Microwave-assisted synthesis of functionalized spirohydantoins as 3-D privileged fragments for scouting the chemical space

Article abstract of DOI:10.1016/j.tetlet.2016.05.065

Fragment-based drug design has been successfully applied to a large set of proteins, however in order to expand this concept to the most demanding targets, such as protein-protein interactions, it is required to enrich current fragment libraries with new and original 3D privileged fragments. Our goal was to develop a rapid microwave-assisted synthesis of 27 new privileged spirohydantoin fragments. Among them 24 compounds showed a high water solubility. These molecules were plotted according to the normalized principal moments of inertia of their minimized conformers, and most of the compounds were prone to occupy under-populated regions of the triangular plot. Finally we demonstrated that the hydantoin ring can be selectively N-monoalkylated providing the access to rapid functionalization for further elaboration.

Full text of DOI:10.1016/j.tetlet.2016.05.065

Tetrahedron Letters 57 (2016) 2888–2894
Contents lists available at ScienceDirect
Tetrahedron Letters
journal homepage: www.elsevier.com/locate/tetlet
Microwave-assisted synthesis of functionalized spirohydantoins
as 3-D privileged fragments for scouting the chemical space
Hugues Prevet a, Marion Flipo a, Pascal Roussel b, Benoit Deprez a, Nicolas Willand a,
⇑
a Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
b Unité de Catalyse et Chimie du Solide (UCCS), CNRS UMR 8181, Ecole Nationale Supérieure de Chimie de Lille, Université Lille Nord de France, Villeneuve d’Ascq F-59652, France
a r t i c l e i n f o
a b s t r a c t
Article history:
Fragment-based drug design has been successfully applied to a large set of proteins, however in order to
expand this concept to the most demanding targets, such as protein–protein interactions, it is required to
enrich current fragment libraries with new and original 3D privileged fragments. Our goal was to develop
a rapid microwave-assisted synthesis of 27 new privileged spirohydantoin fragments. Among them 24
compounds showed a high water solubility. These molecules were plotted according to the normalized
principal moments of inertia of their minimized conformers, and most of the compounds were prone
to occupy under-populated regions of the triangular plot. Finally we demonstrated that the hydantoin
ring can be selectively N-monoalkylated providing the access to rapid functionalization for further
elaboration.
Received 27 April 2016
Revised 13 May 2016
Accepted 17 May 2016
Available online 18 May 2016
Keywords:
Fragment library
3-D shape analysis
Spiranic center
Spirohydantoin
Microwave synthesis
Ó 2016 Elsevier Ltd. All rights reserved.
Introduction
interactions. Therefore, an increase in the proportion of fragments
that contain sp3 Carbon atoms has been proposed to raise the
Fragment-based lead discovery relies on the screening of low-
molecular-weight molecules, that show lower complexity in con-
trast to lead-like or drug-like libraries commonly used in High
Throughput Screening. Fragment hits are then optimized using
rational design to improve not only their affinity toward the tar-
geted protein but also all other required drug properties.1–4 In this
process, the selection of fragments is a key element to ensure nov-
elty, high hit-rates and chemical tractability. Rules such as the
accepted Rule of 3 (Ro3) proposed by Congreve et al.5 are now
commonly used to select fragments based on their physicochemi-
cal properties (MW < 300, clogP 6 3, the number of hydrogen bond
donors and acceptors each 63). More recently these rules have
been relaxed and incorporation of functional groups to help further
optimization has also been suggested.6 Solubility is also important
because fragments, of low expected affinity or potency, are gener-
ally tested at high concentrations (0.1–1 mM). Finally, in order to
fit diverse biological targets and pockets, a fragment collection of
diverse shapes and chemical functions is essential. Many fragment
libraries contain mostly planar aromatic scaffolds. This lack of geo-
metrical and chemical diversity jeopardizes the success in discov-
ering hits for more challenging targets,7 such as protein–protein
number of more complex8 motifs compared to highly aromatic
compounds.9
In that purpose, spirocyclic scaffolds show today a significant
interest due to the conformational restriction that is imposed by
the spiranic center.10 In addition, a careful selection of these spiro-
cyclic scaffolds can provide a rapid access to 3-D diversity.11–14
Therefore, we report here an illustration of this concept of privi-
leged structures15 in the context of fragments.
The concept of privileged fragments lies on the use of a minimal
central scaffold, here based on a spirohydantoin motif that can pro-
vide/accept H-bonds, together with the presence of a spiranic car-
bon atom able to provide rigidity and sphericity and to spread
pharmacophores in the three dimensions (Fig. 1). In this work we
explored a straightforward microwave-assisted synthetic pathway
for the preparation and functionalization of spirohydantoins. We
also illustrated how the selective modifications of these building
blocks might result in a wider range of lead-like compounds that
cover more efficiently the 3-D chemical space.
Results and discussion
The first synthesis of hydantoins was described by Bucherer and
Bergs in 1934 and consisted in reacting carbonyl compounds with
sodium cyanide and ammonium carbonate in a refluxing mixture
of ethanol and water. This method was then applied for the
⇑
Corresponding author. Tel.: +33 3 20 96 49 91; fax: +33 3 20 96 47 09.
E-mail address: nicolas.willand@univ-lille2.fr (N. Willand).
URL: http://www.deprezlab.fr (N. Willand).
http://dx.doi.org/10.1016/j.tetlet.2016.05.065
0040-4039/Ó 2016 Elsevier Ltd. All rights reserved.

