Quantitative analysis of hydrogen and chalcogen bonds in two pyrimidine-5-carbonitrile derivatives, potential DHFR inhibitors: An integrated crystallographic and theoretical study

Article abstract of DOI:10.1039/d0ra07215j

Two potential bioactive pyrimidine-5-carbonitrile derivatives have been synthesized and characterized by spectroscopic techniques (1H and 13C-NMR) and the three dimensional structures were elucidated by single crystal X-ray diffraction at low temperature (160 K). In both structures, the molecular conformation is locked by an intramolecular C-H?C interaction involving the cyano and CH of the thiophene and phenyl rings. The intermolecular interactions were analyzed in a qualitative manner based on the Hirshfeld surface and 2D-fingerprint plots. The results suggest that the phenyl and thiophene moieties have an effect on the crystal packing. For instance, the chalcogen bonds are only preferred in the thiophene derivative. However, both structures uses a common N-H?O hydrogen bond motif. Moreover, the structures of 1 and 2 display 1D isostructurality and molecular chains stabilize by intermolecular N-H?O and N-H?N hydrogen bonds. The nature and extent of different non-covalent interactions were further characterized by the topological parameters derived from the quantum theory of atoms-in-molecules approach. This analysis indicates that apart from N-H?O hydrogen bonds, other non-covalent interactions are closed-shell in nature. A strong and linear N-H?O hydrogen bond shows intermediate bonding character between shared and closed-shell interactions. The molecular docking analysis suggests that both compounds display potential inhibitory effect against the dihydrofolate reductase (DHFR) enzyme from humans and Staphylococcus aureus.

Full text of DOI:10.1039/d0ra07215j

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Quantitative analysis of hydrogen and chalcogen
bonds in two pyrimidine-5-carbonitrile derivatives,
potential DHFR inhibitors: an integrated
Cite this: RSC Adv., 2020, 10, 36806
crystallographic and theoretical study†
a
b
a
Lamya H. Al-Wahaibi, Kushumita Chakraborty, Nora H. Al-Shaalan,
b
c
d
Mohamed Yehya Annavi Syed Majeed, Olivier Blacque,
Ali A. El-Emam, M. Judith Percino
Aamal A. Al-Mutairi,
e
f
b
and Subbiah Thamotharan
*
Two potential bioactive pyrimidine-5-carbonitrile derivatives have been synthesized and characterized by
1
13
spectroscopic techniques ( H and C-NMR) and the three dimensional structures were elucidated by
single crystal X-ray diffraction at low temperature (160 K). In both structures, the molecular
conformation is locked by an intramolecular C–H/C interaction involving the cyano and CH of the
thiophene and phenyl rings. The intermolecular interactions were analyzed in a qualitative manner based
on the Hirshfeld surface and 2D-fingerprint plots. The results suggest that the phenyl and thiophene
moieties have an effect on the crystal packing. For instance, the chalcogen bonds are only preferred in
the thiophene derivative. However, both structures uses a common N–H/O hydrogen bond motif.
Moreover, the structures of 1 and 2 display 1D isostructurality and molecular chains stabilize by
intermolecular N–H/O and N–H/N hydrogen bonds. The nature and extent of different non-covalent
interactions were further characterized by the topological parameters derived from the quantum theory
of atoms-in-molecules approach. This analysis indicates that apart from N–H/O hydrogen bonds, other
non-covalent interactions are closed-shell in nature. A strong and linear N–H/O hydrogen bond shows
intermediate bonding character between shared and closed-shell interactions. The molecular docking
analysis suggests that both compounds display potential inhibitory effect against the dihydrofolate
reductase (DHFR) enzyme from humans and Staphylococcus aureus.
Received 22nd August 2020
Accepted 27th September 2020
DOI: 10.1039/d0ra07215j
rsc.li/rsc-advances
Introduction
Pyrimidine and its related derivatives have long been known as
1
efficient chemotherapeutic agents. The chemotherapeutic
potency of pyrimidine-based drugs is attributed to their inhib-
Department of Chemistry, College of Sciences, Princess Nourah Bint Abdulrahman itory effect on the biosynthesis of vital enzymes responsible for
a
University, Riyadh 11671, Saudi Arabia
nucleic acids such as thymidylate synthetase (TSase), thymidine
phosphorylase (TPase), dihydrofolate reductase (DHFR) and
reverse transcriptase (RTase). Several pyrimidine-based drugs
b
Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of
Chemical and Biotechnology, SASTRA Deemed University, Thanjavur-613401, India.
E-mail: thamu@scbt.sastra.edu
2–6
are currently used as efficient anticancer and antiviral agents
c
Department of Chemistry, University of Z u¨ rich, Winterthurerstrasse 190, 8057 Z u¨ rich,
7
–10
against human immunodeciency viruses (HIV),
hepatitis B
herpes simplex virus (HSV) and SARS-CoV
In addition, several pyrimidine-based drugs are
Switzerland
11,12
13
d
virus (HBV),
Department of Chemistry, College of Sciences, Imam Mohammad Ibn Saud Islamic
14
University (IMSIU), Riyadh 11671, Saudi Arabia
virus.
