Design, synthesis, and conformational analysis of 3-: Cyclo -butylcarbamoyl hydantoins as novel hydrogen bond driven universal peptidomimetics

Article abstract of DOI:10.1039/c7ob02680c

A collection of systematically substituted 3-cyclo-butylcarbamoyl hydantoins was synthesized by a regioselective multicomponent domino process followed by easy coupling reactions. Calculations, NMR studies and X-ray analysis show that these scaffolds are able to project their side chains similar to common secondary structures, such as the α-helix and β-turn, with favourable enthalpic and entropic profiles.

Full text of DOI:10.1039/c7ob02680c

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Takeharu Haino et al.
Solvent-induced emission of organogels based on tris(phenylisoxazolyl)
benzene
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Design, Synthesis, and Conformational Analysis of 3-Cyclo-
Butylcarbamoyl Hydantoins as Novel Hydrogen Bond Driven
Universal Peptidomimetics
Received 00th January 20xx,
Accepted 00th January 20xx
M. C. Bellucci,a M. Frigerio,b C. Castellano,c F. Meneghetti,d A. Sacchetti*,b and A. Volonterio*,b
DOI: 10.1039/x0xx00000x
www.rsc.org/
A collection of systematically substituted 3-cyclo-butylcarbamoyl against different targets, overall when the target binding
hydantoins was synthetized by a regioselective multicomponent conformation is not well characterized.3
domino process followed by easily coupling reactions. Inspired by minimalist hydrogen bond driven β-turn mimetic
Calculations, NMR studies and X-ray analysis show that these trans-pyrrolidine-3,4-dicarboxamide developed by Boger et
scaffolds are able to project their side chains similar to common al.,7 we hypothesized that the introduction of two carbonyl
secondary structures, such as the α-helix and β-turn, with groups in the five-membered ring could 1) generate alternative
favourable enthalpic and entropic profiles.
hydrogen bond networks facilitating the mimicry of different
secondary structures, and 2) improve the “druggability” of the
mimics. Accordingly, we designed 3-cyclo-butylcarbamoyl
In modern medicinal chemistry, a well-established strategy to
overcome the drawbacks associated with the use of peptides
as drugs is the synthesis of peptidomimetics that efficiently
mimic protein secondary structures.1 Recently, this strategy
became increasingly important, even if challenging, in the
design of protein-protein interaction (PPI) inhibitors, since PPIs
are involved in most biological processes. Despite the large
and shallow surface area of contact, the PPI free Gibbs energy
binding depends mainly on the interaction of certain protein
side chains present in secondary structural elements, i.e hot
spots.2 In particular, structural mimetics, where small-
molecule scaffolds replace the entire peptide backbone
encompassing minimalist and universal mimetics, have
hydantoin scaffold
1 (Figure 1a) as structural privileged
universal mimetic scaffold that would possess the following
properties: 1) presentation of the side chains mimicking
secondary protein structures, such as the
α-helix and β-turn;
2) sufficient flexibility for adapting to a broad range of
kinetically and thermodynamically accessible conformations,
but also 3) limited degrees of freedom (favourable entropic
profile); 4) facile synthesis and easily incorporation of a wide
range of amino acid side chains, suitable for a combinatorial
approach (Figure 1b,c).8 Taken together, all these features will
possibly facilitate the synthesis of libraries of compounds
HTS against different targets.6
1 for
received great attention.3 Since early examples of structural
turns4 and -helix5 mimetics, several minimalist mimetics
β-
3-Cyclo-butylcarbamoyl hydantoins
7, precursors of final
α
mimetics were synthesized exploiting a regioselective
1
,
mimicking all type of secondary structures, as well as some
universal mimetics, have been developed in the last decade.6
In particular, the development of new universal
peptidomimetics is highly intriguing because, being able to
mimic different protein secondary structures and to adapt
their conformations through rotation around a few degrees of
freedom, they facilitate high throughput screening (HTS)
sequential multicomponent (MC) domino process recently
developed by us (Table 1. For the detailed mechanism of the
MC process, see Scheme S1).9 Reaction between
α
-azido-cyclo-
in the presence of
, which react in situ with fumaric
butyl carboxylic esters
2 and isocyanates 3
Ph3P affords carbodiimides
4
acid monoesters producing the 3-cyclo-butylcarbamoyl
hydantoin scaffold. In this work, we introduce the fumaric acid
mono-p-nitrophenyl ester
in situ when an equimolar amount of an amine is added to the
reaction medium, once intermediate is formed (see SI).