H. Prevet et al. / Tetrahedron Letters 57 (2016) 2888–2894
2889
synthesis of spirohydantoins.16–18 However, long reaction time,
high temperature and large quantities of cyanide are required to
get acceptable yields. This limits the use of less stable chemical
functions and could lead to the formation of toxic hydrogen cya-
nide. In order to circumvent these drawbacks, we report the opti-
mization of
a
microwave-assisted synthesis using milder
conditions and we extend its scope to quickly and quantitatively
obtain a set of original functionalized spirohydantoins. The exper-
imental conditions were optimized using the cyclohexanone as
starting material.19,20 The desired spirohydantoin 1d was obtained
by reacting the cyclohexanone with 3 equiv of ammonium carbon-
ate and only 1.5 equiv of potassium cyanide in a 1:1 mixture of
methanol and water. The solution was heated in a sealed tube
under microwave irradiation at 90 °C. Under these conditions,
the reaction was complete after only 10 min and led to the desired
spirohydantoin with a 98% yield. A shorter reaction time did not
lead to full conversion and the replacement of methanol by ethanol
led to a lower conversion. As a comparison, the completion of the
Figure 1. Structure of the spirohydantoin privileged fragment scaffold (HBA: H-
bond acceptor, HBD: H-bond donor, FS: functionalization site).
Table 1
Functionalized spirohydantoins synthesized using microwave-assisted Bucherer–Berg reaction
O
KCN (1.5 eq)
O
(NH4)2CO3 (3 eq)
HN
NH
H2O/MeOH
µW - 10 min - 90°C
O
R
R
Entry
1
Compd
Structure
Yielda (%)
Solubilityb (mM)
O
HN
NH
1a
60
0.7
O
O
HN
NH
2
3
4
5
6
1b
1c
1d
1e
1f
91
50*
98
0.8
>1
O
O
HN
NH
N
O
O
HN
NH
0.8
0.9
O
O
CH3
HN
71*
NH
H3C
O
O
HN
NH
95
>1
O
O
(continued on next page)

2890
H. Prevet et al. / Tetrahedron Letters 57 (2016) 2888–2894
Table 1 (continued)
Entry
Compd
Structure
Yielda (%)
Solubilityb (mM)
O
HN
NH
7
1g
76
0.4
N
H
O
O
HN
NH
8
1h
1i
98
100
75
>1
>1
>1
>1
>1
>1
>1
>1
Me
N
O
O
HN
HN
HN
HN
HN
NH
9
Et
Pr
iPr
N
O
O
NH
10
11
12
13
14
15
1j
N
O
O
NH
NH
1k
1l
75
N
O
O
80
Ac
N
O
O
NH
1m
1n
1o
100
58*
55*
Boc
N
N
O
O
HN
NH
Et
O
O
HN
NH
N
Boc
O
O
HN
97*
>1
NH
16
1p
N
O
Boc
a
Isolated yield after purification.
Measured solubility in PBS at pH 7.4.
Compound obtained as a racemic mixture.
b
*
same reaction under thermal conditions required 4 h. In addition,
the reaction mixture was more complex and its purification led
to the desired compound with a significantly lower yield (63%).
These optimized microwave-assisted conditions were then applied
to a broad range of commercially available cyclic ketones with
different ring sizes and substituents.
16 spirohydantoins (Table 1) with four (entry 1, 1a), five
(entries 2 and 3, 1b, 1c), six (entries 4–15, 1d–1o) or seven

