl in dioxane (4 M), rt, 6 h, or Pd/c (10%), DMSO, rt, 2 h.
Table 1
Substrates and yield of oxadiazoles derivatives
Entry
Substrate (R)
Substrate (R1)
NO2
Products
Yielda (%)
97
H2N
H
N
O
H2N
NO2
1
N
N
20
O
O
NH2
O
O
N
H
H
N
O
2
3
92
HN
NH2
N
N
21
O
O
O
NH2
NO2
H
N
O
N
N
H
O
NH2
96
94
H
N
N
22
H2N
H
O
N
H2N
NO2
N
N
4
23
O
O
a
Isolated yields.
Table 2
The results of the optimal cyclization conditions
results in the formation of 29 and 33 in good yields, respectively.
The hydrolysis of ester derivative of 30 and 34 produced corre-
sponding amino acid derivatives which on further reacting at the
reaction conditions (Table 2, entry 5) afforded the desired macro-
cycles 31 and 35, respectively in good yield (Scheme 3).
No extensive effort was made to optimize the synthesis of these
macrocycles and the yield of the purified macrocycles was poor
across the series. A single reaction trying to form the macrocycle
with T3P and Et3N in DCM was attempted23 (Table 2, entry 2),
but no product was observed by LC–MS analysis. Indeed, no final
product was identified for the few attempted macrocyclization
reactions. The yields of the chromatographically-pure macrocycles
are shown in Table 3. Importantly, we did not observe any trend
relating stereochemistry or size of the side chain in preventing
the formation of the macrocycle. Hence it would be possible to ex-
pand this library in the future to include a greater diversity in these
areas. This synthetic strategy necessitated 14 steps as the longest
Entry
Substrate
Conditions
Yielda (%)
1
2
3
4
5
7 + 20
7 + 20
7 + 20
7 + 20
7 + 20
EDC, HOAt, TEA, DCM, rt
T3P, TEA, DCM, rt
PyBOP, DIPEA, DMAP, DMF, rt
BOP chloride, TEA, DCM, rt
HATU, DIPEA, DMAP, DMF, rt
12
NRb
7
21
65
PyBOP: (benzotriazol-1-yl-oxytripyrrolidinophosphonium hexafluorophosphate)
BOP chloride: bis(2-oxo-3-oxazolidinyl) phosphinic chloride.
a
Isolated yield.
No reaction.
b
groups. The protected amino groups using BOC (tert-butyloxycar-
bonyl anhydride) in 21 and 22 were condensed with 7 to produce
amides 28 and 32, respectively with good yield (92–96%).
Subsequent deprotection of 28 and 32 under acidic conditions

308
S. Poojari et al. / Tetrahedron Letters 55 (2014) 305–309
H
H
N
HN
N
H
N
HN
HN
HN
O
HN
O
a
b
c
O
d
d
O
O
7 + 20
O
O
O
N
N
N
N
HN
N
HN
N
HN
HN
N
N
N
OH
N
O
N
N
OH
O
O
O
O2N
N
H
27
O
O2N
H2N
25
24
26
H
H
H
N
HN
HN
HN
N
N
HN
HN
NH
N
NH
N
O
O
NH
N
a
N
H
N
O
e
O
b
7 + 21
O
O
O
O
N
N
N
N
O
N
N
O
N
OH
N
O
O
O
O
N
H2N
H2N
BocHN
H
29
30
28
31
H
N
HN
H
N
HN
HN
HN
HN
O
HN
O
NH
N
NH
N
a
b
NH
N
O
N
H
N
e
O
d
7 + 22
O
O
O
O
O
H
N
N
N
N
N
N
O
BocHN
N
O
N
OH
N
O
O
O
NH2
O
NH2
35
34
32
33
O
HN
O
O
H
HN
HN
H
HN
O
HN
N
H
N
N
N
N
N
O
O
O
N
b
c
a
N
d
O
N
N
7 + 23
O
O
N
HN
O
N
O
NH
NH
N
NH
N
OH
NH
O
N
OH
O2N
O
H2N
O
O2N
O
36
39
37
38
Scheme 3. Reagents and conditions: (a) EDCÁHCl (2.0 equiv), HOBT (1-hydroxy benzotriazole) (1.5 equiv), TEA (2.0 equiv), DMF, rt, 8 h; (b) LiOHÁH2O (3 equiv), MeOH/THF/
H2O (8:2:1), 60 °C, 1 h; (c) Pd/C (10%), DMSO/MeOH (4:6), 4 h; (d) HATU (1-[bis(dimethylamino)methylene]-1H-1,2,3-triazolo[4,5-b]pyridinium 3-oxid hexafluorophosphate)
(2.0 equiv), DIPEA (diisopropylethylamine) (3 equiv), DMAP (4-dimethylamino pyridine, catalytic), DMF, rt, 18 h; (e) HCl in dioxane (2 M), rt, 6 h.
