Insight into structural description of novel 1,4-Diacetyl-3,6-bis(phenylmethyl)-2,5-piperazinedione: synthesis, NMR, IR, Raman, X-ray, Hirshfeld surface, DFT and docking on breast cancer resistance protein

Article abstract of DOI:10.1016/j.molstruc.2021.131435

In this work, novel 1,4-diacetyl-3,6-bis(phenylmethyl)-2,5-piperazinedione (2) is prepared exclusively as the (R,S)-stereoisomer evidenced and confirmed by X-ray diffraction analysis. In addition, spectroscopic (NMR, IR, Raman) analyses were used to characterize the new compound. 2 crystallizes in the Pbca orthorhombic space group, with a symmetry center located at the centroid of the diketopiperazine ring. The structure of 2 is compact with the two phenyl rings folded over and under the diketopiperazine ring, conferring thereby a unique S shape to the molecule. The crystal structure is stabilized by intramolecular interactions, whereas the crystal packing is stabilized by intermolecular H-bond and C?H···π interactions. The different intermolecular interactions were confirmed using Hirshfeld surface analysis and molecular fingerprint. Molecular 2D fingerprint that quantify the different interactions highlights that H···H (58.2%), H···O/O···H (24.8%) and C···H/H···C (14.2%) account for 97.2% of all contacts. The topology of the interaction energy in the crystal structure is obtained and described. The Cremer and Pople puckering parameters indicate that the diketopiperazine ring adopts a flattened chair conformation with Θ = 0.00 ° and Q = 0.2233 (11) ?. Moreover, a computational investigation revealed that the optimized structure of 2 using DFT calculation shows excellent agreement with the experimental data. As potential pharmacological active molecule, the molecular docking on breast cancer resistance protein (BCRP) reveals that 2 could interacts with the binding domain residues Phe728, Tyr949, Ser975 and Val978 and could be consider as promising BCRP inhibitor.

Full text of DOI:10.1016/j.molstruc.2021.131435

Journal of Molecular Structure 1248 (2022) 131435
Contents lists available at ScienceDirect
Journal of Molecular Structure
journal homepage: www.elsevier.com/locate/molstr
Insight into structural description of novel
1,4-Diacetyl-3,6-bis(phenylmethyl)-2,5-piperazinedione: synthesis,
NMR, IR, Raman, X-ray, Hirshfeld surface, DFT and docking on breast
cancer resistance protein
Koffi Sénam Etsèa,∗, Guillermo Zaragozab
a Laboratory of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines (CIRM), University of Liège, Quartier Hôpital B36 Av. Hippocrate 15
B-4000 Liège, Belgium
b Unidade de Difracción de Raios X, RIAIDT, Universidade de Santiago de Compostela, Campus VIDA, 15782 Santiago de Compostela, Spain
a r t i c l e i n f o
a b s t r a c t
Article history:
In this work, novel 1,4-diacetyl-3,6-bis(phenylmethyl)-2,5-piperazinedione (2) is prepared exclusively as
the (R,S)-stereoisomer evidenced and confirmed by X-ray diffraction analysis. In addition, spectroscopic
(NMR, IR, Raman) analyses were used to characterize the new compound. 2 crystallizes in the Pbca or-
thorhombic space group, with a symmetry center located at the centroid of the diketopiperazine ring.
The structure of 2 is compact with the two phenyl rings folded over and under the diketopiperazine ring,
conferring thereby a unique S shape to the molecule. The crystal structure is stabilized by intramolecular
interactions, whereas the crystal packing is stabilized by intermolecular H-bond and C−H···π interactions.
The different intermolecular interactions were confirmed using Hirshfeld surface analysis and molecular
fingerprint. Molecular 2D fingerprint that quantify the different interactions highlights that H···H (58.2%),
H···O/O···H (24.8%) and C···H/H···C (14.2%) account for 97.2% of all contacts. The topology of the interac-
tion energy in the crystal structure is obtained and described. The Cremer and Pople puckering param-
eters indicate that the diketopiperazine ring adopts a flattened chair conformation with ꢀ = 0.00 ° and
Received 30 July 2021
Revised 30 August 2021
Accepted 1 September 2021
Keywords:
diketopiperazine
crystal structure
puckering parameters
DFT calculations, Hirshfeld surface, breast
cancer resistance protein
˚
Q = 0.2233 (11) A. Moreover, a computational investigation revealed that the optimized structure of 2 us-
ing DFT calculation shows excellent agreement with the experimental data. As potential pharmacological
active molecule, the molecular docking on breast cancer resistance protein (BCRP) reveals that 2 could
interacts with the binding domain residues Phe728, Tyr949, Ser975 and Val978 and could be consider as
promising BCRP inhibitor.
© 2021 Elsevier B.V. All rights reserved.
1. Introduction
change in structural and physical characteristics, DKPs can confer
more drug-like properties to molecules and enhance favorable in-
Diketopiperazines (DKPs) are a class of compounds displaying a
wide range of biological activities [1–2] as antibacterial [3–4], an-
tifungal [5,6], antitumoral [7–9] and antiviral agents [10,11]. Some
DKP derivatives exhibit radical-scavenging and antioxidant activi-
ties [12,13]. 3,6-disubstituted 2,5-diketopiperazines, whether natu-
ral or synthetic, are the most abundant and have received enor-
mous attention because of their structure related to cyclodipep-
tides [14–17]. Unlike linear (di)peptides, constraining the nitrogen
atoms of an α-amino amide into a DKP ring modify physical prop-
erties, reduces susceptibility to metabolic amide bond cleavage re-
actions and reduces conformational mobility. As a result of the
teractions with biological macromolecules [15].
The symmetrical cyclic dipeptide (L-Phe-L-Phe) with two
phenylalanine residues was originally isolated from Penicillium ni-
gricans [18] and then from a marine mangrove endophytic fungus
[19]. cyclo(L-Phe-L-Phe) also occurs in a variety of beverages and
foods such as beef, cheddar cheese, cocoa, white wine, yeast ex-
tract [20] and chicken essence [21]. It has been shown to exhibit
good anthelmintic activity against Hymenolepis nana and Schisto-
soma mansoni [22] and antidepressant and antidementia effects
in mice [23] as well as moderate antioxidant efficiencies against
the standard antioxidants ascorbic acid (natural) and butylated hy-
droxyanisole (a synthetic ingredient used in food, cosmetics, and
medicine) [13].
Tryprostatin-A (TPS-A; ((3S,8aS)-3-[[6-methoxy-2-(3-methylbut-
∗
Corresponding author.
2-enyl)-1Hindol-3-yl]
methyl]-2,3,6,7,8,8a-hexahydropyrrolo[1,2-
E-mail address: ks.etse@uliege.be (K.S. Etsè).
https://doi.org/10.1016/j.molstruc.2021.131435
0022-2860/© 2021 Elsevier B.V. All rights reserved.