H. Prevet et al. / Tetrahedron Letters 57 (2016) 2888–2894
2891
Table 2
Spirohydantoin privileged fragments synthesized starting from substituted and hindered cyclic ketones
O
KCN (1.5 eq)
O
(NH4)2CO3 (3 eq)
HN
NH
H2O/MeOH
µW - 10 min - 90°C
O
R
R
Entry
Compd
Structure
Ratioa (%)
Yieldb (%)
Solubilityc (mM)
O
H
N
H
2a
28
22
0.8
>1
NH
EtO2C
O
1
O
H
N
EtO2C
H
2a0
NH
72
74
49
O
O
HN
NH
2b
50*
0.8
O
CO2Et
H
2
O
HN
NH
2b0
26
16*
>1
H
O
CO2Et
O
HN
NH
2c
25
75
10
61
>1
>1
H
O
CO2Et
3
O
HN
NH
2c0
EtO2C
O
H
O
HN
93*
76*
3*
0.1
0.8
NH
4
5
6
2d
2e
2f
>98
>98
>98
O
O
HN
NH
O
O
CH3
O
HN
tBu
NH
0.9
O
(continued on next page)

2892
H. Prevet et al. / Tetrahedron Letters 57 (2016) 2888–2894
Table 2 (continued)
Entry
Compd
Structure
Ratioa (%)
100
Yieldb (%)
Solubilityc (mM)
O
HN
NH
7
2g
40
>1
N
O
O
HN
NH
8
2h
100
60
0.9
Boc
N
O
a
Ratio determined by LC/MS.
Isolated yield after purification.
Measured solubility in PBS at pH 7.4.
Compound obtained as a racemic mixture.
b
c
*
As hydantoins are known to possess low water solubility21 we
evaluated the impact of the introduction of a spiranic center on
this physico-chemical property. Water solubility of the 27 spirohy-
dantoins synthesized was measured (Tables 1 and 2). Interestingly,
24 functionalized spirohydantoins, including the most hydropho-
bic compounds 1d, 1e, 2f, and 2h display high solubility
>0.8 mM. This first observation is in agreement with our hypothe-
sis that incorporation of a spiranic center into the structures of our
privileged fragments may be beneficial for the solubility.
To further characterize the 3D shapes of representative frag-
ments, compounds 2a0, 2b, and 2c0 were recrystallized in MeOH
or EtOH. The 3D-structures of these three fragments were solved
by X-ray crystallography (see Supplementary data). Interestingly
spirohydantoins 2a0 and 2c0 spread their structure mainly in two
dimensions whereas spirohydantoin 2b, as expected, displays a
more spherical structure (Fig. 2).
Next we analyzed the molecular shape of our entire set of frag-
ments using the principal moment of inertia plots.22 Normalized
principal moments of inertia (NPR1 and NPR2) were determined.
These two values were then plotted to provide the triangular chart
where each corner indicates compounds that tend to have rod-like,
disk-like, or sphere-like features (Fig. 2).
Figure 2. Molecular shape analysis of the spirohydantoin set using normalized
principal moment of inertia (PMI).
The data obtained for the entire set of spirohydantoins were
compared to our entire library of fragments. The triangular plot
shows that the majority of our commercially available fragments
(pale blue squares on Fig. 2) are grouped in the left corner of the
plot corresponding to structures with rod-like geometric features.
Interestingly, the spirohydantoin fragments (dark crosses on
Fig. 2) are more scattered in the 3-D space and show a broader
diversity in terms of molecular shape. For example compound 2b
occupies the under-populated central part of the graph.
In addition to their high solubility and their tendency to pop-
ulate in a broader way the 3-D chemical space, the 27 fragments
fulfill the rule of three and most of them have a molecular weight
less than 220 g molꢀ1. More importantly, for all these fragments
functionalization remains possible while keeping fragment prop-
erties. Therefore, we also worked on straightforward sequences
that allow the selective N-monoalkylation of the hydantoin ring
to provide access to fragment-like or more complex lead-like
structures (Scheme 1). Compound 1f was monoalkylated on the
most acidic nitrogen atom using propargyl bromide (1 equiv)
and potassium carbonate (3 equiv) in DMF to afford compound
3. The synthesis of isomer 6, was carried out using a three-step
protocol: 1f was first protected on the most acidic nitrogen atom
with a Boc group. This reaction was complete after only 10 min at
room temperature and led quantitatively to compound 4. Then
membered-ring (entry 16, 1p) were obtained with good to excellent
yields. In addition, Boc or benzyl protected N-heterocycles were
also introduced (entries 3, 13, 15 and 16). The use of free nitro-
gen-containing cyclic ketone was also tolerated, as example the
use of piperidinone led to compound 1g with a 76% yield (entry 7).
The use of substituted and hindered cyclic ketones was also
possible and this led to 11 new spirohydantoins (entries 1–8,
Table 2). Compounds 2a and 2a0 were synthesized in two steps
starting from 3-oxocyclobutanecarboxylic acid then esterified
using thionyl chloride in ethanol. Interestingly, the presence of
ester functions (entries 2 and 3) did not affect the reactivity and
mixtures of diastereoisomers 2b, 2b0, 2c and 2c0 were obtained
with overall good yields. In the cyclohexane series, when the car-
bon in
a or b position of the ketone function was substituted
(entries 4–6) only one diastereoisomer (2d, 2e or 2f) was formed
and isolated. This may be explained by the steric hindrance that
constrained the nucleophilic attack of cyanide on the less hindered
face of the intermediate cyclic imine. This phenomenon was also
observed with the N-methyl or N-Boc tropinone that led to 2g
and 2h with quantitative diastereoisomeric excess. These spirohy-
dantoins were obtained with good yields except for compound 2f
where the tert-butyl group may limit the accessibility to the elec-
trophilic center due to steric hindrance.

