Study of supramolecular self-assembly of pyridone and dihydropyridone co-crystal: Synthesis, crystal structure, Hirshfeld surface, DFT and molecular docking studies

Article abstract of DOI:10.1016/j.molstruc.2021.130214

Dihydropyridone is synthesized by the multicomponent condensation reactions (MCRs), followed by three different oxidation methods to synthesize pyridone. The 3-D self-assemblies of both the compounds were determined using the single-crystal X-ray diffraction method. Dihydropyridone products are found as a racemic mixture in synthesis and crystalized as co-crystal. Similar structural conformations are observed in both the compounds but stabilized with different non-covalent interactions. Hirshfeld surface analysis is done to analyze the various intermolecular interactions in both the structure. This study gives the clue of driving force in the self-assembly of molecules in crystal lattices. The propensity of inter-molecular contacts to construct the supramolecular assembly was further studied using DFT. The geometrical optimizations of both the compounds were done by the electronic structure method using density functional theory (DFT) to identify the active sites and explore the molecules' chemically reactive parameters. Further, both compounds were docked with Survivin Protein and Kinesin Eg5 protein to analyze the binding affinity with targeted protein.

Full text of DOI:10.1016/j.molstruc.2021.130214

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Journal of Molecular Structure 1235 (2021) 130214
Contents lists available at ScienceDirect
Journal of Molecular Structure
journal homepage: www.elsevier.com/locate/molstr
Study of supramolecular self-assembly of pyridone and
dihydropyridone co-crystal: Synthesis, crystal structure, Hirshfeld
surface, DFT and molecular docking studies
Lalhruaizelaa, Brilliant N. Maraka, Dipanta Gogoia, Jayanta Dowaraha, Balkaran S. Sranb,
Zodinpuia Pachuaua, Ved Prakash Singha,∗
a Department of Chemistry, School of Physical Sciences, Mizoram University, Aizawl-796004, Mizoram, India
b Department of Chemistry, Guru Nanak Dev University, Amritsar, Punjab 143005, India
a r t i c l e i n f o
a b s t r a c t
Article history:
Dihydropyridone is synthesized by the multicomponent condensation reactions (MCRs), followed by three
different oxidation methods to synthesize pyridone. The 3-D self-assemblies of both the compounds were
determined using the single-crystal X-ray diffraction method. Dihydropyridone products are found as a
racemic mixture in synthesis and crystalized as co-crystal. Similar structural conformations are observed
in both the compounds but stabilized with different non-covalent interactions. Hirshfeld surface analysis
is done to analyze the various intermolecular interactions in both the structure. This study gives the clue
of driving force in the self-assembly of molecules in crystal lattices. The propensity of inter-molecular
contacts to construct the supramolecular assembly was further studied using DFT. The geometrical opti-
mizations of both the compounds were done by the electronic structure method using density functional
theory (DFT) to identify the active sites and explore the molecules’ chemically reactive parameters. Fur-
ther, both compounds were docked with Survivin Protein and Kinesin Eg5 protein to analyze the binding
affinity with targeted protein.
Received 29 November 2020
Revised 25 February 2021
Accepted 25 February 2021
Available online 5 March 2021
Keywords:
Non-covalent interactions
Docking
Intra-molecular
Intermolecular
DFT
Hirshfeld
Crystal
© 2021 Elsevier B.V. All rights reserved.
Introduction
anti-inflammatory [13]. Cyanopyridines are important intermedi-
ates for synthesizing many biological important analogs like nicoti-
Dihydropyrimidinones (DHPM’s) and their derivatives are het-
erocyclic compounds synthesized by multicomponent reactions
[1,2]. This class of compounds are structural analogs of monas-
trol became important to the field of medicinal chemistry be-
cause monastrol is a very important bio-molecule having many
biological activities [3]. Other DHPMs analogs have been synthe-
sized since then, revealing several other pharmacological proper-
ties [4]. Monastrol is the protagonist of the DHPMs class. Sev-
eral studies have revealed that its inhibitory action on human ki-
nesin Eg5 leads to mitotic arrest and, consequently, to apoptosis
[5]. At first, this was the main action described for this class of
compounds, but some studies have shown other possible targets
for these molecules, such as centrin [6], calcium channels [7] and
topoisomerase I [8].
namide, nicotinic acid, and isonicotinic acid. 3-cyano-2-pyridone
are very significant frameworks in the past few decades. These
are the structural basis of the alkaloid ricinine, the first known
cyano group-containing alkaloid. Milrinone is also a 3- cyano-2-
pyridone derivative used for the treatment of congestive heart fail-
ure [14,15]. Some derivative of 3-cyano2-pyridone has shown an-
ticancer activity [16–18]. 3-cyano-4,6-diaryl-2-pyridone derivatives
I and IV (Fig. 1) possess anticancer activity due to their ability to
act as survivin inhibitors [19]. Undoubtedly, the need to bridge the
gap between minimizing side effects and the mode of action of an-
timitotic drugs encourage us for further investigations towards the
synthesis of the novel potent cytotoxic compound [20,21].
New analogs are designed based on Monastrol kinesin inhibitor
and Survivin inhibitor pharmacophore analysis and bio-isoester
group application (Fig. 2).
2-pyridones are a particular class of compounds with unique
pharmacophores that exhibit several biological activities such as
analgesic [9], antimalarial [10], antitumoral [11], anti-HIV [12], and
Given the pharmacological importance of 2-pyridone deriva-
tives, the investigations of their structural and electronic properties
are fundamental to know the influence of different groups in the
molecule to discover the relationship of these groups with their
biological properties [22–26].
∗
Corresponding author.
E-mail address: vedsinghbhu@gmail.com (V.P. Singh).
https://doi.org/10.1016/j.molstruc.2021.130214
0022-2860/© 2021 Elsevier B.V. All rights reserved.