K.S. Etsè and G. Zaragoza
Journal of Molecular Structure 1248 (2022) 131435
Fig. 1. Synthesis of 1,4-diacetyl-3,6-bis(phenylmethyl)-2,5-piperazinedione (2).
a]pyrazine-1,4-dione)) is a DKP derivative with (cyclo-L-Trp-L-Pro)
backbone. TPS-A is well known as one of the most efficient and
specific inhibitors of breast cancer resistance protein (BCRP) [24].
Indeed, after drug administration, ATP-binding cassette proteins
are produced in organs for absorption, distribution and elimination
of drugs. In serious pathologies like cancers, I was shown that
resistance of cancer cells to anticancer drugs comes from the
increasing production of ATP-binding cassette proteins [25]. It is
therefore suggested that modulation of the activity of these pro-
teins could be beneficial in resistant cancer therapy. BCRP is one of
ATP-binding cassette proteins. Recently, Fani et al. described a new
series of DKP derivatives as simultaneous effective inhibitors of
αβ-tubulin and BCRP proteins [26]. Although most of cyclic dipep-
tides with biochemical properties have been isolated from natural
organisms ranging from bacteria to humans [8,12,27–29], others
[13,30] have been synthesized chemically through a systematic
structure−activity analysis, by taking inspiration from the struc-
ture of lead compounds. The structure of cyclodipeptides could
therefore highly variable, ranging from the simplest, unmodified
cyclic dipeptides [12,31] to heavily modified skeletons [28,32].
The conformations of various DKPs have been experimentally
investigated both in solution and the solid state, as well as by
computational methods [33–37]. It turned out that the molecu-
lar conformation of cyclic dipeptides could depend on the relative
configuration of the two amino acids, the nature of their residue,
and N-acetylation or methylation [33–36]. Furthermore, intra- and
intermolecular hydrogen bondings could be the major contribu-
tors but other intermolecular interactions, such as π-stacking and
C=O/C=O dipole packing forces [35,36] could also contribute sub-
stantially to the crystal structure conformation. In this line, Adler-
Abramovich and coworkers showed that in the case of cyclo(L-
Phe-L-Phe), ordered vertically aligned nanotubes material obtain-
ing could arise from stacking interaction between aromatic moi-
eties providing the energetic contribution needed for the formation
of such well-ordered structures [38].
tained using DFT calculation. Finally, as potential drug candidate,
molecular docking study on breast cancer resistance protein was
performed.
2. Materials and methods
All solvents (ethylene glycol, dichloromethane, petroleum ether)
and reagents (L-phenylalanine and acetic anhydride) were pur-
chased from TCI or Sigma-Aldrich. Solvents for chromatography
were used as received without further purification. All reactions
were monitored and analyzed by TLC using Macherey-Nagel 0.2
mm pre-coated Alugram® N/UV254 silica gel or alumina gel plates.
˚
Column chromatography was conducted using 60 A, 70–230 mesh,
63–200 μm silica gel supplied by Grace Davison or Sigma-Aldrich.
Petroleum ether refers to the fraction boiling at 40–60 °C. Analyses
by 1H and 13C NMR spectroscopy were achieved at 298 K using a
Bruker DRX 400 NMR spectrometer operating at 400.13 and 100.61
MHz, respectively. Chemical shifts, δ, were quoted in parts per mil-
lion downfield from TMS and were referenced from the residual
solvent peaks (CHCl3: 7.26 ppm; CHCl3: 77.36 ppm; CDCl3: 77.16
ppm) or TMS. Spin multiplicities were indicated by the following
symbols: s (singlet), t (triplet), m (multiplet). The melting point
was determined in an open glass capillary using an OSI 9100 Elec-
trothermal digital melting point apparatus, and was uncorrected.
High resolution mass spectrometry analyses were performed on a
Bruker DaltonicsSolariX FT-ICR spectrometer operating at 9.4 Tesla
in the Laboratory of Mass Spectrometry of the University of Liège.
The Raman spectrum was recorded directly through the glass vial
with a Labram 300 (Horiba) Raman spectrometer interfaced with
a He-Ne laser (laser line at 632.8 nm) with a power of 4 mW on
the sample. The infrared spectrum was obtained with an IS5 in-
strument (Thermo Scientific) interfaced with an ID7 ATR module
equipped with a monolithic diamond ATR crystal.
2.1. Synthesis, crystallization and characterization of
As part of our studies on development of new diketopiperazine
derivatives and the molecular structure determination, we became
interested in N,N’-diacetyl-cyclodiphenylalanine (2) (Fig. 1). This
work aims to investigate the effects of the acetyl groups and to de-
termine if the starting residues chirality affects the structural con-
formation of the cyclopeptide 2 [39]. According to literature, this
goal could be achieved by the full characterization and the deter-
mination of the molecular structure of 2 [40,41]. Furthermore, the
experimental results will be compared to similar reported struc-
tures that could provide a critical comparison analysis of the data.
The scope of this work will finally expand to the biological poten-
tiality of this new DKP. This work report therefore on the synthesis
and the full characterization of 1,4-diacetyl-3,6-bis(phenylmethyl)-
2,5-piperazinedione by NMR, infrared and Raman spectroscopy.
Furthermore, full description of the molecular structure obtained
by X-ray diffraction analysis and interactions stabilizing the crystal
structure of this DKP are described. Particular attention was paid
to analyze the conformation adopted by the diketopiperazine ring
thanks to Cremer and Pople parameters. The conformation adopted
by the new DKP was also compared to the optimized structure ob-
1,4-Diacetyl-3,6-bis(phenylmethyl)-2,5-piperazinedione (2)
In a one-neck round-bottomed flask equipped with a magnetic
bar, was added 3.3 g of L-phenylalanine (2 mmol) and 40 mL of
ethylene glycol. The suspension was stirred at 170 °C for 4 h. Af-
terward, the resulting brown solution was concentrated under high
vacuum and cooled at −20 °C overnight. The obtained light brown
precipitate was collected by filtration and washed with 50 mL of
ethanol and dried under high vacuum. The crude product was al-
lowed to react in the next step without further purification.
To obtain compound 2, 30 mL of acetic anhydride was added
to the collected solid of the previous step and refluxed for 6h. Af-
ter this period, the solvent is removed by distillation. The crude
solid was dissolved in 50 mL of dichloromethane and washed three
times with 30 mL of a saturated solution of NaHCO3 and once with
50 mL of water. The organic fraction was dried over MgSO4, filtered
and the solvent removed under vacuum to give a viscous orange
oil. Silica-gel column chromatography of the oil using as eluent a
mixture of petroleum ether and ethyl acetate (8:2.5 v/v) gave 2 as
a white crystalline solid (87% overall yield).
2