5. The activated ester readily reacts
6
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The ester function of compounds 7a-g can be easily hydrolysed
by base (X = Et) or through hydrogenolysis (X = Bn), and the
resulting carboxylic acids coupled with different amines
affording final mimetics 1
(Table 2).10
Table 2. Synthesis of mimetics 1.
R3
NH
H
H
N
O
2N NaOH, MeOH, 40 °C, 12h
when X = Et
O
N
R2
R3-NH2, HBTU
XOOC
R2
O
N
O
N
O
N
or
N
DIPEA, DMF
rt, 12h
R1
R1
H2/C, Pd(OH)2, MeOH
when X = Bn
7
O
1
O
Entry Ester R3
Product
Yield
(%)a
81
1
2
3
7a
7a
7a
benzyl
c-hexyl
74
89
Figure 1. a) General structure and flexibility of 3-cyclo-butylcarbamoyl
hydantoin scaffold
R2 = R3 = Me, grey) and its superimposition with an ideal
(orange); c) simulated low energy
-turn conformer (R1 = R2 = R3 = Me,
grey) and its superimposition with an ideal -turn (orange).
1
; b) simulated low energy
α
-helix conformer (R1 =
-helix
α
butyl
β
β
65b
76
Table 1. MC domino synthesis of intermediates 7.
4
5
7a
7b
HO-Gly-
hexyl
COOX
N3
O
PPh3
O
COOX
N
5
2
+
XOOC
C
N
R1
N
NO2
O
CH3CN
TMP
N
4
R1
R1-NCO
6
O
3
H
NO2
O
N
O
R2
R2-NH2
XOOC
N
HOOC
O
O
N
R1
6
7c
tryptamine
69
5
7
O
Entry R1
R2
X
Product
Yield
(%)a
73
1
Et
p-MeO-
Et
benzyl
7
8
7d
7d
tryptamine
tyramine
65c
64
77
75
2
3
Et
phenethyl
phenethyl
Bn
Bn
Bn
69
4
Bn
Bn
tryptamine
Bn
9
7e
7f
phenethyl
triptamine
78
81
81
77
5
6
c-hexyl
n-hexyl
Bn
Bn
10
1-naphthyl
63
7
-CH2CO2Et
phenethyl
Bn
11
7g
tyramine
74
aIsolated yields.
In this way, we were able to obtain 3-cyclo-butylcarbamoyl
hydantoins 7a-g in good yields, through a sequential four-
component process.
2 | J. Name., 2012, 00, 1-3
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aIsolated yields. bVia coupling with BnO-Gly-H followed by hydrogenolysis;
cVia coupling with N-Boc-1,6-hexamethylendiammine followed by Boc
removal with TFA.
For model compound A, 17% of conformers can adopt a α-helix
conformation, whereas another 25% of structures are able to mimic
a
β-turn (a total of 42% of the conformers are potential
peptidomimetics). Similar results were obtained for all compounds,
thus confirming the ability of the scaffold to induce a preferential
requirements to be used for the preparation of a wide library conformation regardless the nature of the residues. The highest
The synthetic procedure presented possess the suitable
success was recorded for the i-i+4 distance. For compounds 1b, 1i,
1k and model compound A, a more accurate study was performed
and the results summarized in Table 4. The first five low energy
conformers (for both α-helix and β-turn structures) were submitted
to HF/3-21G* full optimization followed by DFT/B3LYP-6-31G*
single point energy calculation. The α-helix motif is the most stable
for all compounds, but the β-turn conformations are easily
accessible at room temperature being only 0.048 to 0.246 kcal/mol
higher in energy. This feature is essential in designing
minimalist/universal peptidomimetics.