H. Prevet et al. / Tetrahedron Letters 57 (2016) 2888–2894
2893
NOE correlations
O
O
H
Br
1
H
H
N
HN
1
(1 eq.)
N
NH
2
2
O
K2CO3 (3 eq.)
DMF
O
O
O
RT - 2h
1f
3
MW = 170 g.mol-1
65%
MW = 208 g.mol-1
solubility > 1 mM
(Boc)2O (1 eq.)
DMAP (0.035 eq.)
Et3N (1 eq.)
MeCN
83%
RT - 10min
NOE correlations
H
O
H
H
H
Br
1
MeONa (4 eq.)
MeOH
O
HN
O
1
N
1
N
(3 eq.)
Boc
N
O
O
2
K2CO3 (3 eq.)
DMF
N
H
2
O
N
µW
2
O
10min - 60°C
O
O
Boc
RT - 3h30
4
5
6
88%
86%
MW = 208 g.mol-1
solubility > 1 mM
Scheme 1. Selective preparation of N-monoalkylated analogs 3 and 6.
alkylation of the free remaining Nitrogen atom with propargyl
bromide (3 equiv) was performed as previously. Finally com-
pound 5 was deprotected using sodium methoxide in MeOH
under microwave irradiation to afford compound 6 in a 63% over-
all yield. NMR experiments (1H, 13C and 1D-NOESY) allowed us to
confirm the structures of the two isomers 3 and 6 (Scheme 1).
Finally, we confirmed that the substitution of the hydantoin ring
did not impact the solubility, as the two compounds showed sol-
ubility higher than 1 mM.
Crystallographic data
Crystallographic data for compounds 2a0 (CCDC 1465076), 2b
(CCDC 1465078) and 2c0 (CCDC 1465077) have been deposited
with the Cambridge Crystallographic Data Centre. Copies of the
data can be obtained, free of charge, on application to CCDC, 12
Union Road, Cambridge CB2 1EZ, UK, (fax: +44 (0)1223 336033
or e-mail: deposit@ccdc.cam.ac.Uk).
The introduction of alkyne functions opens the way to further
functionalization via Huisgen-type click-chemistry or Sonogashira
coupling. In addition, the benzyl and Boc protecting groups of
spirohydantoins 1c, 1m, 1o, 1p, and 2h could be removed to pro-
vide a third anchoring point, making these privileged spirohydan-
toin fragments very useful to probe the chemical space in a broader
way.
Acknowledgments
We are grateful to the institutions that support our laboratory:
Inserm, Université Lille Nord de France, Institut Pasteur de Lille, EU,
Région Nord-Pas de Calais, and PRIM Pôle de Recherche Interdisci-
plinaire du Médicament. This project is funded by ANR (ANR-13-
JSV5-0010-01).
Conclusion
Supplementary data
We report here a rapid and convenient microwave-assisted syn-
thesis of functionalized privileged spirohydantoin fragments
which are able to probe more efficiently the 3-D chemical space
than flat aromatic scaffolds. The optimization of the synthetic
route using microwave irradiation allowed the rapid synthesis of
analogs and led to 27 compounds with moderate to excellent
yields. 24 of our privileged fragments displayed an aqueous solu-
bility higher than 0.8 mM suggesting that this physico-chemical
property is generic to the spirohydantoin scaffold and warrants
biological screening at high concentrations. Analysis of the shape
of our privileged fragments showed that they adopt preferentially
rod-like and sphere-like conformations. Moreover we were able to
selectively alkylate each of the two Nitrogen atoms of the hydan-
toin ring providing accessibility to further functionalization. The
enrichment of fragment libraries with these 3-D scaffolds may
allow finding compounds that bind to a larger set of targets and
hits will be of great interest to kick-start fragment-based lead
discovery.
Supplementary data (experimental procedures, analytical and
spectral data of all synthesized compounds) associated with this
article can be found, in the online version, at http://dx.doi.org/10.
1016/j.tetlet.2016.05.065.
References and notes
1. Baker, M. Nat. Rev. Drug Disc. 2013, 12, 5.
2. Villemagne, B.; Flipo, M.; Blondiaux, N.; Crauste, C.; Malaquin, S.; Leroux, F.;
Piveteau, C.; Villeret, V.; Brodin, P.; Villoutreix, B. O.; Sperandio, O.; Soror, S. H.;
Wohlkönig, A.; Wintjens, R.; Deprez, B.; Baulard, A. R.; Willand, N. J. Med. Chem.
2014, 57, 4876.
3. Murray, C. W.; Verdonk, M. L.; Rees, D. C. Trends Pharmacol. Sci. 2012, 33, 224.
4. Scott, D. E.; Coyne, A. G.; Hudson, S. A.; Abell, C. Biochemistry 2012, 51, 4990.
5. Congreve, M.; Carr, R.; Murray, C.; Jhoti, H. Drug Discovery Today 2003, 8, 876.
6. Köster, H.; Craan, T.; Brass, S.; Herhaus, C.; Zentgraf, M.; Neumann, L.; Heine, A.;
Klebe, G. J. Med. Chem. 2011, 54, 7784.
7. Morley, A. D.; Pugliese, A.; Birchall, K.; Bower, J.; Brennan, P.; Brown, N.;
Chapman, T.; Drysdale, M.; Gilbert, I. H.; Hoelder, S.; Jordan, A.; Ley, S. V.;
Merritt, A.; Miller, D.; Swarbrick, M. E.; Wyatt, P. G. Drug Discovery Today 2013,
18, 1221.