K.S. Etsè and G. Zaragoza
Journal of Molecular Structure 1248 (2022) 131435
electron density maps. All secondary CH2 and aromatic CH hydro-
gen atoms were refined using a riding model with Uiso(H) = 1.2
Ueq(C). The methyl hydrogen atoms were refined as a rigid group
with torsional freedom [Uiso(H) = 1.5 Ueq(C)] and the hydrogen H8
atom as a free atom.
Crystal data, data collection and structure refinement details ta-
ble (Table 1) is constructed using WinGX software [46,47]. The CIF-
file for compound 2 containing the supplementary crystallographic
data has been deposited into CCDC with number 1870902. These
data can be obtained free of charge via http://www.ccdc.cam.ac.uk/
conts/retrieving.html (or from the Cambridge Crystallographic Data
Centre, 12, Union Road, Cambridge CB2 1EZ, UK; fax: +44 1223
336033).
2.4. Hirshfeld surface analysis
The intermolecular interactions present in the crystal structure
of compound 2 were evaluated by drawing contact and shape de-
scriptors using Hirshfeld surface analysis. Molecular Hirshfeld sur-
faces were calculated using a standard (high) surface resolution
and with the three-dimensional dnorm surfaces mapped over a
˚
fixed colour scale from −0.1369 (red) to 1.1914 A (blue) with the
program CrystalExplorer17 [48].
2.5. Computational details
Geometry optimization of the molecular structure of 2 in the
gas phase was performed with the GAUSSIAN 09 revision D.01 at
0 K [49,50]. The DFT method with CAM-B3LYP functional was used
and all atoms were described with the 6-311G (D) basis set [51].
The simulated IR spectrum of compound 2 was obtained by ap-
plying the fully-automated, second-order vibrational perturbation
approach implemented in the GAUSSIAN 09. The uniform scaling
factor (0.9456) was used to correct the calculated harmonic fre-
quencies computed at the DFT level.
Fig. 2. Scanning electron micrographs of compound 2.
Analytical data for compound 2: RF (dichloromethane) 0.7; m.p.
189−192 °C. 1H NMR (400.13 MHz, CDCl3): δ 7.25−7.22 (m, 6H,
H3 + H4 + H5), 6.91−6.89 (m, 4H, H2 + H6), 4.44 (t, J = 8 Hz, 2H,
H8), 3.16−3.14 (m, 4H, H7), 2.52 (s, 6H, H11). 13C NMR (101.61 MHz,
CDCl3): δ 171.09 (C10), 167.78 (C9), 134.11 (C1), 129.91 (C2 + C6),
128.85 (C3 + C5), 128.09 (C4), 58.42 (C8), 39.99 (C7), 27.69 (C11)
(see Figures S1−S5 in the Supplementary Materials). MS (ESI): m/z
+
calculated for C22H23N2O4 = 379.16578 [M+H]+, found 379.16682
2.6. Molecular docking studies
[M+H]+. IR (ν, cm−1): 3396, 3072, 2949, 1703, 1386, 1361, 1223,
1134, 1035, 744, 707, 615 [Fig. 2(b)].
Molecular docking calculations were performed with
AUTODOCK 4.2 [52] according to the reported method [53].
The cocrystal structure of QZ59 with P-Glycoprotein (PDB code
2.2. Scanning electron microscopy
˚
3G60, resolution of 4.40 A) retrieved from the protein data bank
Scanning electron microscopy (SEM) was used to characterize
the particle size and morphology of different crystals of 2. The
SEM morphological analyses of the samples were performed in the
Laboratoire de Chimie Inorganique Structurale (GreenMAT, CESAM)
of the University of Liège, on a FEG-ESEM XL30 (FEI) apparatus
with an accelerating voltage of 15 kV under high vacuum. Samples
were deposited on carbon tapes. Sputtering deposition was done
with gold target under argon atmosphere (Balzers, SCD004, Sput-
ter coater).
(PDB) was used in the docking study [54]. All the ligand and
water molecules attached to the proteins were removed. The miss-
ing hydrogen atoms were added and non-polar hydrogens were
merged into their corresponding carbon atoms using AutoDock
3
˚
Tools. A grid box size of 50 × 50 × 50 A was defined around the
P-Glycoprotein ligand binding domain. 3D molecular structure of
compound 2 obtained from the X-ray crystal structure data was
used for the docking.
Robust poses population resulting from 100 runs docking sim-
ulation using genetic algorithm were considered for the analyses.
The Docking Parameter File (DPF) was generated with Lamarckian
genetic algorithm by setting the protein as rigid molecule. Finally,
the DLG (Docking Log File) file is created by running Autodock with
DPF as input file. Out of several interactions possible, the best pose
with lowest binding energy and the most probable was considered
for further protein-ligand docking. PyMOL [55] was used for dock-
ing conformation representation.
2.3. Single-crystal x-ray diffraction analysis
A small portion of 2 was dissolved in dichloromethane and
allowed to evaporate slowly at room temperature, yielding crys-
tals suitable for X-ray crystallographic analysis. The data were col-
lected by applying the omega and phi scans method on a Bruker
APPEX−II diffractometer using graphite-monochromated Mo-Kα
˚
radiation (λ = 0.71073 A) from a fine-focus sealed tube source at
100 K following the previous report [42]. The structure was solved
using SHELXT [43] and finally refined by full-matrix least-squares
based on F2 by SHELXL [44]. An empirical absorption correction
was applied using the SADABS program [45]. All non-hydrogen
atoms were refined anisotropically and the hydrogen atom posi-
tions were included in the model on the basis of Fourier difference
3. Results and discussion
3.1. Synthesis and NMR
The title compound (2) was prepared from L-(S)-phenylalanine
using the condensation method [17] followed by acetylation
3