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Lalhruaizela, B.N. Marak, D. Gogoi et al.
Journal of Molecular Structure 1235 (2021) 130214
ica gel (60-120 mesh) was employed, and eluents were ethyl ac-
etate/hexane mixtures. Melting points of all the compounds were
recorded on the electrically heated instrument and are uncor-
rected. The FT-IR spectrum of solid was recorded in reflectance
(ATR) mode with Shimadzu IRAffinity-1S spectrophotometer. 1H
and 13C NMR spectrums were recorded in CDCl3 on Bruker
AVANCE 300 MHz spectrometer. The chemical shifts are expressed
in parts per million (ppm) using tetramethylsilane (TMS) as an in-
ternal standard. Mass spectra were done using 6545 QTOF with
1290 Infinity II HPLC equipped with an ESI source. X-ray data of
compounds 3, 4 enantiomer co-crystal, and 5 were collected on
an Oxford Diffraction Xcalibur CCD and Bruker Axs Smart Apex-1
diffractometer, respectively, at room temperature and processed by
SAINT [27]. Lorentz and polarization effects and empirical absorp-
tion corrections were applied using SADABS from Bruker [28]. The
structure was solved by Intrinsic Phasing methods, using ShelXT
[29], and refined by least-squares refinement methods based on F2,
using ShelXL [30]. All non-hydrogen atoms were refined anisotrop-
ically. All hydrogen atoms were fixed geometrically with their Uiso
values 1.2 times that of the phenylene carbons and 1.5 times that
of the methyl group. The hydrogen atoms of the heteroatoms were
located from the difference Fourier synthesis and were refined
isotropically. All calculations were performed using the Olex2 pack-
age [31].
Fig. 1. Cyanopyridones as anticancer agents.
In this study, we report the synthesis of a new molecule con-
taining 2-pyridone and 2-dihydropyridone. Both compounds are
fully characterized by IR, 1H NMR, 13C NMR spectrometry, and
single-crystal X-ray diffraction (SCXRD). DFT calculations of both
molecules carried to study the molecular geometric structure, vi-
brational frequencies, 1 H & 13C NMR chemical shifts, NBO, ener-
gies, and molecular electrostatic potential (MEP) using DFT/B3LYP
method with 6-311++ G(d,p) basis. Also, Hirshfeld surface analyses
were performed to analyze molecular packing and surface interac-
tions. In silico analysis, it is used to locate small molecules binding
affinity in the target protein’s active site. In other words, molecu-
lar docking investigated the ligand’s most stable conformation in
the protein’s binding package and scored. Therefore, the molecular
docking analyses investigated between compounds 3, 4 & 5 and
the target protein.
Synthesis of ethyl 6-amino-4-(4-chlorophenyl)-5-cyano-2-methyl-4H-
pyran-3-carboxylate
In
a 100 mL RB, ethanol (40 mL) was taken and 4-
Materials and methods
chlorobenzaldehyde (10 mmol) & malononitrile (10 mmol) added
and stirred. The mixture ethyl acetoacetate (10 mmol) was added,
followed by piperidine (0.2 mL, 2 mmol). The mixture was then
stirred at room temperature in an open atmosphere for 10 mins.
The precipitate of ethyl 6-amino-4-(4-chlorophenyl)-5-cyano-2-
methyl-4H-pyran-3-carboxylate was obtained, which was filtered
using vacuum sintered glass funnel and then finally washed with
cold methanol.
Synthesis and crystallization
All Chemicals were purchased from Sigma-Aldrich and Merck.
Reactions were checked with TLC on pre-coated aluminum sheets
of Merck using an appropriate solvent system, and chromatograms
were visualized under UV light. For column chromatography, sil-
Fig. 2. Kinesin inhibitor (Monastrol 1) & Survivin inhibitor (Compound 2) based designed analog.
2

