Expanding Synthesizable Space of Disubstituted 1,2,4-Oxadiazoles

Article abstract of DOI:10.1021/acscombsci.6b00103

One-pot synthesis of 3,5-disubstituted 1,2,4-oxadiazoles from carboxylic acids and nitriles was optimized to parallel chemistry. The method was validated on a 141 member library; the desired products were recovered with a high success rate and in moderate yields. Practical application of the approach was demonstrated in the synthesis of bioactive compound pifexole and agonists of free fatty acid receptor 1. A library of 4 948 100 synthesizable drug-like 3,5-disubstituted 1,2,4-oxadiazoles was enumerated based on the method and available validated reagents.

Full text of DOI:10.1021/acscombsci.6b00103

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Technology Note
Expanding synthesizable space of disubstituted 1,2,4-oxadiazoles.
Andrey Tolmachev, Andrey V. Bogolubsky, Sergey E. Pipko, Alexander V.
Grishchenko, Dmytro V. Ushakov, Anton V. Zhemera, Oleksandr O. Viniychuk,
Anzhelika I. Konovets, Olga A. Zaporozhets, Pavel K. Mykhailiuk, and Yurii S. Moroz
ACS Comb. Sci., Just Accepted Manuscript • DOI: 10.1021/acscombsci.6b00103 • Publication Date (Web): 22 Aug 2016
Downloaded from http://pubs.acs.org on August 23, 2016
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Expanding synthesizable space of disubstituted 1,2,4-oxadiazoles.
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Andrey Tolmachev,†,‡ Andrey V. Bogolubsky,† Sergey E. Pipko,‡,# Alexander V. Grishchenko,† Dmytro V.
Ushakov,† Anton V. Zhemera,† Oleksandr O. Viniychuk,# Anzhelika I. Konovets,†,║ Olga A. Zaporozhets,§ Pavel
K. Mykhailiuk,*,†,§ and Yurii S. Moroz*,‡
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†Enamine Ltd., 78 Chervonotkatska Street, Kyiv, 02094, Ukraine, www.enamine.net.
‡ChemBioCenter, Kyiv National Taras Shevchenko University, 61 Chervonotkatska Street, Kyiv, 02094, Ukraine.
#UkrOrgSyntez Ltd. (UORSY), 29 Schorsa Street, Kyiv, 01133, Ukraine, www.uorsy.net.
║The Institute of High Technologies, Kyiv National Taras Shevchenko University, 4 Glushkov Street, Building 5, Kyiv,
03187, Ukraine.
§Department of Chemistry, Kyiv National Taras Shevchenko University, 64 Volodymyrska Street, Kyiv, 01601, Ukraine.
Keywords one-pot parallel synthesis, 1,2,4-oxadiazoles, nitriles, carboxylic acids, REadily AccessibLe (REAL)
arrays.
Abstract
One-pot synthesis of 3,5-disubstituted 1,2,4-oxadiazoles from carboxylic acids and nitriles was optimized to
parallel chemistry. The method was validated on a 141 member library; the desired products were
recovered with a high success rate and in moderate yields. Practical application of the approach was
demonstrated in the synthesis of bioactive compound pifexole and agonists of free fatty acid receptor 1. A
library of 4,948,100 synthesizable drug-like 3,5-disubstituted 1,2,4-oxadiazoles was enumerated based on
the method and available validated reagents.
High-throughput screening (HTS) has been a valuable tool in many drug discovery projects.1 To expect high
efficiency of HTS, one requires sized libraries of structurally diverse compounds with favorable
physicochemical profiles which are typically delivered by parallel chemistry. Discovering new parallel
synthesis procedures and optimizing to the parallel conditions known “flask” chemistry protocols, therefore,
have been among important goals in facilitating success for drug discovery projects. Additionally, new
parallel chemistry allows for expanding a synthetically accessible area within a virtual chemical space.
For 25 years, we have been participating in the Escape of virtual space by introducing approaches to the
compounds widely exploited in HTS:2–5 sulfonamides,6 ureas,7 secondary amines8,9 – to name a few. The key
point of our research has been to deliver a simple, cost-effective, and highly feasible parallel chemistry. This
goal in part correlates with the guidelines for the “ideal synthesis” suggested by Wender10 and has been
achieved by applying the following criteria to the procedures under development:
- Price, availability, and compatibility of reagents;
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- Simplicity of reaction setup and workup manipulations;
- Applicability to a wide range of substrates.