e
Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, currently used as antibacterial agents. Trimethoprim was early
Mansoura 35516, Egypt
discovered as a potent drug mainly in the treatment of urinary
f
Unidad de Pol ´ı meros y Electr ´o nica Org a´ nica, Instituto de Ciencias, Benem ´e rita
tract infections acting by inhibition of dihydrofolate reductase
Universidad Aut ´o noma de Puebla, Val3-Ecocampus Valsequillo, Independencia O2
1
5
(
DHFR). The next generations of DHFR inhibitors including
Sur 50, San Pedro Zacachimalpa, Puebla-C.P.72960, Mexico
16
17
18
brodimoprim, epiroprim and iclaprim were developed as
†
Electronic supplementary information (ESI) available: Relative contributions of
different atom–atom contacts, selected torsion angles, 2D-ngerprint plots, highly potent antibacterial drugs for the treatment of severe
molecular graphs for intermolecular interactions and experimental details of in respiratory tract infections. DHFR inhibitors bind bacterial
vitro bioactivity. CCDC 2022218 and 2022219. For ESI and crystallographic data
5
DHFR 10 times tighter than it does to vertebrate DHFR. By
in CIF or other electronic format see DOI: 10.1039/d0ra07215j
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virtue of their mechanism of action, antibacterial DHFR including the Hirshfeld surface, 2D-ngerprint plots, energy
inhibitors exert their activity through blocking synthesis of frameworks, PIXEL energy, and Bader's quantum theory of
32
DNA, RNA and proteins, thereby arresting bacterial cell atoms-in-molecules (QTAIM). The rst four criteria ((a)
1
9,20
growth.
Pyrimidine-based DHFR inhibitors are also used as topology, (b) electron density, (c) Laplacian of electron density
21,22
potent antiprotozoal agents for the treatment of malaria,
trypanosomiasis and leishmaniasis. It has been reported atom) of Koch–Popelier have been used to characterize the
and (d) mutual penetration of the hydrogen and the acceptor
23
24
33
that the barbituric acid, a pyrimidine heterocylic nucleus, was nature and strength of non-covalent interactions as previously
34,35
used as a molecular recognition species by non-covalent inter- reported.
In addition, molecular docking study of the title
actions especially hydrogen bonds or via coordination to metal pyrimidine-5-carbonitrile derivatives as DHFR inhibitors is
ions. Using this molecular recognition approach, different types reported.
of receptors that belong to organic, inorganic and organome-
25
tallic have been developed for barbituric acid.
Materials and methods
Synthesis and crystallization
In view of the diverse applications of the pyrimidine deriv-
atives, we have synthesized two pyrimidine-5-carbonitrile
derivatives and crystal structures of these compounds have
been studied in detail in the present investigation. The reported
compounds vary with respect to the thiophene and phenyl
substituents. A CSD (Cambridge Structural Database; CSD
The pyrimidine-5-carbonitrile derivatives 1 and 2 were synthe-
sized starting with the appropriate aldehydes A via condensa-
tion with thiourea B and ethyl cyanoacetate C, in ethanol, in the
presence of anhydrous potassium to yield the intermediates 6-
26
Version 5.41, November 2019; update 1 March 2020) search
36
(
thiophen-2-yl)-2-thiouracil-5-carbonitrile D and 6-phenyl-2-
was conducted using the compound 1 as a template in which
substituents at 2 and 4 positions kept ‘X’ (any) and this search
yielded 8 hits (csd refcodes: GAHTIS, ILEREY, MUTGOY,
MUTGUE, OKUWEY, SEDTAY, XAYLUF and ZAPQEO). In all
37
thiouracil-5-carbonitrile E, which were reacted with bromo-
ethane in the presence of potassium carbonate to yield the
target compounds 1 and 2 (Scheme 1).
Bromoethane (1.1 g m, 0.01 mol) and anhydrous potassium
carbonate (1.38 g, 0.01 mol) were added to a solution of the
appropriate 2-thiouracil-5-carbonitrile D or E (0.01 mol) in DMF
these structures, a strong and directional N–H/O hydrogen
2
2
bonded R
(8) synthon is formed between amino and carbonyl
groups of the pyrimidine ring except in 2-amino-4-(3,4-
dimethyoxyphenyl)-6-oxo-1,6-dihydropyrimidine-5-carbonitrile
(
10 mL) and the mixture was stirred at room temperature for 12
hours. Water (15 mL) was the added to the reaction with stirred
for further 30 minutes. The precipitated crude product was
27
N,N-dimethylformamide solvate (csd refcode: SEDTAY ). This
2
2
self-assembled R (8) synthon was disrupted due to the pres-

ltered, washed with cold water, dried and crystallized from
ence of N,N-dimethylformamide solvate. However, the carbonyl
group of the solvate has participated in a N–H/O bond with
amino group of the pyrimidine moiety.
aqueous ethanol. The pure single crystals of compounds 1 and 2
were obtained by slow evaporation of ethanolic solution at room
temperature.