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Lalhruaizela, B.N. Marak, D. Gogoi et al.
Journal of Molecular Structure 1235 (2021) 130214
Table 1
Crystal data and structure refinement for compound 3 & 4 co-crystal & 5.
Identification code
5 (CCDC 2035459)
16H13ClN2O3
3& 4 (co-crystal) (CCDC 2035460)
Empirical formula
Formula weight
Temperature/K
Crystal system
Space group
C
C16H15ClN2O3
316.73
318.75
296.15
296.15
Triclinic
triclinic
P-1
P-1
˚
A, b, c /A
9.264(5), 9.923(5), 10.327(5)
9.4919(8), 12.9828(11), 14.9912(13)
α/°
β/°
γ /°
64.060(5)
104.030(3)
73.767(5)
106.305(3)
66.810(5)
105.518(3)
3
˚
Volume/A
778.1(7)
1604.6(2)
Z
2
4
ρ
calcg/cm3
1.352
1.319
μ/mm-1
0.259
2.230
F(000)
328.0
664.0
Crystal size/mm3
0.2 × 0.18 × 0.14This is not a pattern of ’ccdc’ external object linking.
0.23 × 0.18 × 0.15
CuKα (λ = 1.54178)
7.524 to 94.034
Radiation
MoKα (λ = 0.71073)
4.424 to 57.932
2ꢀ range for data collection/°
Index ranges
-12 ≤ h ≤ 12, -13 ≤ k ≤ 13, -13 ≤ l ≤ 13
24274
-8 ≤ h ≤ 8, -12 ≤ k ≤ 12, -14 ≤ l ≤ 14
13149
Reflections collected
Independent reflections
Data/restraints/parameters
Goodness-of-fit on F2
Final R indexes [I>=2σ (I)]
Final R indexes [all data]
4048 [Rint = 0.0678, Rsigma = 0.0512]
4048/0/205
2814 [Rint = 0.0279, Rsigma = 0.0231]
2814/0/409
1.057
1.054
R1 = 0.0503, wR2 = 0.1223
R1 = 0.0873, wR2 = 0.1406
0.21/-0.42
R1 = 0.0378, wR2 = 0.0969
R1 = 0.0433, wR2 = 0.1022
0.20/-0.24
−3
˚
Largest diff. peak/hole / e A
precipitate formation. The solution was collected in a conical flask,
sealed with rubber septa, and then placed inside a freezer (-20
to -25°C) for 2 hours. The precipitate of ethyl 4-(4-chlorophenyl)-
5-cyano-2-methyl-6-oxo-1,4,5,6-tetrahydropyridine-3-carboxylate
formed (confirmed by TLC), which was collected by filtration.
The filtrate that contains the remaining product was subjected to
purification by column chromatography. This method facilitates
the pure precipitate of the product and reduces the working time
and solvent required for purification.
1H NMR(300 MHz, CDCl3): δ 1.18 – 1.23 (3H, t, CH3CH2-, J = 7.2
Hz); 2.44 (3H, s, CH3-); 4.08 – 4.17 (3H, m, CH3CH2-, CH,); 4.46
– 4.49 (1H, d, CH-, J = 6.9 Hz); 7.18 – 7.20 (2H, d, Ar-H, J = 8.4
Hz); 7.30- 7.33 (2H, d, Ar-H, J = 8.4 Hz); 8.42 (1H,s, -NH,). 13C
NMR (300 MHz, CDCl3): δ 14.04 (C, CH3), 18.91 (C, CH3), 40.91
(C, CH-Ar), 41.02 (C, CCN),60.90 (C, CH2O), 107.35 (C, CCO2Et),
113.87 (C, CN), 129.18 (C, Ar), 129.21 (C, Ar), 134.36 (C, CCl), 134.44
(C, C-CH), 146.06 (C, CCH3),162.89 (C, CO2Et), 165.16 (C, C=O).
IR (KBr): 3263 (NH), 2252 (CN), 1705 (COOR), 1674 (RCONHR),
733 (CCl). HRMS (ESI) (m/z): calculated for C16 H15O3N2Cl (NH4)
[M+NH4]+ = 336.11095, found 336.11069.
Fig. 3. Ortep Diagram of 3 & 4 enantiomeric co-crystal (a) & 5 (b).
Synthesis of ethyl 4-(4-chlorophenyl)-5-cyano-2-methyl-6-oxo-1,4,5,6-
tetrahydropyri dine-3-carboxylate
General procedure for the synthesis of ethyl 4-(4-chlorophenyl)-5-
cyano-2-methyl-6-oxo-1,6-dihydropyridine-3-carboxylate
To
a
2-neck 150 mL RB the synthesized ethyl 6-amino-
Method A (microwave-assisted reaction)
4-(4-chlorophenyl)-5-cyano-2-methyl-4H-pyran-3-carboxylate
(6.7 mmol) was dissolved in ethanol (50 mL) at 80°C. Iodine
(10 mol %) was added to the reaction vessel and refluxed using
Graham condenser for 2-4 hours monitored by TLC (EtOAc/hexane
3:7). After the reaction was completed, the mixture was con-
centrated under reduced pressure and then treated with hypo
solution (5 mol%) to remove un-reacted iodine. The organic layer
was back-extracted with ethyl acetate (twice), usual workup and
purification over silica gel column using Hexane: EtOAc (70:30)
afforded 3 & 4 enantiomer mixture ethyl 4-(4-chlorophenyl)-5-
cyano-2-methyl-6-oxo-1,4,5,6-tetrahydropyridine-3-carboxylate.
To a solution of ethyl 4-(4-chlorophenyl)-5-cyano-2-methyl-
6-oxo-1,4,5,6-tetrahydropyridine-3-carboxylate (3.52 mmol) in
ethanol (15 mL), DDQ (3.52 mmol) was added and irradiated in
the microwave oven for 2 minutes. The reaction was monitored
by TLC (EtOAc/hexane 1:1). After the reaction was completed,
ethanol (10 mL) was added to the reaction vessel, which allows
for pure crystals of 2-pyridone (which was further collected). The
remaining solvents that contain 2-pyridone were collected and
purified over silica gel by column chromatography Hexane: EtOAc
(1:1).
Method B (thermal assisted reaction)
Additional technique
To a solution of ethyl 4-(4-chlorophenyl)-5-cyano-2-methyl-
The organic layer (ethyl acetate) obtained from the workup
process was concentrated in a rotary evaporator by preventing
6-oxo-1,4,5,6-tetrahydropyridine-3-carboxylate (3.52 mmol) in
ethanol (15 mL), DDQ (3.52 mmol) was added and heated on
3