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A recent project on antidiabetics performed by our biological department was to find agonists of free fatty
acid receptor 1 (GPR40).11 A cell-based HTS identified hits with hitherto unknown for this target 1,2,4-
oxadiazole motif which lack in-stock analogs for hit follow-up. This pushed us to establish parallel chemistry
approach to these compounds. Indeed, 3,5-disubstituted 1,2,4-oxadiazoles have been widely exploited in
medicinal chemistry;12–14 the motif is found in experimental and marketed drugs (Figure 1),15,16 and has an
acceptable ADME profile.17
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Figure 1. Marketed drugs with the 3,5-disubstituted 1,2,4-oxadiazole fragment.15
A literature search revealed several “flask” chemistry approaches to assemble the 3,5-disubstituted 1,2,4-
oxadiazole ring.18–25 To our surprise, some of these methods have been proposed only recently,21,23–25 after
more than 120 years since the first discovery of 1,2,4-oxadiazoles,26 that indicates a growing interest for this
motif. The parallel synthesis, however, has been reported only for the 4+1 assembly reaction between
amidoximes and carboxylic acids (Figure 2).18–20 But this approach had a limitation: amidoximes (254) were
scarcely represented in our stock compared with carboxylic acids (15886) (Figure 2) that is a general trend
for the former reagents.27 The method from amidoximes and carboxylic acids, therefore, would result in low
diversity libraries and ineffective exploration of chemical space. Additional features of amidoximes:
instability and relatively high price, made these reagents and unfavorable in parallel chemistry.
After close examination of the other “flask” procedures, we chose the approach from nitriles and carboxylic
acids. Nitriles are more stable and less expensive reagents than amidoximes. Indeed, our 4061 in-stock
nitriles would support high variation of the substituents at the C(3) position of the ring thus affording more
diverse libraries than the in-stock amidoximes. But the reported “flask” procedure21 from nitriles and
carboxylic acids was not suitable for parallel chemistry:
a) A solvent-free setup would complicate mixing for the reactions on a submillimolar scale;
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b) Acetate anion of the catalyst, 4-(dimethylamino)pyridinium acetate, could react concurrently with
amidoximes resulting in side products, 5-methyl 1,2,4-oxadiazoles;
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c) Scope and limitations of the procedure had not been assessed as the tested reagents were limited to the
phenyl-containing substrates.
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Herein, we present our results on the adaptation of the approach from nitriles and carboxylic acids to the
parallel conditions and on its application to various substrates including GPR40 agonists. We also discuss the
usefulness of the developed method on exploring synthesizable chemical space.
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Figure 2. Parallel synthesis of 3,5-disubstituted 1,2,4-oxadiazoles.
Modification of the method from nitriles and carboxylic acids to the parallel conditions. Most multistep
millimolar- or submillimolar-scale reactions, we have previously established for the parallel chemistry, have
a simple one-pot setup that employs 8 mL sealed vials as the reactors and a shaker or an oven shaker for
mixing or mixing with heating, respectively. To enable this setup, one should account for: solubility and
efficiency of reagents and intermediates, solubility of byproducts, and compatibility of solvents. The
assembly of 3,5-disubstituted 1,2,4-oxadiazoles from nitriles and carboxylic acids is a three-step procedure:
1) a generation of an amidoxime in situ;
2) a condensation of the amidoxime with a carboxylic acid to form an O-acylamidoxime;
3) a cyclodehydration of the O-acylamidoxime.
A closer examination of these transformations revealed that the procedure did not need special reaction
conditions, e.g. dropwise addition of reagents, maintaining low temperature or inert atmosphere, and
would proceed at room or elevated temperatures. Thus, we set the reactions in an oven shaker (Figure S1,
in the Supporting Information).
The “flask” synthesis of amidoximes from nitriles and an excess of hydroxylammonium chloride (NH2OH·HCl)
has been conducted in methanol or ethanol in the presence of a base,28–31 i.e. NaOH, Na2CO3, K2CO3, and
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triethylamine (TEA). We chose ethanol for the amidoxime generation as this solvent supported mild heating
to achieve efficient conversion of the reagents and could help remove water by azeotropic distillation. We
found TEA, an inexpensive ($70/L) and mild base, the most appropriate reagent for this step. TEA and its
hydrochloride are soluble in ethanol while other bases from the list have poor solubility and might prevent
efficient mixing in small volumes. This base was also sufficient to promote the cylcodehydration of O-
acylamidoximes. Our previous experience in the acylation reactions revealed a combination of N-(3-
dimethylaminopropyl)-N’-ethylcarbodiimide (EDC) and 1-hydroxy-7-aza-1H-benzotriazole (HOAt) as the
most efficient condensing agent. EDC32 has been widely employed in the synthesis of drug candidates;33
HOAt34 is an epimerization suppressant, a safe and more stable analogue of 1-hydroxybenzotriazole (HOBt).