of structural mimetics. All the natural (and unnatural) amino
acid side chains are available based on a MC domino process
where the side chains come from easily accessible amines (R2,
R3) and isocyanates (R1). Moreover, compounds 1a-k follow
Lipinsky’s rule of five (Table S1).11 In particular, the octanol-
water partition coefficients (log P) of all compounds are
smaller than 5, rendering them promising candidates in drug
discovery.
In order to evaluate the ability of the scaffolds to mimic
classical peptide secondary structures, we performed a
preliminary computational study of model compound
A
(R1 =
Table 4. Comparison of α-helix/β-turn calculated free energies.
R2 = R3 = Me) and compounds 1a-k using Molecular Mechanics
Merck Force Field (MMFF) for energy minimization. We mainly
mimic
α-helix mimic
energy
(kcal/mol)
0.00
β-turn mimic
focused on the ability to mimic α-helix and β-turn secondary
energy
(kcal/mol)
0.954
structures (a more exhaustive analysis of all the possible
secondary structures mimicked, according to Burgess at al., is
reported in Table S2).3 The three-diversification points of the
scaffold Ci, Ci+4 and Ci+7 were associated to the i, i+4 and i+7
A
1b
1i
0.00
0.067
0.00
0.048
1k
0.00
0.246
residues of an ideal
distances i-i+4 = 6.2 Å, i-i+7 = 10.3 Å and i+4-i+7 = 5.8 Å were
used as parameters. For the -turn conformation, the For the secondary structure stabilization, different
interatomic distance dα < 7Å was used as a limit (Figure 1c). intramolecular hydrogen bonds can be established and two
The absolute value of the dihedral angle C1-C2-C3-N4 < 30° different patterns have been identified: 1) two H-bonds
was also evaluated as a more stringent condition. All the involving both carbonyl oxygens of the hydantoin ring
conformers within 10 kcal/mol from the global minimum from stabilizing the -helix, and 2) another H-bond between
the conformational analysis were kept. Results of the C1=O∙∙∙HAN4, not involving carbonyl of the hydantoin ring,
geometrical measurements are reported in Table 3 as which stabilizes the -turn conformation (Figure 1b,c). To
α-helix (Figure 1b). The ideal interatomic
β
β
α
β
percentage of the structures that meet above requirements.
assess the presence of these intramolecular hydrogen bonds in
solution, we performed variable temperature (VT) 1H-NMR
Table 3. Percentage of conformers that meet specific parameters typical of analysis on compounds 1b and 1k. Typically, solvent accessible
α-helix/β-turn conformations. protons exhibit a Δ /ΔT > 5 ppb/K, whereas Δ /ΔT < 5 ppb/K is
δ
δ
found for protons involved in H-bonds. The values found in 1b
and 1k for NHA (4.0 and 4.4) were smaller than those found for
NHB (4.5 and 5.1), thus indicating a preference for NHA to be
involved in hydrogen bond formation (Figures S1 and S2). This
observation is in agreement with an equilibrium between the
mimic % i-
i+4a
% i-
i+7a
26
13
24
14
20
27
19
19
37
25
11
14
% i+4-
i+7a
46
% α-
helixb
17
% dα
<7Å
25
40
36
41
39
14
35
17
13
19
4
angle
<30°
17
β
A
87
31
78
86
88
56
88
83
84
90
96
71
1a
1b
1c
1d
1e
1f
36
10
15
63
19
15
open (
α
β
-helix, both NHA and NHB are hydrogen bonded) and
-turn, only NHA H-bond is present) conformations in
55
11
19
folded (
65
17
11
solution. The 2D NOESY spectrum of compound 1k was also
recorded. No significant intramolecular long range contact was
detected, thus supporting the conclusion that no preferential
conformation is adopted.12
61
12
14
53
19
21
1g
1h
1i
66
18
16
39
28
24
For compounds 1i and 1k, we were able to obtain suitable
crystals for X-ray analysis from 1:1 water/methanol solutions
as colourless prisms (Figure 2a,b, respectively). Notably, in the
38
20
16
1j
75
11
6
1k
48
9
19
10
solid state, both structures adopted a
β-turn conformation
aValues in the ± 10% range with respect to the ideal distance were
considered; i-i+4 = 5.6-6.8 Å; i-i+7 = 9.3-11.3 Å; i+4-i+7 = 5.2-6.4 Å.