Among 8 hits, 3 structures (6-oxo-4-propyl-2-(propylthio)-1,6-
dihydropyrimidine-5-carbonitrile; csd refcode: ILEREY, 2-[(4-
2
-Ethylsulfanyl-6-(thiophen-2-yl)-3,4-dihydro-4-
28
oxopyrimidine-5-carbonitrile (1). Yellow transparent block crys-
tals; yield 1.87 g m (71%); mp 282–284 C; mol. formula (mol wt):

uorobenzyl)sulfanyl]-4-(2-methylpropyl)-6-oxo-1,6-dihydropyrim
ꢀ
29
1
idine-5-carbonitrile; csd refcode: OKUWEY
and 2-[(2-
C
3
11
H
N OS
9 3 2
(263.34). H NMR (DMSO-d
6
, 700.17 MHz): d 1.28 (t,
, J ¼ 7.4 Hz), 7.32 (t, 1H,
thiophene-H, J ¼ 4.0 Hz), 7.44–7.65 (m, 2H, thiophene-H), 12.90
methoxyethyl)sulfanyl]-4-(2-methylpropyl)-6-oxo-1,6-dihydropyrimi
H, CH
3
, J ¼ 7.4 Hz), 2.88 (q, 2H, CH
2
30
dine-5-carbonitrile; csd refcode: ZAPQEO ) were found to be
closely related structures to the title compounds. In these 3
1
3
(
2
6 3
s, 1H, NH). C NMR (DMSO-d , 176.08 MHz): d 12.08 (CH ),
nd
structures, the S atom is present at the 2 position of the pyrim-
5.88 (CH ), 98.28 (C-5), 114.98 (CN), 125.98, 127.50, 131.90,
2
idine ring. In addition to hydrogen bond donors and acceptors,
two chalcogen atoms (O and S) also present in these 3 structures
and in the title compounds. The chalcogen bond (ChB) is one of
the types of non-covalent interactions and has gained great interest
in studying the role of such a bond in different areas including
crystal engineering, materials science and biological sciences etc.
The chalcogen bond is dened as R–Ch/A, where Ch is the
chalcogen bond donor (electron-poor) and A is the chalcogen bond
acceptor (electron-rich). The lone pair carbonyl and p system
could act as chalcogen acceptors in the title compounds and their
closely related structures. Therefore, a detailed investigation has
been performed to study the nature and strength of chalcogen
136.80 (thiophene-C), 163.32 (C-2), 168.20 (C]O), 177.60 (C-6).
31
bond in the title compounds in addition to conserved and self-
2
2
assembled R
(8) synthon mediated by the N–H/O hydrogen
bond in pyrimidine-5-carbonitrile containing compounds.
To gain qualitative and quantitative insights into intra- and
intermolecular interactions, we performed different analyses, Scheme 1 The synthetic pathway for compounds 1 and 2.
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ꢁ1
FT-IR (in cm ) (NH: 3451, thiophene CH: 3028, aliphatic CH: considered) were performed using CrystalExplorer with B3LYP/
54
2841, CN: 2218, C]O: 1651, C]N: 1522).
6-31G(d,p) level of theory. For the PIXELC calculation, the
2-Ethylsulfanyl-6-phenyl-3,4-dihydro-4-oxopyrimidine-5-
electron density for the monomer of 1 and 2 (both major and
carbonitrile (2). Colorless transparent needle crystals; yield minor disordered components) has been obtained separately at
ꢀ
2
C
.03 g m (79%); mp 250–252 C; mol. formula (mol wt): the MP2/6-31G** level of theory using the Gaussian 09 program.
1
13
H
11
N
3
OS (257.30). H NMR (DMSO-d
t, 3H, CH , J ¼ 7.5 Hz), 7.12–7.24 interactions was carried out using AIMALL package. For this
, J ¼ 7.5 Hz), 2.92 (q, 2H, CH
m, 3H, Ar–H), 7.39 (d, 2H, Ar–H, J ¼ 7.8 Hz), 13.22 (s, 1H, NH). calculation, the wave functions were calculated at normalized
6
, 700.17 MHz): d 1.29
The topological analysis of the intra- and intermolecular
55
(
(
3
2
1
3
C NMR (DMSO-d
6 3 2
, 176.08 MHz): d 13.22 (CH ), 24.80 (CH ), crystal structure geometries with M06-2X-D3/cc-pVTZ level of
9
1
3
1
5.70 (C-5), 115.0 (CN), 127.22, 129.50, 131.20, 136.74 (Ar–C), theory. The dissociation energy (D ) for different non-covalent
e
ꢁ
1
56
62.98 (C-2), 168.40 (C]O), 177.54 (C-6). FT-IR (in cm ) (NH: interactions was obtained by EML formula. Various topolog-
2
450, aromatic CH: 3018, aliphatic CH: 2849, CN: 2219, C]O: ical properties such as r(r), V r(r), V(r), G(r) and H(r) were
657, C]N: 1534). The FT-IR spectra for compounds 1 and 2 are computed for intra and intermolecular interactions at their
given in the ESI.†
bond critical points (BCPs). Further, the wave functions and
cube les were used as input for the molecular electrostatic
potential surfaces of 1 and 2. These surfaces were mapped over
Single crystal X-ray diffraction
57
the electron density at 0.001 au using WFA-SAS suite.
X-ray intensity data were measured at 160 K from single crystals
of 1 and 2 on a Rigaku OD XtaLAB Synergy, Dualex, Pilatus 200
K diffractometer using a single wavelength X-ray source (Cu Ka
Molecular docking analysis
˚
The 3D structures of dihydrofolate reductase (DHFR) enzyme
radiation: l ¼ 1.54184 A). Pre-experiment, data collection, data
38
reduction and analytical absorption correction were per- from two different species (Homo sapiens; PDB ID: 2W3A and
formed with the program suite CrysAlisPro (Version Staphylococcus aureus; PBD ID: 2W9H) were used in the present
.171.40.39a, Rigaku Oxford Diffraction, 2018).Using Olex2,
39
1
study to investigate the anticancer and antibacterial activities of
the structure was solved with the SHELXT structure solution the title pyrimidine derivatives utilizing an in silico molecular
40
program and the structural renement was performed with docking approach. The docking calculation was performed
41
the SHELXL 2018/3 program package. In 2, the phenyl ring was using the Schr ¨o dinger suite 2019-4 (Schr ¨o dinger, LLC, New
disordered over two sets of positions with site-occupancy factors York, NY, 2019). For docking calculation, the protein structure
of 0.501(3) and 0.499(3). For both structures, the position of was prepared using the protein prep wizard module with default
amine H atom was located from a difference Fourier map and settings. Similarly, the title compounds and control inhibitor
rened freely along with its isotropic temperature factors. The (trimethoprim) were prepared using the liprep module with
methyl H atoms were constrained to an ideal geometry with OPLS3e force eld. The grid box was constructed based on the
˚
position of the trimethoprim inhibitor complexed with human
C–H ¼ 0.98 A and U (H) ¼ 1.5U (C), but were allowed to rotate
iso
eq
58
freely about the C–C bond. The remaining H atoms were xed and bacterial enzymes. The glide XP docking was performed to
˚
predict the best binding pose and assess inhibitory potential
by a riding model approach with C–H ¼ 0.95–0.99 A and Uiso(H)
¼
1.2Ueq(C). PLATON was used to check the result of the X-ray using docking scores.