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Lalhruaizela, B.N. Marak, D. Gogoi et al.
Journal of Molecular Structure 1235 (2021) 130214
Fig. 4. (a) Hydrogen bonding between enantiomer in crystal packing (b) extended hydrogen bonding network (c) crystal packing in unit cell (d) alternate packing architecture
(e) packing pattern of around both enantiomer 3 & 4.
Table 2
˚
Non-covalent interactions (A) for 3, 4 & 5 in crystals. Cg is the centroid of the rings
D-H…A
D-H
H…A
D….A
D-H...A
Symmetry Operation
Compound 3 & 4
N(2)..H(2A)…O(1)
C(8)..H(8)…O(2)
0.783
0.980
0.803
0.930
0.960
0.930
0.980
2.266
2.447
2.245
2.722
2.700
2.481
2.367
3.376
3.938
2.928
3.036
3.307
3.044
3.353
3.553
3.294
3.211
168.27
146.34
173.59
125.85
148.43
146.11
143.85
3-x,1-y,1-z
3-x,1-y,1-z
x,y,z
N(5)..H(5)…O(2)
C(21)..H(21)…N(1)
C(32)..H(32C)…N(4)
C(1)-H(1)…O(4)
2-x,1-y,1-z
-x,1-y,-z
1+x,y,z
C(24)-H(24)…O(5)
C(16)- H(16A)…Cg (C1-C6)
C(18)- H(18)…Cg (C1-C6)
C(12)- H(12C)…Cg (C17-C22)
Intramolecular
1-x,1-y,-z
C(12)..H(12B)…O(2)
C(28)..H(28B)…O(5)
Compound 5
0.960
0.960
2.274
2.238
2.931
2.938
124.85
129.05
N2-H2…O1
0.961
0.960
0.930
1.836
2.662
2.385
3.384
2.761
2.784
3.481
3.259
167.99
143.48
156.48
-x,1-y,-z
-x,1-y,-z
1-x,-y,1-z
C12-H12C….O1
C5-H5…O2
C4-H4… Cg(C1-C6)
C1-H1… Cg(N2, C7, C8, C10, C11, C13)
Intramolecular
C(12)..H(12A)…O(2)
C(12)..H(12B)…O(2)
0.960
0.960
2.801
2.617
2.920
2.920
98.64
87.45
4