bPercentage of conformers having the three interatomic distances in
the correct range.
with the presence of the characteristic intramolecular
C1=O∙∙∙HAN4 H-bond, with N-H∙∙∙O distances in the range of 2.0
and 2.3 Å (Table S3). The intramolecular hydrogen bond
persisted during the crystal formation even under the
influence of relatively large intermolecular packing forces and
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the presence of a highly competitive protic solvent (MeOH) in accurate modeling studies suggest a slight propensity for a
the crystallization solution. The solid state parameters, such as helix conformation.
α-
interatomic distance dα, virtual torsion angle
β
were compared to ideal butylcarbamoyl hydantoin scaffold 1
, and dihedral In conclusion,
a
route for the synthesis of 3-cyclo-
was devised that involves
angles ϕ and φ of compounds 1i
,
k
β
-
turn conformations (Table 5).
a regioselective, multicomponent domino process followed by
facile couplings. The synthetic pathway is modular, thus
Table 5. Comparison of the main geometrical features between an suitable for the combinatorial synthesis of these compounds,
ideal type II
Compound
Ideal value < 7
β
-turn and crystal structures of 1i
|(°)
< 30 -60
,
k
.
and a variety of natural and unnatural amino acid side chains
can be easily placed in key positions. Molecular modeling
showed that these scaffolds could adopt kinetically and
thermodynamically accessible conformations mimicking those
of the secondary structures with only moderate loss of
entropy. In particular, conformations where R2, R1, and R3
dα
(Å
)
|β
ϕi+1
φi+1
ϕi+2 φi+2
120
80
0
1i
5.259(1) 1(1)
5.265(1) 4(1)
-53(1) 125(1) 77(1) 19(1)
-47(1) 122(1) 86(1) 20(1)
substituents overlap with the i, i+4, and i+7 side-chains in a
helix are slightly favoured according molecular mechanics,
whereas the -turn conformation is adopted in solid state, as
evidenced by X-ray analysis. For the features stated above, 3-
cyclo-butylcarbamoyl hydantoin scaffold could be considered
a new class of effective universal peptidomimetics. Application
of mimics , as well as the synthesis, conformation analysis,
α-
1k
β
1
The values of the distances d
fully comply with the
of the and dihedral angles defines the presence of the β-
turn conformation of type-II′. The values of φ i+1 ϕ i+1 and φ i+2
ϕ i+2 show a higher distortion with respect to the ideal values
for the second couple, that may be related to the geometrical
constraint of the five-membered ring, which is almost planar.
α
and of the virtual torsion angle
β
β-turn arrangement. A detailed analysis
1
φ
ϕ
and application of similar mimetics having other carbocycles in
position 3 will be reported in due course.13
,
,
We thank Politecnico di Milano and Università degli Studi di
Milano for financial support.
Conflicts of interest
There are no conflicts to declare.
Notes and references
1
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,
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J. Matusik, J.-M. Ahn, G. V. Ray, Mol. Cancer Res. 2014, 12
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Angew. Chem. Int. Ed. Engl. 2015, 54, 8896.
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Hirschmann, K. C. Nicolau, S. Pietranico, J. Salvino, E. M.