42
analysis.
Results and discussion
Details of theoretical calculations
The present work probes the role of two substituents (thiophene
and phenyl moieties) at the 4 position of the pyrimidine ring
For all the density functional theory (DFT) calculation, the M06-
th
43
44
2
X functional and cc-pVTZ basis set was used with the
on the intermolecular interactions, crystal packing, evaluation
of non-covalent interactions, energy frameworks and inhibitory
potential against DHFR enzyme from human and methicillin
resistant Staphylococcus aureus. Further, a detailed evaluation of
the intermolecular interactions using the QTAIM approach is
presented.
45
incorporation of Grimme's dispersion correction (D3). The
geometry optimization carried out using the rened models of 1
and 2 (major disordered component) with Gaussian 09
46
program. Further, the optimized structures were subjected to
vibrational frequency calculation in order to conrm the energy
minima on the potential energy surface.
The H involving bond lengths were adjusted to their typical
Description of crystal structures of 1 and 2
˚
˚
neutron diffraction values (C–H ¼ 1.083 A and N–H ¼ 1.009 A).
Aer resetting the bond lengths, the resultant molecular Single crystal data and renement parameters for 1 and 2 are
geometries were used for the following analysis: (i) qualitative presented in Table 1. Compound 1 {systematic name: 2-
analysis of intermolecular interactions using Hirshfeld (ethylthio)-1,6-dihydro-6-oxo-4-(thiophen-2-yl)pyrimidine-5-carbo
47
48
surface
and 2D-ngerprint plots
with the program nitrile} crystallizes in the monoclinic system with the space group
CrystalExplorer-17.5 (ref. 49) and (ii) intermolecular interaction P2 /n. Compound 2 {systematic name: 2-(ethylthio)-1,6-dihydro-
1
energies (Etot) for dimers of 1 and 2 using PIXELC module of 6-oxo-4-phenylpyrimidine-5-carbonitrile} crystallizes in the
50–53
ꢀ
CLP program package.
The energy frameworks of these two triclinic system with the centrosymmetric P1 space group.
structures (for 2, the major disordered component was Thermal ellipsoidal plots of compounds 1 and 2 are shown in
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Table 1 Crystal data and refinement parameters for crystals 1 and 2
1
2
Crystal data
Chemical formula
C
11
H
9
N
3
OS
13 11 3
C H N OS
M
r
263.33
Monoclinic, P21/n
160 (1)
257.31
Crystal system, space group
Temperature (K)
a, b, c (A)
a, b, g ( )
V (A )
Triclinic, P1ꢀ
160 (1)
˚
ꢀ
14.5546 (2), 4.9907 (5), 17.1813 (3)
4.6908 (2), 9.2376 (3), 14.6613 (3)
94.308 (2), 93.766 (2), 100.924 (3)
619.95 (4)
2
90, 113.268 (2), 90
1146.50 (12)
4
3
˚
Z
Radiation type
Cu Ka (l ¼ 1.54184)
Cu Ka (l ¼ 1.54184)
ꢁ1
m (mm
)
4.10
2.25
ꢁ3
rCalc (g cm
)
1.526
0.09 ꢂ 0.09 ꢂ 0.03
1.378
0.13 ꢂ 0.03 ꢂ 0.02
3
Crystal size (mm )
Data collection
Diffractometer
XtalLab Synergy, Dualex, Pilatus
XtalLab Synergy, Dualex,
Pilatus 200K diffractometer
Analytical
200K diffractometer
Absorption correction
Analytical
Tmin, Tmax
0.745, 0.908
0.848, 0.960
No. of measured, independent
11 447, 2336, 2147
13 068, 2524, 2219
and observed [I > 2s(I)] reections
R
int
0.027
0.625
0.037
0.625
ꢁ1
˚
(sin q/l)max (A
)
Renement
R[F > 2s(F )], wR(F ), S
No. of reections
2
2
2
0.025, 0.069, 1.06
0.033, 0.089, 1.02
2336
2524
No. of parameters
H-atom treatment
159
205
H-atom treated by a mixture of independent
and constrained renement
0.29, ꢁ0.23
H-atom treated by a mixture of independent
and constrained renement
0.30, ꢁ0.31
ꢁ
3
˚
Drmax, Drmin (e A
)
CCDC no.