These reagents35 support acylation even with electron deficient carboxylic acids and tolerate aqueous
workup because unreacted EDC, N-(3-dimethylaminopropyl)-N’-ethyl urea (the byproduct from EDC), and
HOAt are water-soluble. The acylation reaction occurs at room temperature but the following
cylcodehydration of the O-acylamidoxime required elevated temperatures of 100-120oC. So, we chose DMF
as a solvent for these steps.
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We compared the designed three-step procedure from nitriles and carboxylic acids to the known two-step
approach from amidoximes and carboxylic acids. For the test experiments, we selected from our stock
seven amidoximes (Figure 3, chemset 1a) and the corresponding nitriles (chemset 1n), and 14 carboxylic
acids (Figure 4, chemset 2). Then, we performed 40 randomly chosen parallel reactions on a millimolar scale
(20 from the amidoximes, method A, and 20 from the nitriles, method B, Table 1, chemset 3). The synthesis
of the full combinatorial set (98 members, 196 reactions) was unnecessary for the method development.
We ran the experiments in a semi-parallel mode monitoring each step by LC-MS or NMR to assure that the
chosen conditions were optimal. Briefly, we prepared amidoximes (first step in method B) as follows: a
mixture of a nitrile 1n (1 equiv), NH2OH·HCl (1.5 equiv), and TEA (2 equiv) in ethanol was shaken in a sealed
vial at room temperature for 6 hours and at 70oC for 16 hours. The solvent was subsequently removed in
vacuum. The aforementioned conditions were sufficient to achieve full conversion of the nitriles. The
amidoximes were acylated with carboxylic acids (method A, second step in method B) in the presence of
EDC (1.5 equiv) and HOAt (1 eq) by shaking the vials at room temperature for 24 hours. The prolonged
reaction time ensured complete transformation to the O-acylamidoximes and was necessary for parallel
o
chemistry. The cyclodehydration to 1,2,4-oxadiazoles at 100 C in the presence of TEA (1 equiv) was
completed in 3 hours. Compatibility of reagents and solvents enabled a one-pot procedure. The workup,
extraction of aqueous solution with CHCl3, resulted in the crude products that were analyzed with LC-MS or
1H NMR.
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R
NH2
OH
R
N
N
1a{1}ꢀ1a{7}
1n{1}ꢀ1n{7}
6
7
8
9
O
R=
S
S
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{1}
{2}
{3}
O
N
N
N
N
N
{4}
{5}
{6}
{7}
Figure 3. Amidoximes and nitriles, chemset 1a and chemset 1n.
O
R1
HO
2{1}ꢀ2{14}
N
O
N
N
O
R1=
N
S
N
O
O
N
H
NH
{1}
{2}
{3}
{4}
{5}
O
N
O
S
NO2
N
O
N
O
NH2
O
O
{6}
{7}
{8}
{9}
{10}
O
NH
N
N
N
N
O
{11}
{12}
{13}
{14}
Figure 4.Carboxylic acids, chemset 2.
Analysis of the crude mixtures revealed high efficiency of both methods (Table 1): the aqueous workup
afforded pure compounds (>90 % product content) in most of the experiments. The product content was
higher in the two-step reactions (>75 %) than those in the three-step ones (>65 %, Figures S2-S7). The
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mixtures with product content below 90 % were subjected to reversed phase HPLC; identity and purity of
the synthesized compounds were confirmed by 1H, 13C NMR and LC-MS. Not surprisingly, the isolated yields
were also higher for method A than those for method B. This fact, however, had a minor influence on
selection of the method for parallel chemistry because the determining factors are availability, variety and
price of the reagents (Table 1). Nonetheless, the three-step procedure afforded 3,5-disubstituted 1,2,4-
oxadiazoles in sufficient quantities (> 50 mg) for biochemical assays.