K.S. Etsè and G. Zaragoza
Journal of Molecular Structure 1248 (2022) 131435
Table 1
Crystal data of 1,4-diacetyl-3,6-bis(phenylmethyl)-2,5-piperazinedione (2).
Identification code
NIQHON
Empirical formula
Formula weight
Temperature
C22 H22 N2 O4
378.42
100 K
˚
Wavelength
0.71073 A
Crystal system
Space group
Orthorhombic
Pbca
˚
Unit cell dimensions
a = 7.8241(3) A
α = 90 °
β = 90 °
γ = 90 °
˚
b = 12.3441(5) A
˚
c =19.2615(8) A
3
˚
Volume
1860.30(13) A
Z
4
Density (calculated)
Absorption coefficient
F(000)
1.351 mg/m3
0.094 mm-1
800
Crystal size
0.52 × 0.43 × 0.16 mm3
Theta range for data collection
Index ranges
2.1 to 28.3 °
-10<=h<=10, -16<=k<=16, -25<=l<=24
16262
Reflections collected
Independent reflections
Completeness to theta = 28.282 °
Absorption correction
Max. and min. transmission
Refinement method
Data / restraints / parameters
Goodness-of-fit on F2
Final R indices [I>2sigma(I)]
R indices (all data)
Extinction coefficient
Largest diff. peak and hole
2315 [R(int) = 0.038]
100 %
Semi-empirical, Multi-scan
0.888 and 0.959
Full-matrix least-squares on F2
2315 / 0 / 132
1.057
R1 = 0.0388, wR2 = 0.0643
R1 = 0.0472, wR2 = 0.0977
n/a
-3
˚
0.29 and -0.21 e.A
Table 2
(Fig. 1). In the first step of the synthesis, a suspension of L-
phenylalanine in ethylene glycol was heated at 170 °C with stirring
for 4 h to give the corresponding cyclodipeptide. The cyclodipep-
tide intermediate was then acetylated in the presence of acetic
anhydride to provide its N,N’-diacetylated derivative. Extraction of
the product with dichloromethane followed by purification by col-
umn chromatography gave 2 as a white crystalline solid in 87%
overall yield.
1H and 13C NMR analyses (see Figures S1−S6 in the Supple-
mentary Materials) of compound 2 provided evidence for the pres-
ence of the phenyl rings, as indicated by two multiplets in the
range δ 7.25−6.89 ppm in 3:2 proportions, and four signals in 13C
NMR between 135 and 128 ppm. As expected, the methyl group
of the acetyl substituents resonated as singlets around 2.5 ppm
(1H NMR) and 28 ppm (13C NMR). On 13C NMR spectroscopy, the
carbonyl groups led to two deshielded singlets at ca. 168 and 171
ppm. The four protons of the two C6H5-CH2- linker are observed
as a multiplet around 3.15 ppm. The zoom in of the benzyl protons
peaks is provide in Figure S2. Of note, assignment of all the peaks
was corroborated by 2D NMR spectroscopy (Figure S5). Finally, the
electron-spray ionization mass spectrum showed a peak at m/z
379.16 corresponding to the protonated molecular ion [M+H]+.
˚
Selected bond lengths (A) and bond angles ( °) in compound 2.
˚
Bond lengths (A)
Bond angles ( °)
C1-C7
1.5064 (16)
1.5547 (16)
1.4690 (14)
1.5160 (16)
1.2122 (13)
1.3855 (14)
1.4235 (15)
1.2104 (14)
1.4957 (16)
C1−C7−C8
N1i−C8−C9
N1i−C8−C7
C9−C8−C7
O1−C9−N1
O1−C9−C8
N1−C9−C8
C9−N1−C10
C9−N1−C8i
C10−N1−C8i
O2−C10−N1
113.01 (9)
116.51 (9)
110.38 (9)
107.34 (9)
123.95 (10)
117.87 (10)
117.86 (9)
124.49 (9)
120.98 (9)
114.52 (9)
118.21 (10)
C7−C8
C8−N1i
C8−C9
C9−O1
C9−N1
N1−C10
C10−O2
C10−C11
In round brackets are the estimated standard deviations. Symmetry code: –x, −y,
−z.
1,4-diacetyl-3,6-bis(phenylmethyl)-2,5-piperazinedione (2), the two
stereocentres are of opposite configuration, R and S, whereas ini-
tially only L-(S)-phenylalanine was used for the synthesis. Obtain-
ing the meso compound was confirmed by its zero optical rotation.
Inversion of stereochemistry at the chiral carbon in the α-position
of a carbonyl group is quite common and has been described sev-
eral times in the synthesis of DKPs [16]. The X-ray diffraction anal-
ysis also reveals that product 2 crystallizes in the centrosymmetric
orthorhombic space group (Pbca), with half of the molecule in the
asymmetric unit around an inversion centre located at the centroid
of the diketopiperazine ring. A perspective view and atom labelling
of the X-ray crystal structure of 2 is shown in Fig. 3a. Selected in-
teratomic bond distances and angles are given in Table 2.
3.2. Scanning electron microscopy
The morphology of the crystals obtained after column chro-
matography was characterized by scanning electron microscopy
(SEM). As shown in Fig. 2, the particle sizes are not uniform. The
particles exhibit plate-like shape and their thickness is about 40
μm. All the particles possess clean and smooth surface facets, sug-
gesting that they are well crystallized. Moreover, they have similar
irregular polyhedral morphologies.
From the data collected in Table 2, it is apparent that all the
C−N bond distances are different, especially those of the C9−N1
˚
˚
[1.3855 (14) A] and N1−C10 [1.4235 (15) A] bonds of the imide
group. Comparative study with similar derivatives highlight a dis-
tinctive characteristic of the 1,4-diacetyl-2,5-piperazinedione core.
As in the analogues 3 - 6 (Fig. 4) [33,34] the endocyclic C(O)−N
bond is shorter compared to the exocyclic one. The increased
double-bond character in the endocyclic C(O)−N bond presumably
3.3. Crystal structure of 1,4-diacetyl-3,6-bis(phenylmethyl)-
2,5-piperazinedione (2)
The X-ray diffraction analysis of high quality crystals ob-
tained by slow evaporation of dichloromethane reveals that in
4