2022218
2022219
Fig. 1. As mentioned in the experimental section, the phenyl ring structures of 1 and 2 are in close agreement with their corre-
of 2 was disordered over two orientations with nearly equal site sponding X-ray structure geometry.
occupancy factors. The thioethyl moiety is nearly coplanar with
the pyrimidine ring in both 1 and 2. The dihedral angle formed
ꢀ
Intramolecular interactions
between the mean planes of these groups being 7.28 in 1 and
ꢀ
ꢀ
6
.37 in 2. It should be noted that the phenyl ring (27.45–28.20
The molecular conformation of 1 and 2 is stabilized by an
intramolecular C–H/C interaction involving one of the protons
in minor and major disordered components) is more twisted
ꢀ
than the thiophene ring (5.51 ) with respect to the mean plane of
(H11) of the thiophene ring and the C9 atom of cyano group. A
the pyrimidine ring.
similar intramolecular interaction has also been observed in
The structural superimposition of X-ray structures of 1 and 2
is given in Fig. 1. As can be seen from Fig. 1, the phenyl ring is
slightly twisted compared to thiophene ring. The optimized
many cyano containing organic compounds reported earlier from
59–61
our group.
This intramolecular interaction was further
examined in both X-ray and optimized structures using QTAIM
analysis. In the X-ray geometry of 1, the bond path is established
between H and cyano carbon (hence it is a C–H/C interaction)
whereas in the corresponding optimized structure, the bond path
is shied to cyano N from cyano carbon (hence it is a C–H/N
interaction). The molecular graphs showing the intramolecular
interaction in X-ray and optimized structures of 1 and 2 are
depicted in Fig. 2. The topological parameters for these interac-
tions are summarized in Table S1.† From the analysis, we note
that the intramolecular interaction observed in X-ray and opti-
mized structures of 1 and 2 shows van der Waals type nature
Fig. 1 ORTEP diagrams of compounds (a) 1, (b) major disordered
component of 2 and (c) minor disordered component of 2 drawn at
the 50% probability level. Atom-numbering scheme is given.
(based on KP-4 rule) except C–H/N interaction in the optimized
structure of 1. This intramolecular C–H/N interaction displays
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Fig. 2 Molecular graphs showing intramolecular interactions in (a) X-
ray structure of 1 (b) optimized structure of 1, (c) X-ray structure of 2
(
major disordered component), (d) X-ray structure of 2 (minor disor-
dered component) and (e) optimized structure of 2.
hydrogen bonding character. Moreover, intramolecular C–H/C
interaction is slightly stronger in the X-ray structure of 2
compared to 1 and the optimized structure of 2. It is of interest to
note that the intramolecular C–H/C interaction is absent as
Fig. 3 Short intermolecular interactions visualized using Hirshfeld
surfaces mapped over dnorm for (a) 1 and (b) 2 and (c) the relative
contribution of different intermolecular interactions observed in 1 and
2
(d) the relative contribution of two chalcogen contacts (S/C/O) in
evident from the topological analysis in related structures in 1 and 2.
nd
which aliphatic groups are present at the 2 position of the
28–30
pyrimidine nucleus.
interaction is found to be 0.1%. In one of the closely related
structures, the corresponding contact contributes about 1.7% to
In 1, the highly directional N1–H1/O6 hydrogen-bonded dimer the crystal packing. The existence of chalcogen and other
is showing bright red areas on the HS, whereas the intermo- intermolecular interactions in 1 and 2 is further evaluated by
lecular C7–H72/N2 interaction and S2/S2 (lp/lp) contact are QTAIM analysis.
Hirshfeld surface (HS) and 2D-ngerprint plots
30
also visible on the HS with pale red marks. In 2, two intermo-
lecular hydrogen bonding interactions (N1–H1/O6 and C8–
H81/N2) are visible on the HS and large red areas appeared
Analysis of molecular electrostatic potential surface
over the phenyl ring due to disorder. Fig. 3 highlights the short The molecular electrostatic potential surface maps for X-ray and
intermolecular interactions observed in 1 and 2 and these optimized structures of 1 and 2 were generated. The distribution of
features suggest that these interactions play an essential role in electrostatic potentials is very similar in both structures including
the stabilization of crystal structure.
their corresponding optimized structures (Fig. 4). However, the
To explain the effect of thiophene and phenyl substituents values of positive (Vs,max) and negative (Vs,min) electrostatic poten-
on the intermolecular interactions observed in the solid state, tials are varied. In 1, the most positive electrostatic potential has
we obtained 2D-ngerprint plots (2D-FP) (Fig. S1†). The result occurred at the amine proton of the pyrimidine ring with the Vs,max
ꢁ
1
shows that the intermolecular H/H contacts have a signicant value of 53.5 kcal mol and at other important protons H72 and
ꢁ
1
contribution to both structures. The intermolecular H/N/C/O H12 have Vs,max values of 23.2 and 21.4 kcal mol , respectively.
interactions provide substantial contributions toward crystal The most negative electrostatic potential observed for carbonyl
ꢁ
1
packing and the relative contributions of these contacts are oxygen (O6; Vs,min: ꢁ46.3 kcal mol ) followed cyano nitrogen (N2;
ꢁ
1
comparable in 1 and 2. However, there is a substantial increase
of H/H (16.2%) contacts in 2 compared to 1 due to the pres-
V
s,min: ꢁ41.1 kcal mol ).