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Evaluation of the method. Next step in the development process is the application of the established
approach to produce at least a 100 member set. The substrates, randomly selected from our stock, included
reagents with different reactivity and those with additional functionalities. In the case of 1,2,4-oxadiazoles,
we probed combinations of nitriles and carboxylic acids to generate 3-alkyl-5-alkyl-, 3-alkyl-5-aryl-, 3-aryl-5-
aryl-, and 3-aryl-5-alkyl-derivatives. We chose 30 nitriles (Figures S8, S9) and 23 carboxylic acids (Figures
S10, S11) with attractive medicinal chemistry motifs and set up 120 parallel reactions on millimolar and
submillimolar (0.2 mmol) scale utilizing method B (40 examples are included in the paper, Tables 2-5,
chemsets 3.1-3.4). The subsequent workup and isolation afforded products in moderate yields; identity and
purity of the compounds were validated by NMR and LC-MS. Most reagents and especially those with
additional functionalities were tolerated under the reaction conditions (for example, 3{3,1}, 3.2{8,10}, and
3.4{7,10}). Among the synthesized compounds, a known bioactive substance pifexole, 5-(2-chlorophenyl)-3-
(pyridin-4-yl)-1,2,4-oxadiazole, was isolated in a 55% yield (Entry 8 in Table 4) that is on par with the
previously reported method from the corresponding amidoxime (71% if the amidoxime preparation and
isolation step is included).13,36,37 Overall, the products were recovered with 82 % success rate, an acceptable
value for a three-step three-component process. Thus, the developed method met all requirements of
parallel chemistry: high success rate, simplicity, and applicability.
The applicability factor reveals the major difference between the “ideal” and the parallel synthesis: in the
latter methodology the yields are far from being quantitative. Indeed, the parallel chemistry aims to
produce sized screening compound libraries in short periods of time and in sub-optimal yields rather than to
spend resources on optimization of the reaction conditions and thus obtain fewer compounds in high
yields.38 This trend is supported by recent modernization of screening techniques and assays which resulted
in minimization of material required for HTS and by introduction of approaches to screen crude mixtures.39
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Table 1. Parallel synthesis of 3,5-disubstituted 1,2,4-oxadiazoles: comparing two approaches.
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12
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Product in crude
Yield (%),*
method
Price† ($/g),
sample# (%),
method A/method
B
Entry
Product 3
n | a
A/method B
1
2
3{1,2}
3{1,6}
85/80
51/45
72/57
4 | 57
>90/88
3
4
3{2,5}
3{2,7}
>90/>90
>90/>90
84/66
87/70
6 | 56
5
6
3{2,13}
3{3,1}
>90/>90
77/85
90/76
52/44
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3{3,3}
3{3,6}
3{4,3}
3{4,5}
3{4,9}
3{4,12}
>90/80
81/70
73/56
20 | 122
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60
51/43
47/40
66/57
54/47
48/60
9
88/65
10
11
12
>90/>90
>90/75
83/>90
5 | 67
13
14
3{5,7}
>90/>90
>90/87
60/74
81/63
2 | 85
3{5,14}
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3{6,10}
3{6,12}
>90/75
75/56
87/71
22 | 300
>90/>90
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17
3{7,4}
>90/>90
84/63
18
19
20
3{7,8}
3{7,11}
3{7,14}
89/70
85/88
83/80
51/54
69/79
65/69
4 | 31
# - product content was determined by LC-MS or 1H NMR; * - isolated yield, † - source: eMolecules database.
Synthesis of GPR40 agonists. We utilized the developed procedure to prepare precursors for the project
focused on the search for potential agonists of GPR40: 14 derivatives of chloroacetic or 1-chloropropionic
acids were synthesized and further modified to afford 21 1,2,4-oxadiazoles. The cell-based assay conducted
on these compounds revealed micromolar to submicromolar potency for most studied 1,2,4-oxadiazoles,
pharmacokinetic experiments proved selectivity against other GPRs and favorable ADME profiles (Figure
S12).11
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Table 2. 3,5-disubstituted 1,2,4-oxadiazoles derived from aliphatic nitriles and aliphatic acids.