K.S. Etsè and G. Zaragoza
Journal of Molecular Structure 1248 (2022) 131435
Table 3
H-Bond interactions in compound 2.
D−H···A
C6−H6···O1
C7−H7B···O2
[Symm]
[−1/2 − x, 1/2 + y, z]
[−1 + x, y, z]
0.99
˚
D−H (A)
0.95
˚
H···A (A)
2.52
2.55
˚
D···A (A)
3.3368 (14)
144
3.4413 (14)
150
D−H···A ( °)
angles C9i−N1i−C8−C9 and N1i−C8−C9−N1 are also close to 25 °
[−24.69 (15) ° and 23.90 (15) °, respectively], but opposite in sign,
thus leading to a succession of internal rotation angles around
the ring with alternating positive and negative signs, suggesting
a flattened chair conformation of the diketopiperazine ring. Fur-
ther examination of the parameters given in Table 2 shows that
the internal bond angle N1i−C8−C9 is 116.51 (9) °, a value close to
that measured for related compounds, and that the internal bond
angle C9−N1−C8i is slightly compressed in 2 as in analogues 5
and 6 (Fig. 4), i.e. 120.98 (9) ° vs 119.8 and 120.3 ° [58]. On the
other hand, a very low deviation of the acetyl group from the
plane C9−N1−C8i was observed as evidenced by the torsion an-
gle C9−N1−C10−C11 of −2.05 (16) °.
The crystal packing of 2 is stabilized by short intermolecular in-
teractions along the ab plane (Fig. 3b). Thus, H-bond interactions
(C7−H7B···O2, Table 3) are present along the a axis, between a
benzyl H atom of one molecule and the oxygen atom of the acetyl
group of an adjacent molecule. In addition, there is another inter-
molecular H-bond interaction between each carbonyl oxygen of the
DKP ring of one molecule and the hydrogen at C6 of the phenyl
group of another molecule (C6−H6···O1). These interactions lead to
a succession with right, then inverted disposition of the molecules
in the cell providing thereby high stabilisation to the crystal pack-
ing.
Furthermore, examination of X−H···Cg(π-ring) distances reveals
the existence of an additional interaction between C4−H4 and the
π electrons of the aromatic ring (C1→C6) [51] of a neighboring
molecule (0.5 + x, y, 0.5 − z). This contact is characterized by
˚
short distances (dπcH) of 2.88 A between H4 and the centroid of
the phenyl ring with an angle of 136 ° between the C4−H4 bond
and the ring center (Figure S7). The perpendicular distance (Hperp
)
˚
between H4 and the plane of the phenyl ring is 2.79 A and the
angle of approach of the vector Hπc to the plane of the aromatic
ring (θ) is 75.97 °, indicating that hydrogen H4 is located above the
center of the ring and that the C4−H4 bond points towards a ring
carbon. Altogether, this interaction as well as the dihedral angle
C1−C7−C8−C9 (54.54 °) could explain why the molecule adopts a
folded S shape with the two phenyl rings folded over and under
the diketopiperazine ring.
Fig. 3. (a) The molecular structure of compound 2, showing the atom-labelling
scheme. Displacement ellipsoids are drawn at the 50% probability level. Symme-
try code: –x, -y, -z. (b) Intermolecular C7-H7B···O2 (violet) and C6-H6···O1 (cyan)
H-bond interactions along the ab plane of the crystal packing of compound 2.
3.4. Conformational and DKP ring puckering analysis
The particular folded conformation adopted by compound 2
let us to investigate the DKP ring puckering. The calculated Cre-
mer and Pople puckering parameters [59,60] indicate that the DKP
ring of compound 2 adopts a flattened chair conformation with
ꢀ = 0.00 ° and a total puckering amplitude (Q) = 0.2233 (11)
Fig. 4. Structures of some reported 1-acetyl- and 1,4-diacetyl-2,5-piperazinedione
analogues.
˚
A. Very close values were found for trans-(R,S)-1,4-diacetyl-3,6-
reflects the enhanced delocalization of the lone pair of electrons
of the nitrogen atom onto the endocyclic imide linkage. The third
dimethylpiperazine-2,5-dione (6) (Fig. 4), in which positions 3 and
6 of the DKP ring are substituted by methyl groups in the trans
configuration, implying therefore that intermolecular interactions
do not play a significant role in the conformation of the DKP
ring. This is in contrast to the boat conformations adopted by
1,4-diacetylpiperazine-2,5-dione (3) [61] and cis-(S,S)-1,4-diacetyl-
3,6-dimethylpiperazine-2,5-dione (5) (Fig. 4). Importantly, in these
compounds, carbons 3 and 6 are not substituted (compound 3) or
i
˚
C−N bond, C8−N1 , is the longest with a length of 1.4690 (14) A
in the range of those observed for related compounds [56,57].
From the value of the torsion angle C8−C9−N1−C8i which
measures the deviation of the amide bond from planarity, it is
apparent that the endocyclic amide linkage C9−N1 is twisted as
characterized by the large ω value [−25.01 (16) °]. The dihedral
5