It is of interest to note that the pyrimidine N3 atom has a weak
ence of phenyl substituent and its disorder. Further, the inter- accepting tendency as evident from the V
molecular S/C(p) contact described as a chalcogen bond, is ꢁ5.0 kcal mol . The sulphur atoms in 1 show distinct features of
reduced in 2 by 6.6% towards the crystal packing compared to 1. electrostatic potentials and the thiophene S2 atom has relatively
value of
s,min
ꢁ1
ꢁ1
It is worthy to note that the 3.6% increase of S/S contacts to the more negative electrostatic potential (Vs,min: ꢁ2.6 kcal mol
)
ꢁ
1
total HS area due to the presence of additional S atom in 1 and compared to S1 atom (Vs,min: 2.2 kcal mol ). As mentioned
its participation in the intermolecular interaction. The corre- above, compound 2 possesses similar electrostatic potentials and
˚
sponding contact appeared around 3.4 A in the FP plot and this the values of Vs,max and Vs,min are comparable in the X-ray
contact contributes about 1.0% towards the crystal packing of structures of 1 and 2. As shown in Fig. 4, the values of positive
29
a related structure.
and negative electrostatic potentials vary between X-ray and
It should be pointed out that the chalcogen bond (S/O) optimized structure for some of the donor and acceptors atoms.
contributes 1.1% to the total HS area in 1 and the corresponding This variation is indicating the effect of crystal packing.
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Fig. 5 Different dimers observed in the crystal structure of 1.
synthon. The contribution of electrostatic energy was calculated to
be 86% towards the stabilization of this cyclic synthon. The dimer
ꢁ
1
D2 (Etot: ꢁ7.6 kcal mol ) is stabilized by intermolecular C–H/p
(
centroid of the pyrimidine ring) and stabilization is further sup-
Fig. 4 Molecular electrostatic potential of (a) X-ray structure of 1 (left)
and its optimized structure (right) and (b) X-ray structure of major
disordered component of 2 (left) and its optimized structure (right)
ported by a weak chalcogen bond S/C(p) contact. This weak
chalcogen bond is established by sum of vdW radii of S and C
˚
mapped over the electron density isosurface at 0.001 au. Colour scale atoms +0.03 A. It should be noted that this dimer is predominantly
in kcal mol ): red: greater than 20; yellow: between 20 and 0; green: dispersive with a contribution of 76%. It is realized that this one of
ꢁ1
(
0
to ꢁ20 and blue: greater than ꢁ20. The important most positive
the rare chalcogen bonds formed between thiophene S and cyano
C atom. To support this statement, a CSD search was performed
(Vs,max) and negative (Vs,min) electrostatic potentials are given.
˚
using sum of the vdW radii of S and C +0.03 A cut-off and we found
that 46 hits contain this contact and the contact distance ranging
Dimers in the crystal structure of 1
˚
from 3.359 to 3.529 A.
The intermolecular interactions energies calculated by the
It is to be noted that adjacent D1 dimers are interlinked by
PIXEL method for dimers of 1 are summarized in Table 2 and dimer D2 which is further extended along the crystallographic
ꢁ
1
ꢁ1
these energies are ranging from ꢁ20.9 to ꢁ4.3 kcal mol
.
b axis. Dimer D3 (Etot: ꢁ6.0 kcal mol ) supports by a weak and
These dimers (Fig. 5 and 6) are stabilized by both classical and long intermolecular C/C (involving C11 and C12) contact. This
non-classical non-covalent interactions such as N–H/O, C–H/ contact only appears when the distance being sum of vdW radii of
p, C–H/N, C/C, S/S, S/C and S/O]C interactions. The interacting atoms +0.09 A. The electrostatic and dispersion ener-
˚
latter two non-covalent interactions can be classied as chal- gies contribute 42% and 58%, respectively towards the stabiliza-
cogen bonds.
tion of this dimer. Moreover, each molecule in this dimer (D3)
ꢁ1
The strong dimer (D1; E : ꢁ20.9 kcal mol ) forms by a linear interacts with the neighbouring molecule via S/S (involving
tot
N–H/O hydrogen bond involving amine group (N1–H1) and thiophene S2 atoms) contact (dimer D6). The intermolecular
2
2
carbonyl O6 atom and this hydrogen bond produces a cyclic R
(8)
ꢁ
1
Table 2 Intermolecular interaction energies (in kcal mol ) obtained by the PIXEL method for various molecular pairs observed in the crystals of 1
a
and 2. Cg1 is the centroid of the pyrimidine ring
Important
interactions
Geometry
H/A (A)/:D–H/A ( )
˚
ꢀ
Dimer
CD
Symmetry
E
Coul
E
pol
E
disp
E
rep
E
tot
Compound 1
D1
D2
8.353
4.991
ꢁx + 1, ꢁy, ꢁz + 1
x, y ꢁ 1, z
N1–H1/O6
C7–H71/Cg1
S2/C9
1.75/179
2.90/156
3.520 (4)
3.487 (3)
2.63/129
3.683 (4)
3.497 (4)
2.57/132
ꢁ29.3
ꢁ2.8
ꢁ13.9
ꢁ2.4
ꢁ7.1
29.4
10.6
ꢁ20.9
ꢁ7.6
ꢁ13.0
D3
D4
D5
D6
D7
9.058
10.092
7.068
6.827
9.017
ꢁx + 2, ꢁy + 1, ꢁz + 1
ꢁx + 2, ꢁy, ꢁz + 1
C11/C12
ꢁ3.0
ꢁ3.8
ꢁ2.7
ꢁ2.2
ꢁ3.2
ꢁ0.9
ꢁ1.4
ꢁ1.5
ꢁ2.0
ꢁ0.9
ꢁ5.3
ꢁ3.0
ꢁ5.5
ꢁ9.0
ꢁ2.5
3.2
2.7
4.9
8.5
2.3
ꢁ6.0
ꢁ5.4
ꢁ4.9
ꢁ4.6
ꢁ4.3
C12–H12/N2
S1/O6]C6
S2/S2
ꢁx + 1, ꢁy + 1, ꢁz + 1
ꢁx + 3/2, y ꢁ 1/2, ꢁz + 1/2
ꢁx + 1/2, y + 1/2, ꢁz + 1/2
C7–H72/N2
Compound 2
D1
D2
D3
D4
8.266
10.071
9.535
ꢁx + 1, ꢁy + 1, ꢁz + 2
ꢁx + 2, ꢁy + 1, ꢁz + 1
x ꢁ 1, y ꢁ 1, z
N1–H1/O6
1.72/177
2.67/121
2.67/131
2.45/161
ꢁ29.2
ꢁ4.2
ꢁ1.5
ꢁ2.9
ꢁ13.9
ꢁ1.6
ꢁ0.5
ꢁ0.8
ꢁ6.8
ꢁ4.6
ꢁ1.9
ꢁ1.3
32.8
3.9
0.9
2.0
ꢁ17.2
ꢁ6.4
ꢁ3.1
ꢁ3.0
C12A–H121/N2
C8–H83/O6
C8–H81/N2
11.853
x ꢁ 2, y ꢁ 1, z
a
Neutron values are given for all D–H/A interactions. CD: centroid-to-centroid distance of the molecular pair.