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Yield*
(%)
Entry
1
Product 3.1
3.1{1,5}
3.1{3,5}‡
44
2
47
3
4
3.1{4,4}
3.1{4,6}
48
52
#
5
3.1{6,2}‡
58
6
7
3.1{7,7}
3.1{9,8}
49
69
$
8
3.1{10,2}‡
55
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3.1{10,3}
3.1{13,6}‡
47
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10
45
#
* - isolated yield; ‡ - reactions were set on a submillimolar scale; # - mixture of isomers, 20/80, cis/trans, $ -
mixture of isomers, 21/79, cis/trans.
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Table 3. 3,5-disubstituted 1,2,4-oxadiazoles derived from aliphatic nitriles and aromatic or heteroaromatic acids.
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6
7
8
1) EDC, HOAt,
NH2OH, TEA
1) rt, 6h
2) 70 oC, 16h
rt, 24h
2) TEA,
100 oC, 3h
Alk
NH2
OH
O
N
Alk
Alk
Ar
9
+
Ar
EtOH
N
DMF
N
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N O
HO
1.1
2.2
3.2
Yield*
(%)
Entry
1
Product 3.2
3.2{2,3}‡
3.2{5,9}
3.2{7,8}‡
44
41
74
50
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3
4
3.2{7,13}‡
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3.2{8,10}
42
57
3.2{11,13}
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8
3.2{12,4}‡
3.2{13,4}
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Table 4. 3,5-disubstituted 1,2,4-oxadiazoles derived from aromatic or heteroaromatic nitriles and aromatic or heteroaromatic
acids.
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Yield*
(%)
Entry
1
Product 3.3
3.3{2,7}
75
2
3.3{3,12}‡
73
4
5
3.3{4,13}
3.3{5,6}
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43
3
6
7
3.3{6,5}‡
3.3{10,1}
3.3{12,4}
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3.3(13,2)
Pifexole
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Table 5. 3,5-disubstituted 1,2,4-oxadiazoles derived from aromatic or heteroaromatic nitriles and aliphatic acids.
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Yield*
(%)
Entry
1
Product 3.4
O
S
O
HN
3.4{1,1}‡
46
N
N O
2
3
3.4{7,10}
3.4{8,4}
44
72
N
4
3.4{9,2}‡
44
N
N
N
S
N O
5
6
3.4{10,5}
3.4{10,7}
88
52
N
N
7
8
3.4{11,4}‡
3.4{12,9}‡
49
44
O
N O
N
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3.4{14,4}
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* - isolated yield; ‡ - reactions were set on a submillimolar scale.
Charting a feasible region in a virtual chemical space. High-throughput virtual screening (HTVS) has
provided a valuable support to HTS at the early stages of many drug discovery projects. Recent
improvements in molecular docking has enabled effective hit identification thus making HTVS an alternative
to HTS.40,41 The major difference between two screening strategies is that HTVS is not limited to the
compounds on hand and allows virtual structures. The use of virtual sets greatly expands a screenable space
but also raises an important question: which virtual compounds can be actually made for biochemical
evaluation?
To address this question, we have developed REadily AccessibLe (REAL) arrays. The structures included in
REAL arrays are indeed highly feasible because:
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they are made of only in-stock reagents careful selected based on the years of experience in
synthetic organic and parallel chemistry;
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they are made by applying only in-house established and validated transformations.
These features distinct REAL arrays from similar virtual databases42,43 making them a pool of readily
synthesizable molecules extracted from the virtual chemical space.
A classical combinatorial approach gave 4,061x15,886 = 64,513,046 theoretically possible structures of 3,5-
disubstituted 1,2,4-oxadiazoles. Applying to this virtual space the REAL criteria (>12 g of in-stock available
tested substrates, reactivity clash), drug-like criteria44,45 and PAINS filtering,46 we generated 4,948,100
feasible molecules, a 4.9M set.
In order to show utility of the 4.9M set to drug discovery, we analyzed its overlap with 1073 drug-like
bioactive (activity 10μM or better) and 31009 in-stock 1,2,4-oxadiazoles47 using principal components
analysis. Since the 4.9M set was too large for processing, we reduced it to a 49K representative sample48 (1
%, 49,481 molecules) that respected the heterogeneity of the 4.9M set (Figures S13). The analysis revealed
substantial overlap in both cases (Figure 5) that made the REAL set a tool for structure-activity relationship
studies or for hit follow-up. Additionally, many molecules from the representative sample occupied the
space where the known compounds are absent indicating potentially novel molecules.