2894
H. Prevet et al. / Tetrahedron Letters 57 (2016) 2888–2894
8. Beghyn, T.; Deprez-Poulain, R.; Willand, N.; Folleas, B.; Deprez, B. Chem. Biol.
Drug Des. 2008, 72, 3.
15. Mason, J.; Morize, I.; Menard, P.; Cheney, D.; Hulme, C.; Labaudiniere, R. J. Med.
Chem. 1999, 42, 3251.
9. Lovering, F.; Bikker, J.; Humblet, C. J. Med. Chem. 2009, 52, 6752.
10. Zheng, Y.; Tice, C. M.; Singh, S. B. Bioorg. Med. Chem. Lett. 2014, 24, 3673.
11. Tran, N. C.; Dhondt, H.; Flipo, M.; Deprez, B.; Willand, N. Tetrahedron Lett. 2015,
56, 4119.
16. Sarges, R.; Schnur, R. C.; Belletire, J. L.; Peterson, M. J. J. Med. Chem. 1988, 31,
230.
17. Brouillette, W. J.; Brown, G. B.; DeLorey, T. M.; Liang, G. J. Pharm. Sci. 1990, 79,
871.
12. Lüthy, M.; Wheldon, M. C.; Haji-Cheteh, C.; Atobe, M.; Bond, P. S.; O’Brien, P.;
Hubbard, R. E.; Fairlamb, I. J. S. Bioorg. Med. Chem. 2015, 23, 2680.
13. Deprez-Poulain, R.; Willand, N.; Boutillon, C.; Nowogrocki, G.; Azaroual, N.;
Deprez, B. Tetrahedron Lett. 2004, 45, 5287.
14. Willand, N.; Beghyn, T.; Nowogrocki, G.; Gesquiere, J.-C.; Deprez, B. Tetrahedron
Lett. 2004, 45, 1051.
18. Naydenova, E.; Pencheva, N.; Popova, J.; Stoyanov, N.; Lazarova, M.; Aleksiev, B.
Farmaco 2002, 57, 189.
19. Rivero, I. A.; Reynoso, E. A.; Ochoa-Teran, A. Arkivoc 2011, 260.
20. Safari, J.; Gandomi-Ravandi, S.; Javadian, L. Synth. Commun. 2013, 43, 3115.
21. Stella, V.; Higuchi, T. J. Pharm. Sci. 1973, 62, 962.
22. Sauer, W. H.; Schwarz, M. K. J. Chem. Inf. Comput. Sci. 2003, 43, 987.