K.S. Etsè and G. Zaragoza
Journal of Molecular Structure 1248 (2022) 131435
Table 4
Table 5
Calculated and experimental torsion angles ( °) in compound 2.
Global reactivity descriptor of compound 2.
Angle
Definition
Optimized structure
X-ray structure
Parameters (eV)
Values
ω1
ω2
ψ1
ψ2
φ1
φ2
α1
α2
β1
β2
γ 1
γ 2
C8−C9−N1−C8i
C8i−C9i−N1i−C8
N1−C8i−C9i−N1i
N1i−C8−C9−N1
C9−N1−C8i−C9i
C9i−N1i−C8−C9
C8−C9−N1−C10
C8i−C9i−N1i−C10i
C1−C7−C8−C9
−21.72
21.72
−25.01 (16)
25.01 (16)
−23.89 (15)
23.90 (15)
24.69 (15)
−24.69 (15)
156.06 (10)
−156.06 (10)
54.54 (12)
−54.54 (12)
−17.21 (17)
17.21 (17)
ELUMO
EHOMO
Energy band gap |EHOMO-ELUMO
Ionization potential (I = -EHOMO
-1.885
-9.012
7.127
9.012
1.885
3.563
0.140
8.069
-8.069
9.128
2.265
−20.57
20.57
|
)
21.24
Electron affinity (A = -ELUMO
)
−21.24
158.71
−158.71
60.26
Chemical hardness (η = (I-A)/2)
Chemical softness (z = 1/2η)
Electronegativity (c = (I + A)/2)
Chemical potential (μ = -(I + A)/2)
Electrophilicity index ω = μ2/2η
Maximum charge transfer index (ꢁNmax = - μ / η)
C1i−C7i−C8i−C9i
O1−C9−N1−C10
O1i−C9i−N1i−C10i
−60.26
−15.67
15.67
Symmetry code: –x, −y, −z.
are not at the origin of the S form adopted by the molecule, as
suggested above. Furthermore, one can suggest an interactions be-
tween the acetyl oxygen O2 and hydrogen H8 located in the α
position of the amide group. Indeed, atoms O1, H8, and O2 are
practically aligned (angle O1···H8···O2 = 170.8 °). With an angles
C8−H8···O1 of 70.27 ° and C8−H8···O2 of 100.57 °, this disposi-
tion is probably due to internal geometrical constraints. These in-
tramoleculars orientation in compound 2 have also the effect of
moving the methyl group away from the DKP ring and thus avoid-
ing steric repulsion between the methyl and phenyl substituents.
possess a methyl group in the cis position (compound 5), demon-
strating thereby the crucial role played by N and/or α-C sub-
stituents in determining the conformations of diketopiperazines.
The preference for an aromatic part of an amino acid residue
like phenylalanine and tyrosine to fold over the DKP skeleton is
previously reported [62]. The folded conformation has been ob-
served both in the solid state and in solution. This phenomenon
is not well understood and plausible explanations have been pro-
posed. First, NMR studies reported by Kopple and Marr [63] indi-
cated that this folded form was favored over other possible con-
formations of the arylmethyl side chain by an enthalpy change
resulting from a direct rather than solvent-mediated interaction
between the aryl and DKP rings [64]. Because of the aromatic
nature of phenylalanine, attractive forces between the two rings
[64] as well as dispersion forces favoring, among others, CH···π
non-covalent interactions [39] have also been recognized as im-
portant factors in the stabilization of the folded conformation. In
the case of compound 2, the CH···π interaction could not be sug-
3.6. Frontier molecular orbital
The frontier molecular orbitals formed by the Highest Occupied
Molecular Orbital (HOMO) and the Lowest Unoccupied Molecular
Orbital (LUMO) are the most important molecular orbitals con-
tributing in the chemical reactivity. The energy of the HOMO level
is linked to the ionization potential, whereas the LUMO energy
level is linked to the electron affinity. The gap between HOMO
and LUMO energies level of a selected compound characterizes
therefore the molecular chemical stability [65]. A large gap sug-
gests good stability and lower reactivity of the compound in chem-
ical reactions. Other parameters of reactivity relative to these or-
bitals and the relation are reported in Table 5. The HOMO and
LUMO molecular orbitals of 2 have been calculated and presented
in Fig. 5c and 5d. The LUMO orbitals are mainly localized over the
DKP ring and acetyl units. The results gave and HOMO and LUMO
orbitals energies levels values of -9.012 eV and -1.885 eV respec-
tively giving an energy gap of 7.127 eV. This gap value reveals a
good stability of 2.
˚
˚
gested (C8−H8···π; dπcH = 3.805 A; d = 1.275 A; α = 96.65 °,
θ = 70.42 °). Budesinsky also suggested that, to escape repul-
sion with the vicinal carbonyl group, the benzyl side-chain of
the phenylalanine residue prefers the pseudo-axial orientation
and is stacked over the DKP ring, consistent with a presumed
face-to-face attractive interaction between the phenyl and DKP
rings [37]. For compound 2, the calculated geometric parameters
˚
(Cg−Cg = 3.625 A, α = 44 °, β = 8.8 °, γ = 45 °, CgI_Perp = 2.562
˚
˚
A, CgJ_Perp = −3.562 A) are compatible with an intramolecular in-
teraction between the phenyl and DKP rings and this could finally
explain why complete inversion of stereochemistry at one chiral C
α
carbon center occurred during its synthesis from optically pure L-
3.7. IR and Raman spectroscopy
(S)-phenylalanine.
3.5. DFT molecular modeling
The new compound is also characterized by IR and Raman spec-
troscopy. In the IR and Raman spectra of compound 2 (Fig. 6), the
most intense absorption located around 1710 cm−1 was assigned
to the stretching of the carbonyl groups [66–68]. Note that only
one strong absorption (1714 cm−1 in Raman and 1703 cm−1 in IR)
is obtained for both endocyclic and exocyclic carbonyl groups in
2 (Figs. 6a and 6b), while two strong bands resulting from asym-
metric and symmetric stretch were normally expected as in imides
[56,69,70] and anhydrides [71]. In addition, the in-plane defor-
mation vibrations of C=O that is expected in the region 625
70 cm−1 is obtained at 707 cm−1 in IR (692 cm−1 in Raman).
The only one peack obtained in Raman and infrared spectroscopy
for carbonyl group can be attributed to the symmetry present in
the molecule in addition to the C=O bond lengths (C9−O1 and
C10−O2) that are practically identical [1.2122 (13) and 1.2104 (14)
The structure of the DKP 2 was optimized at the 6-311G (D)
level using CAM-B3LYP functional of the DFT method in the gas
phase. The optimized structure of 2 was obtained showing “trans-
phenyl conformations” (Fig. 5a). Superimposition of the crystallo-
graphic (in black) with optimized (in grey) structures of compound
2 presented in Fig. 5b show good agreement. The slight differences
with the experimental X-ray structure comes from the effects of
crystal packing. Actually, the conformations assumed by the dike-
topiperazine ring are best described by the values of the torsion
angles ω, ψ, and φ (Fig. 5e), and these are summarized in Table 4.
For the optimized structure, all ωi, ψi, and φi values (i = 1
or 2) are generally close to those obtained from the X-ray data
of compound 2 (Table 4). These similarities reveal that the opti-
mized structure is symmetrical as the crystal structure of 2. Fig. 8b
shows the satisfactory match between the theoretical and the crys-
tal structure of 2, which indicates that intermolecular interactions
˚
A, respectively]. The strecking corresponding to N–C bond is ob-
served at 1386 cm−1 in IR and 1372 cm−1 in Raman. The aromatic
C=C-C and C=C stretching vibrations of phenyl in 2 correpond to
6