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Figure 5. Analysis of the drug-like chemical space of 3,5-disubstituted 1,2,4-oxadiazoles: the bioactive (green), the in-stock (red),
and the 49K REAL (blue) sets. The two principal components cover 63 % of the total variance: pc1 explains 42% and pc2 explains
21%.
We compared the 4.9M set with the bioactive and drug-like in-stock 1,2,4-oxadiazoles in more details: for
each compound from the 4.9M set, the distance to the nearest bioactive or the in-stock compound was
calculated employing ECFP4 fingerprints49 (Figures S14). For the bioactive, the distribution of similarity is
centered around a Tanimoto score of 0.35. Most feasible compounds were novel compared to the bioactive
set: 10 % had a Tanimoto score > 0.5, which is known as a good discriminative cutoff between similar and
dissimilar molecules for ECFP4 fingerprint. Not all entries from the bioactive set had similar feasible
compounds: for example, Gr-175737 (ZINC000000006638) that hits Histamine H3 receptor50 had more than
350 analogues (Figure 6) while Taniplon (ZINC000000010613) that is a GABAA receptor agonist,51 - none.
Indeed, almost 65 % of the bioactive compounds had at least one feasible 1,2,4-oxadiazole. For the in-stock
1,2,4-oxadiazoles, the distribution of similarity is centered around a Tanimoto score of 0.45 showing that
most of the feasible compounds are novel. These results correlated with the PCA positioning the 4.9M set as
a source for finding analogues and novel chemical entities.
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N
N
N
4
5
O
N
Cl
6
7
Tanimoto score = 0.68
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9
S
N
O
N
N
N
NH
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N
N
N O
N O
O
O
Cl
Cl
Cl
Gr-175737
Tanimoto score = 0.65
Tanimoto score = 0.6
N
N
N
N
O
N O
Cl
Tanimoto score = 0.56
Figure 6. REAL analogues of Gr-175737.
In conclusion, we established a facile one-pot parallel synthesis approach to 3,5-disubstituted 1,2,4-
oxadiazoles. Verification on a set of 141 reactions (61 are presented in the paper) applying millimolar or
submillimolar conditions showed that the approach completely satisfied the parallel synthesis criteria:
1) It is based on the starting reagents available as numerous collections from commercial sources that
would support good alteration of the substituents at the 3rd and the 5th positions of the 1,2,4-oxadiazole
ring.
2) It had a simple setup utilizing general labware, an oven shaker, and a simple workup, extraction;
3) It could be applied to various reagents and tolerate additional functionalities.
The method was employed in the synthesis of bioactive compound pifexole and in the synthesis of
precursors for novel GPR40 agonists.
The procedure was included in REadily AccessibLe (REAL) arrays that resulted in 4,948,100 feasible 3,5-
disubstituted 1,2,4-oxadiazoles. The 4.9M set contains analogues of the known bioactive 1,2,4-oxadiazoles
and novel chemical entities.
We believe that our approach will be helpful for researchers who look for a simple and quick access to sized
sets of 3,5-disubstituted 1,2,4-oxadiazoles and are ready to employ parallel chemistry for achieving the goal.
Experimental
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General. All chemicals and solvents were obtained from Enamine and used without further purification.
NMR spectra were acquired on Bruker Avance DRX 400 and Bruker Avance DRX 500 spectrometers using
DMSO-d6 as a solvent and tetramethylsilane (TMS) as an internal standard. IR spectra were recorded on
Perkin-Elmer Spectrum BX II. Elemental analysis was performed on a Vario MICRO Cube elemental
microanalyzer (Elementar). Melting points were determined on Buchi melting point apparatus and are
reported as uncorrected. LC-MS data were acquired on Agilent 1100 HPLC system equipped with diode-
matrix and mass-selective detector, column: Zorbax SB-C18, 4.6 mm × 15 mm. Eluent, A, acetonitrile −
water with 0.1 % of TFA (95:5); B, water with 0.1% of TFA. Crude samples with product content below 90 %
were purified mass-triggered Agilent 1200 HPLC systems utilizing various gradients depending on a ClogP
value of a particular compound.
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Principal components analysis (PCA). Representative REAL (49K), drug-like active, in-stock available 1,2,4-
oxadiazoles from ZINC15 database were compared utilizing PCA function as implemented in Data Warrior
software.35 Seven molecular descriptors were included: molecular weight, logP, number of H-bond donors,
number of H-bond acceptors, number of rotatable bonds, topological polar surface area, and molecular
complexity.