Table 3
Supplementary data
Yield and melting point of the macrocycles
Entry
Macrocycle
Mol.wt
MP (°C)
Yield (%)
Supplementary data (experimental and spectral data for all the
compounds) associated with this article can be found, in the online
version, at http://dx.doi.org/10.1016/j.tetlet.2013.08.099.
1
2
3
4
27
31
35
39
593.6
545.6
531.6
651.7
220.1–225.7
236.4–239.9
169.4–172.8
216.2–219.3
65
58
51
62
References and notes
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chromatography.
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In summary, the critical ring closure was achieved in 51–65%
yield by intramolecular condensation. The purity of each step
was monitored by LC–MS analysis and in a few cases the structure
of compounds were confirmed by NMR. Due to insolubility issues
in some steps with the product purity less than 90% were taken
for next step without further purification. The concise and diver-
sity-oriented synthesis of macrolactam described here would be
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Acknowledgments
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The authors are grateful for the support provided by Syngene
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21. General procedure for the synthesis of amides 24, 28, 32, 36: To a solution of 5-[4-
(4-carboxybenzylamino)-phenyl]-nicotinic acid methyl ester 7 (1 mol) and
amines 20, 21, 22, 23 (1.5 mol) in anhydrous DMF (10 ml) was added TEA
(3 mol), EDCÁHCl (2 mol) and HOBT (1 mol). The reaction mixture was stirred at
room temperature for 16 h. and it was poured into ice water and extracted
with ethyl acetate (2 Â 500 ml) and the combined organic phase was washed
with water, brine solution and dried over anhydrous magnesium sulfate. The
solvent was removed under vacuum and the brown residue was purified by
column chromatography on silicagel using petroleum ether/ethyl acetate (6:4)
to afford 24, 28, 32, 36 as a yellow solid.
22. General procedure for the synthesis of macrocycles 27, 31, 35, 39: A mixture of
aminoacids 26, 30, 34, 38 (1 mol) in anhydrous DMF (10 ml) was added DIPEA
(3 mol) and DMAP (catalytic) followed by HATU (1.5 mol). The reaction
mixture was stirred at room temperature for 18 h. The reaction mixture was
concentrated and extracted with ethyl acetate (2 Â 25 ml) and the
combined organic phase was washed with water, brine solution and dried
over anhydrous magnesium sulfate. The solvent was removed under
vacuum and the brown residue was purified by column chromatography on
silica gel using chloroform/methanol (8:2) to afford 27, 31, 35, 39 as required
products.
16. General procedure for the synthesis of 5-[4-(4-carboxy-benzylamino)-phenyl]-
nicotinic acid methyl ester 7: To a solution of 5-(4-amino-phenyl)-nicotinic acid
methyl ester 6 (5 g, 21.9 mol) and 4-carboxy benzaldehyde (5.4 g, 32.8 mol) in
anhydrous DMF/THF (50 ml) was added acetic acid (6.7 g, 109.6 mol) and
sodium triacetoxyborohydride (9.2 g, 43.8 mol). The reaction mixture was
stirred at room temperature for 12 h. Once the substrate was completely
consumed (as monitored by TLC), the reaction mixture concentrated in vacuo
to obtain an acid. The crude product was extracted with ethyl acetate
(2 Â 100 ml) and the combined organic phase was washed with water, brine
solution and dried over anhydrous magnesium sulfate. The solvent was
removed under vacuum and the brown residue was purified by column
chromatography on silica gel using petroleum ether/ethyl acetate (1:1) to
afford 5.9 g (84%) of 7 as a pale yellow solid.
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19. General procedure for the synthesis of oxadiazoles derivatives 16, 17, 18, 19: A
mixture of hydrazides (1 mol), isothiocyanates (1.5 mol) in anhydrous DMF
(25 ml) was added TEA (3 mol) and reaction mixture was stirred at 60 °C for
30 min. Then to this added EDC and the resulting reaction mixture was stirred
at 90 °C for 16 h. The reaction mixture was poured into ice and the solid
separated was washed with cold water, dried under vaccum to afford the
yellow solid as required products.
23. Poojari, S.; Parameshwara, N. P.; Krishnamurthy, G. Tetrahedron Lett. 2012, 53,
4639–4643.