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Am. Chem. Soc. 1992, 114, 9217; (c) L. Lomlin, J. Einsiedel, F.
Figure 2. Crystal structure (grey) of 1k (a) and 1i (b), and their
superimposition with an ideal type-II’ β-turn (green) and optimized
W. Heinemann, K. Meyer, P. Greiner, J. Org. Chem. 2008, 73
3608.
,
calculated structure (orange)
.
5
6
(a) B. P. Orner, J. T. Ernst, A. D. Hamilton, J. Am. Chem. Soc.
2001, 123, 5382; (b) A. Volonterio, L. Moisan, J. Rebek, Org.
Lett. 2007, 9, 3733; (c) L. Moisan, S. Odermatt, N.
Gombosuren, A. Carella, J. Rebek, Eur. J. Org. Chem. 2008,
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(a) A. Raghuraman, E. Ko, L. M. Perez, T. R. Ioeger, K.
Burgess, J. Am. Chem. Soc. 2011, 133, 12350; (b) D. Xin, L. M.
Perez, T. R. Ioeger, K. Burgess, Angew. Chem. Int. Ed. Engl.
2014, 53, 3594.
L. R. Whitby, Y. Ando, V. Setola, P. K. Vogt, B. L. Roth, D. L.
Boger, J. Am. Chem. Soc. 2011, 133, 10184.
Finally, X-ray crystal structures of 1i and 1k were
superimposed with an ideal type-II’ -turn and -turn
β
β
conformer of the same compound as obtained by DFT
calculations (Figure 2a,b, respectively). We found a significant
geometrical correspondence between the three-dimensional
arrangements of the structures, as provided by the RMSD
(root-mean-square deviation) values of 0.26Å/0.18Å (with type
II’
for the superimposition of the heavy atoms. Overall, these
results confirm that 3-cyclo-butylcarbamoyl hydantoins have
-turn conformation, even if
β-turn) and 0.68Å/0.65Å (with DFT structures), respectively,
7
8
A hydantoin oligomer as β-strand mimetic has been
previously reported: A. G. Jamieson, D. Russel, A. D.
Hamilton, Chem. Comm. 2012, 48, 3709-3711.
1
a strong tendency to adopt a
β
4 | J. Name., 2012, 00, 1-3
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9
(a) T. Marcelli, F. Olimpieri, A. Volonterio, Org. Biomol. Chem.
2011, , 5156; (b) F. Olimpieri, M. C. Bellucci, T. Marcelli, A.
9
Volonterio, Org. Biomol. Chem. 2012, 10, 9538; (c) M. C.
Bellucci, G. Terraneo, A. Volonterio, Org. Biomol. Chem.
2013, 11, 2421.
10 An alternative synthetic procedure based on liquid-liquid
extractions (see ref. 7) has been used successfully starting
from purified intermediate
forthcoming full paper.
6. Details will be described in a
11 C. A. Lipinsky, F. Lombardo, B. W. Dominy, P. J. Feeney, Adv.
Drug Delivery Rev. 1997, 23, 3.
12 P. Tosovska, P. S. Arora, Org. Lett. 2010, 12, 1588.
13 In order to preliminary validate our scaffold, we have
accordingly superimposed the β-turn conformation of
compound 1i with the x-ray structure of macrocyclic β-turn
mimic active toward the ghrelin receptor (see: H. R.
Hoveyda, E. Marsault, R. Gagnon, A. P. Mathieu, M. Vézina,
A. Landry, Z. Wang, K. Benakli, S. Beaubien, C. Saint-Louis, M.
Brassard, J.-F. Pinault, L. Ouellet, S. Bhat, M. Ramaseshan, X.
Peng, L. Foucher, S. Beauchemin, P. Bhérer, D. F. Veber, M. L.
Peterson, G. L. Fraser J. Med. Chem. 2011, 54, 8305–8320).
The two structures overlay each other very well, with a
RMSD = 0.301 in the β-turn region.
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