K.S. Etsè and G. Zaragoza
Journal of Molecular Structure 1248 (2022) 131435
Fig. 5. Calculated optimized structures (a), overlay of the crystallographic (in black) with optimized (in grey) structures of compound 2. Frontiers HOMO (c) and LUMO (d)
molecular orbital of 2 and torsion angle definition (e).
the peacks at 1223 and 1134 cm−1 respectively in IR spectrum.
The HS mapped over di shows multiple red spots distributed
These vibrations are observed at 1212 and 1116 cm−1 respectively
on the surface (Fig. 7), revealing that most of the atoms of 2 are
closed to the surface. The same tendency is observed on the sur-
face mapped over de (Fig. 7) demonstrating that neighbor’s nuclei
are also close to the surface. The intermolecular interactions were
then analyzed through the mapping of dnorm by considering the
contact distances di and de from a point on the surface to the near-
est nucleus inside and outside the surface, respectively. The surface
mapped over dnorm highlights well-defined red spots correspond-
ing to intermolecular distances shorter than the sum of the van der
Waals radii (Fig. 7). These dominant interactions are intermolecular
C−H···O and O···H−C hydrogen bonds. The white spots and blue re-
gions on the surface reveal distances equal to and longer than the
sum of the van der Waals radii, respectively [74,77].
in Raman. Much less informative absorptions included weak C–H
stretching vibration bands between 2800 and 3100 cm−1 for the
various alkyl and phenyl substituents. The very low intensity band
observed around 3396 cm−1 in IR spectra could be attributed to
water O-H vibration coming from the adsorption of water by com-
pound 2 [72,73]. The simulated IR spectrum present in Figure 10c
shows very good agreement with the experimental. By the way, a
single peak in the ν(CO) stretch region at 1700 cm−1 was also dis-
played in the simulated IR spectrum of 2 (Fig. 6c). The similarity
between the experimental and theoretical IR spectra reflect also a
good agreement of the obtained theoretical structure.
According to the Hirshfeld surface of compound 2 mapped with
3.8. Hirshfeld surface analysis
˚
the shape index (−1.0 to 1.0 A) (Fig. 7), convex blue regions cor-
respond to hydrogen-donor groups, whereas concave red regions
correspond to hydrogen-acceptor groups. In addition, the decom-
position of the Hirshfeld surface mapped over shape index con-
firms the existence of C4−H4···π interactions as discussed in the
X-ray structural description section (Fig. 7). The curvedness that
measures ‘‘how much shape’’ property was obtained on the HS
and shown in Fig. 7. The absence of large flat areas on the surface
(low values of curvedness) reveals a lack of π–π planar stacking
The nature and amount of intermolecular interactions in the
crystal packing of compound 2 were described using Hirshfeld sur-
face (HS) analysis. The dnom (normalized contact distance) is ob-
tained by considering the global relation between the distances of
any surface point to the nearest interior (di) and exterior (de) atom
and the Van der Waals radii of the atoms. In addition, HS mapped
with shape index and curvedness (Fig. 7) were used to complete
the non-covalent interactions in the molecular packing [74–76].
7

K.S. Etsè and G. Zaragoza
Journal of Molecular Structure 1248 (2022) 131435
Fig. 6. Experimental Raman (a) and infrared (b) spectra of compound 2, together with its simulated infrared spectrum (c).
contact. In contrary, many curvatures domains divide the surface
into patches that could associated with low interaction with other
molecules.
3.9. Electrostatic potential and crystal voids
In addition to molecular orbital, molecular properties could be
described by mapping the molecular electrostatic potential that
play a key role for identify reactive positions on the molecular
surface [79]. This map is useful to predict the position of nucle-
ophile and electrophile attack. The molecular electrostatic potential
of compound 2 is calculated at B3LYP/6–31G(d,p) level of theory
and mapped on the Hirshfeld surfaces (Fig. 7). The blue and red
regions around the different atoms observed on the surface corre-
spond to positive and negative electrostatic potentials respectively.
It appears clearly that, the electron-rich site are mainly localized
around the oxygen atoms.
The distances from the HS to the nearest nucleus inside the sur-
face (di) and outside the surface (de) are used in CrystalExplorer
program to generate a 2D histogram named molecular fingerprint
[77,78]. Since there is the immediate environment providing the
various contacts of the selected molecule is used to construct the
fingerprint, this latter is unique and allows to evaluate the con-
tributions of interatomic contacts to the HS. The full and decom-
posed fingerprint plots with the percentage values calculated for
all intermolecular contacts are shown in Fig. 7. The results re-
veal that the major contributions to the Hirshfeld surface are from
H···H contacts (58.2%), H···O/O···H (24.8%) and C···H/H···C interac-
tions (14.2%). The other intermolecular contacts contribute little to
the overall fingerprint plot and appear insignificant.
The folding observed in the conformation adopted by the de-
scribed DKP, the intermolecular contact and the position of elec-
tron rich sites provide particular stacking in the crystal that could
8

K.S. Etsè and G. Zaragoza
Journal of Molecular Structure 1248 (2022) 131435
Fig. 7. Three-dimensional Hirshfeld surface of compound 2 mapped over di (in the range 1.0532 to 2.4216 A, de (in the range 1.0546 to 2.191 A), dnorm (in the range -0.1370
to 1.1914), shape-index (-1.000 to 1.000), shape index highlighting C4-H4···Cg contacts as red spots (Symmetry: 0.5 + x, y, 0.5 – z) and curvedness (in the range of -4 to 4).
The two-dimensional fingerprint plots of compound 2 and the decomposed contributions. Molecular electrostatic potential (-0.0567 to 0.0450 a.u.) and crystal voids present
in the title compound 2. The surfaces are transparent to allow visualization of the molecule.
9

K.S. Etsè and G. Zaragoza
Journal of Molecular Structure 1248 (2022) 131435
Fig. 8. The color-coded interaction energy frameworks of compound 2 viewed along the crystallographic a, b and c axes. Energy framework diagram for electrostatic,
dispersion and total interaction energy. The energy factor scale is 80 and the cut-off is 5.00 kJ/mol.
describe by analyzing the voids in the crystal structure. A view of
crystal voids present in 2 is shown in Fig. 7. The voids parame-
ters of the title compound gave void volume of 193.70 A3, an area
of 649.81 A2, a globularity of 0.249 and asphericity value of 0.183.
Thank to these values, low voids percentage of 10% was obtained
attesting the effect of molecular folding and a compact stacking of
the molecules in the crystal structure.
coded according to their interaction energy within a cluster of ra-
˚
dius of 3.8 A. As defined by Spackman and Mackinzie, the total in-
termolecular energy Etot (kJ/mol) relative to the reference molecule
(in black) is obtained by summing the energies of four main com-
ponents, comprising electrostatic (Eele), polarization (Epol), disper-
sion (Edis) and exchange-repulsion (Erep) with scale factors of 1.057,
0.740, 0.871 and 0.618, respectively [81,82]. The different energy
components are resumed in Table S1.
The graphical representation of Coulomb interaction energy
(red), dispersion energy (green) and total interaction energy (blue)
of 2 viewed down a, b and c axes are presented in Fig. 8. The val-
ues of the total energy components are -34.4 kJ/mol, -9.0 kJ/mol,
-104.9 kJ/mol, 71.6 kJ/mol for Eele, Epol, Edis and Erep respec-
tively. Altogether, the total interaction energy of -90.1 kJ/mol is
obtained. Thanks to the symmetry present in the crystal pack-
ing only four different interactions color coded molecules are ob-
served. The interaction with molecules colored in green is the
much stronger (-40.1 kJ/mol) and is characterized by the low-
3.10. Interaction energy framework
The various intermolecular contacts depicted in the structural
and packing stabilization of this novel DKP are governed by inter-
action energies that could be computed and present graphically as
energy diagrams. Therefore, the intermolecular interactions ener-
gies of 2 were calculated using CE-B3LYP/6–31G(d,p) energy model
available in CrystalExplorer [80]. The 3D topology of the energy
framework of compound 2 is presented on Fig. 8. The radii of the
cylinders are proportional to the magnitude of interaction energy.
The selected compound (in black) is surrounded by molecules color
˚
est distance between molecular centroids (7.31 A) with the mu-
10