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weaker than dimer D1 in 1 due to the repulsion contribution as
ꢁ
1
compared to 1. The dimer D2 (Etot: ꢁ6.4 kcal mol ) forms by an
intermolecular C–H/N interaction in which cyano N2 atom
functions as an acceptor, as observed in 1. Though the donor
moiety is different in 1 (thiophene ring) and 2 (phenyl ring),
2
2
a cyclic synthon (R
(16)) formed by this interaction is the same.
Further, the electrostatic and dispersion energies contribute
about 56 and 44% towards stabilizing D2 dimer in 2. The dimers
D1 and D2 are arranged in an alternate fashion that runs parallel
to the crystallographic c axis (Fig. 7(a)). Unlike in 1, the carbonyl
group is also involved as an acceptor for the intermolecular
ꢁ
1
C–H/O interaction (dimer D3, Etot: ꢁ3.1 kcal mol ). This
interaction links the molecules into a C(8) chain which runs
parallel to the b axis (Fig. 7(b)). Further, the intermolecular
C–H/N interaction stabilizes the dimer D4 (Etot
:
ꢁ
1
ꢁ
3.0 kcal mol ). The adjacent molecules of 2 interlinked via this
Fig. 6 Molecular sheets formed by various combinations of motifs in
the crystal structure of 1.
interaction forms as one-dimensional chain with the graph-set
motif of C(10) which extended along the b axis (Fig. 7(b)). It is
important to emphasize that the contribution of electrostatic
ꢁ
1
interaction energy for dimer D6 being ꢁ4.6 kcal mol and the
dispersion energy contributes 68% towards the stabilization of D6.
Intermolecular C–H/N interaction (involving H12 and N2)
(
51%) and dispersion (49%) energies are nearly the same towards
the stabilization of dimer D3. In contrast, dimer D4 is predomi-
nantly electrostatic in nature with the contribution of 74%
towards the stabilization.
ꢁ1
stabilizes the dimer D4 (Etot: ꢁ5.4 kcal mol ) with 63% of
electrostatic energy contribution towards the stabilization. This
2
As mentioned above, the phenyl ring has participated in an
intermolecular C–H/N (involving C12A–H121 and N2) inter-
action in the major disordered component of 2. The equivalent
atoms are also engaged in an intermolecular C–H/N (involving
C12B–H122 and N2) interaction in the minor disordered part.
The remaining interactions come from the non-disordered
atoms of 2 which are identical with those of interactions
observed in the major disordered component.
dimer generates a R
2
(16) motif. Interestingly, another chal-
cogen bond of the type S/O]C (involving S1 and O6) stabilizes
the dimer D5 with an intermolecular interaction energy value of
ꢁ
1
ꢁ
4.9 kcal mol . It should be noted that this chalcogen bond is
established only when distance cutoff is relaxed i.e. sum of the
˚
vdW radii of S and O +0.23 A. The electrostatic and dispersion
energies contribute 43 and 57%, respectively, towards the
stabilization of this dimer. It is also pointed out that dimer D5 is

anked by on both sides by dimer D4. A CSD search identies
this chalcogen bond in 993 structures.
Crystal packing and energy frameworks
ꢁ
1
The energetically least dimer D7 (Etot: ꢁ4.3 kcal mol with
The crystal packing of 1 can be described as a typical herring-
bone (viewed down a axis) or columnar (viewed down b axis).
Molecules of 2 also packed as a columnar fashion (viewed down
a and b axes). Recently, the energy frameworks have received
considerable attention to understanding the polymorphism,
effect of substituents on the crystal packing and mechanical
properties of the crystals. The 3D topology of the energy
frameworks for crystals 1 and 2 are depicted in Fig. 8. Overall,
6
2% contribution of electrostatic energy towards stabilization)
forms by an intermolecular C–H/N (involving H72 and N2)
interaction. This non-covalent interaction links the molecules
of 1 into a zigzag C(9) chain which runs parallel to the c axis.
Further, dimers D4, D6 and D7 collectively generate two
different closed synthons and these synthons are alternately
arranged in a zigzag manner in the solid state (Fig. 6).
Dimers in the crystal structure of 2
PIXEL energy analysis was carried out for both major and minor
disordered components. For the major component, four
molecular dimers were identied and the intermolecular
interactions for these dimers are ranging from ꢁ17.2 to
ꢁ
1
ꢁ
3.0 kcal mol
(Table 2). These dimers are stabilized by
intermolecular N–H/O, C–H/O and C–H/N interactions
Fig. 7). No non-classical contacts including chalcogen bond
(
exist in this structure.