One-pot parallel synthesis of 3,5-disubstituted 1,2,4-oxadiazoles from amidoximes and carboxylic acids
(method A). A mixture of thiophene-2-amidoxime 1a{2} (1 mmol), 2-(3-methyl-2-oxopyridin-1(2H)-yl)acetic
acid 2{5} (1 mmol), EDC (1.5 mmol), and HOAt (0.7 mL of 20 wt% solution in DMF) was shaken at room
temperature for 24 hours. The cyclodehydration was performed in the presence of triethylamine (1 mmol)
by heating the reaction vial at 100 oC for 3 hours. Then, 3 mL of water was added and the mixture was
extracted with CHCl3. The chloroform phase was washed with water thrice and evaporated to afford 3-
methyl-1-((3-(thiophen-2-yl)-1,2,4-oxadiazol-5-yl)methyl)pyridin-2(1H)-one 3{2,5} as yellowish solid. Yield:
229 mg, 84 %, m.p.: 166-168 oC; FTIR (KBr): 3119, 3087, 2985, 2945, 2915, 1648, 1591, 1559, 1214; 1H NMR
(500 MHz, DMSO-d6): δ 1.99 (s, 3H), 5.47 (s, 2H), 6.28 (m, 1H), 7.25 (m, 1H), 7.40 (d, J = 6.5 Hz , 1H), 7.74 (d,
J = 6.5 Hz, 1H), 7.77 (d, J = 3.5 Hz, 1H), 7.88 (d, J = 4.5 Hz, 1H); 13C NMR (125.7 MHz, DMSO-d6): δ 17.2, 45.8,
106.2, 127.6, 128.9, 129.2, 130.8, 131.5, 1373, 138.6, 162.5, 164.5, 176.7; MS (APSI) m/z [M+H]+ calculated
for C13H11N3O2S: 274.1; found: 274.2. Anal. Calcd. For C13H11N3O2S: C, 57.13; H, 4.06; N, 15.37; found: C,
57.00; H, 4.20; N, 15.25. The essentially identical conditions were applied to the remaining compounds from
chemset 3 when synthesized from amidoximes.
One-pot parallel synthesis of 3,5-disubstituted 1,2,4-oxadiazoles from nitriles and carboxylic acids
(method B). A mixture of thiophene-2-carbonitrile 1n{2} (1 mmol), NH2OH·HCl (1.5 mmol), and TEA (2
mmol) in ethanol was shaken in a sealed 8 mL vial at room temperature on an orbital shaking platform for 6
hours. Then, the reaction mixture was heated at 70 oC in an oven for 16 hours. The solvent was removed
after the heating utilizing a rotary evaporator. To the in situ formed amidoxime, 2-(3-methyl-2-oxopyridin-
1(2H)-yl)acetic acid 2{5} (1 mmol), EDC (1.5 mmol), and 0.7 mL of 20 wt% HOAt in DMF were added and the
mixture was shaken at room temperature for 24 hours. The cyclodehydration was performed in the
o
presence of triethylamine (1 mmol) by heating the reaction vial at 100 C for 3 hours. Then, 3 mL of water
was added and the mixture was extracted with CHCl3. The chloroform phase was washed with water thrice
and evaporated. Yield: 180 mg, 66 %. The essentially identical conditions were applied to the remaining
compounds from chemset 3 when synthesized from nitriles. For the reactions on a submillimolar scale, the
amounts of reagents were scaled down accordingly.
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ASSOCIATED CONTENT
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Supporting Information. Details of experimental setup, lists of starting reagents, analytical data, analysis of
enumerated (REAL) set of 3,5-disubstituted 1,2,4-oxadiazoles, LC-MS and NMR spectra for synthesized
compounds.
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AUTHOR INFORMATION
Corresponding Author
* E-mail: ysmoroz@gmail.com.
* E-mail: Pavel.Mykhailiuk@mail.enamine.net; Pavel.Mykhailiuk@gmail.com.
Notes
A.V.B., A.T., P.K.M., A.V.G., D.V.U., A.V.Z., and A.I.K. work at Enamine Ltd.; S.E.P. and O.O.V. work at UOrSy.
Both companies are suppliers of reagents and screening compounds.
AKNOWLEDGEMENT
Dedicated to the 25th anniversary of Enamine Ltd. The authors are grateful to Enamine Ltd for providing
financial and technical support.
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