K.S. Etsè and G. Zaragoza
Journal of Molecular Structure 1248 (2022) 131435
In addition, one oxygen of Ser975 is pointed toward the center of
one phenyl ring of 2 leading to a probable π···π interaction. A
relative suitable binding energy (-8.96 kcal/mol), ligand efficiency
(-0.32) and inhibition constant (0.272 μM) were obtained for the
best pose used for the analysis. The binding domain occupied by
2 in BCRP and the relative energy are consistent with the studies
of Fani et al. for another DKP derivatives [26]. The docking results
suggest clearly that compound 2 can interact with BCRP active site
and could therefore could be consider as inhibitor candidate of this
protein.
4. Conclusion
In this study,
a
novel N,N’-diacetylated cyclodipeptide 1,4-
has been
diacetyl-3,6-bis(phenylmethyl)-2,5-piperazinedione
2
prepared exclusively as the (R,S)-stereoisomer starting from the
optically pure L-(S)-phenylalanine. X-ray diffraction analysis con-
firm the optical rotation result establishing complete inversion of
stereochemistry at the chiral carbon center of one phenylalanine
residue. The intermolecular H-bond interactions with oxygen
atoms as well as intermolecular C−H···π interactions with the
phenyl rings stabilizing the crystal packing are discussed. In ad-
dition, suggested intramolecular π···π interaction information is
provided and its analysis combined to describe the compact “S”
shaped conformation observed in 2 with the two phenyl residues
folded facing the diketopiperazine ring. Results demontrated that
the title compound possesses a symmetry center located at the
centroid of the DKP ring. Analyses of DKP ring puckering using the
Cremer and Pople puckering parameters gave values of ꢀ = 0.00 °
˚
and Q = 0.2233 (11) A highlighting a flattened chair confor-
mation. DFT calculations of the structural features and infrared
spectroscopy results show very good agreement with the X-ray
structure and experimental measurements. The energy gap of the
HOMO and LUMO orbitals (7.127 eV) reveals a good stability of the
described DKP. To get more insight on compound 2, the various
intermolecular interactions in the crystal packing were further
analyzed by mapping contact descriptors (dnom, di, de) and shape
property (shape-index, curvedness) on the Hirshfeld surface and
the 2D fingerprint. The analysis of the fingerprint revealed that
interactions are dominated by H···H, H···O/O···H and C···H/H···C
contacts. In addition, the calculated ESP surface of 2 showed
that electron rich domains are mainly located around the oxygen
atoms. The first topology of interaction energies stabilizing the
structural and packing were obtained and presented graphically
as energy framework diagrams. Finally, as potential anticancer
molecule, this study provide the molecular docking of 2 with
BCRP. The results showed that 2 could bind with the BCRP active
site especially with residues Phe728, Tyr949, Ser975 and Val978
and could be consider as inhibitor candidate of this protein.
Fig. 9. (a) Cartoon representation of the docked DKP 2 (in magenta) with BCRP. (b)
Zoom on the modulator binding site containing compound 2. (c) Superimposition
of the domain occupancy of 2 (in magenta) and TPSA (in yellow). (d) View showing
amino acids that could interact with the docked molecule and the probable inter-
actions highlighted as dash black dots lines.
tual C7−H7B···O2/O2···H7B−C7 intermolecular HBs as described
above. Although the topology of the coulomb and dispersion en-
ergy frameworks seems to be similar, an additional interaction are
present in the second one forming a diagonal line within the prin-
cipal rectangular grid. As a main contributor in the total interaction
energy, the same topology of the dispersion energy is observed for
the total energy.
3.11. Molecular docking study
Other symmetric with or not acetylated DKP are currently in
preparation in view to elucidate their structure. In addition, the
binding mode of 2 with BCRP reported here will be confirmed by
pharmacological in vitro testing. Since cyclo Phe-Phe is described
to exhibit antidepressant and antidementia activity and thanks to
the wide range of biological activity exhibited by DKP derivatives,
in vitro and in vivo studies will be conducted to depict the ability
of 2 to cross blood brain barrier and especially as neuroprotective
agent, but also to study its interaction with AMPA receptors.
Numerous DKP derivatives are described to exhibit anticancer
activity. In this work, we explore the possible binding mode of the
DKP 2 as novel inhibitor of breast cancer resistance protein (BCRP).
The molecular docking results showed that compound 2 can easily
enter the BCRP active site (Fig. 9a and 9b). The docking solution of
2 in the active site is therefore compared to the position of TPSA
a well know DKP inhibitor of BCRP. As shown in Fig. 9c, the acety-
lated DKP 2 occupy the same binding domain like TPSA. In the ac-
tive site, the compound 2 is surrounded by various close residues
(Met67, Tyr303, Phe332, Ser725, Phe725, Phe728, Tyr949, Ser975,
Val978). One oxygen atom of the acetyl group of 2 could form a
hydrogen bond with the residue Tyr949. Furthermore, the contact
between one endocyclic oxygen of the DKP ring with Val978 is
suggested (Fig. 9d). This contact and the proximity of Phe728 are
interesting since Aller and coworkers showed that these residues
play an important role in drugs binding mechanism of BCRP [54].
Author Contributions
Koffi Sénam Etsè: Investigation; Conceptualization; Data cura-
tion; Formal analysis; Writing – original draft; Writing – review &
editing;
Guillermo Zaragoza: Crystal data collection and analyses.
11

K.S. Etsè and G. Zaragoza
Journal of Molecular Structure 1248 (2022) 131435
Declaration of Competing Interest
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cyclic dipeptides: Occurrence in natural products, synthesis, and sensory eval-
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Flavors, 1042, 2010, pp. 111–120.
The authors declare that there are no conflicts of interest re-
garding the publication of this article.
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the identification of diketopiperazines in chicken essence, Eur. Food Res. Tech-
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Acknowledgments
The authors thank the University of Liège for supporting this
research work by letting us to access to most of the platform facil-
ities, C. Malherbe (Laboratoire de Chimie Analytique Inorganique,
MolSys, University of Liège) for IR and Raman analyses, and C.
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Supplementary material associated with this article can be
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