ꢁ1
As observed in 1, the strong dimer (D1; Etot: ꢁ17.2 kcal mol
)
stabilizes by an intermolecular N–H/O hydrogen bond with
2
2
a cyclic R (8) synthon. The contribution of electrostatic energy
Fig. 7 (a) Molecular ribbon formed by motifs D1 and D2 and (b) one-
dimensional molecular chain formed by motifs D3 and D4 in the crystal
was calculated to be 86% towards the stabilization of this
hydrogen-bonded dimer. Moreover, this dimer is relatively structure of 2.
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C–H/N interaction. Although 3D topology of the energy
frameworks looks similar for both 1 and 2, there is a difference
in the large cylinders geometry. In 2, these cylinders are
oriented in a parallel fashion in the same layer and as well as in
the adjacent layers. These features are different in 1 i.e. the large
cylinders are oriented in a parallel fashion in the same layers
and not in the adjacent layers. Desiraju and co-workers inves-
tigated the bending behavior of a large number of structures.
They found that the bending behavior was well correlated with
the shortest crystallographic axis of ca. 4 A˚ . As shown in Fig. 8,
62
˚
˚
the crystal packing of 1 (b ¼ 4.99 A) and 2 (a ¼ 4.69 A) viewed
along the respective shortest crystallographic axis and these
structures showed similar 3D topology of the energy frame-
works. Based on the energy frameworks, one can conclude that
Fig. 8 Energy frameworks for the crystal structures of (a and b) 1 and the bending behavior could be similar to 1 and 2.
c and d) 2 (major disordered component). The electrostatic (red) and
(
total interaction energy (blue) components are shown as cylinders.
Analysis of isostructurality
The concept of supramolecular constructs (SC) which are
subcomponents of a complete crystal structure was introduced
both electrostatic (red) and total interaction energy (blue) show
similar topology for crystals 1 and 2. The large and small
cylinders are placed alternately in the horizontal layer. In 1, the
large cylinders represent intermolecular N–H/O hydrogen
bond and a weak chalcogen bond (S/O]C). A small cylinders
in each horizontal layer represent intermolecular C–H/N
interaction. The large cylinders in two adjacent layers are
further interconnected by a small cylinder which represents
a weak S/S interaction.
63,64
by Gelbrich and Hursthouse.
In this study, we used this
concept to identify the similar packing arrangements in the title
compounds and their closely related structures. The common
packing motifs observed in the title compounds and their
closely related structures are depicted in Fig. S2 and S3.† The
structures 1 and 2 show 1D isostructurality (molecular chain)
and the molecular chain has alternate N–H/O and C–H/N
bonded synthons. The structures of 1 and ILEREY display 2D
isostructurality and in both structures respective molecule
forms as layers. These layers are primarily stabilized by N–H/O
and C–H/N interactions. It is important to note that structures
OKUWEY and ZAPQEO share 0D isostructurality (N–H/O
In 2, the large cylinders belong to intermolecular N–H/O
hydrogen bond and a small cylinder which links neighbouring
large cylinders in the horizontal layer represent intermolecular
ꢁ1
ꢁ3
Table 3 Topological parameters for intermolecular interactions in dimers of 1 [values of V(r), G(r) and H(r) are expressed in kJ mol bohr and
¼ ꢁ0.5 ꢂ V(r) in kcal molꢁ
1
]
D
e
ꢀ
ꢀ
ꢀ
ꢁVðrÞꢀ
Interaction
R
r(r) (e A˚ 3
ꢁ
)
V r(r) (e A
2
ꢁ5
˚
)
V(r)
G(r)
H(r)
ꢀ
ꢀ
ꢀ
D
e
˚
ij (A)
ꢀ
GðrÞ
D1
N1–H1/O6
1.772
0.281
2.676
ꢁ108.6
90.8
ꢁ17.9
1.20
13.0
D2
C7–H71/N1
S2/C9
2.825
3.614
0.043
0.041
0.517
0.482
ꢁ8.5
ꢁ7.5
11.3
10.3
2.8
2.8
0.75
0.73
1.0
0.9
D3
C11/C12
3.874
2.666
3.571
3.512
2.599
0.034
0.048
0.038
0.055
0.055
0.412
0.631
0.419
0.633
0.704
ꢁ5.9
ꢁ9.4
8.5
13.3
9.3
2.7
3.9
2.1
3.1
4.1
0.69
0.70
0.77
0.78
0.73
0.7
1.1
0.9
1.3
1.3
D4
C12–H12/N2
D5
S1/O6]C6
ꢁ7.1
D6
S2/S2
ꢁ11.0
ꢁ10.9
14.1
15.0
D7
C7–H72/N2
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Table 4 Topological parameters for intermolecular interactions in dimers of 2 (major disordered component) [values of V(r), G(r) and H(r) are
ꢁ1
ꢁ3
ꢁ1
]
expressed in kJ mol bohr and D
e
¼ ꢁ0.5 ꢂ V(r) in kcal mol
ꢀ
ꢀ
ꢀ
ꢁVðrÞꢀ
ꢁ
2
ꢁ5
˚
ꢀ
ꢀ
ꢀ
ꢀ
˚
Interaction
R
ij (A)
r(r) (e A˚ 3
)
V r(r) (e A
)
V(r)
G(r)
97.7
12.7
11.2
18.1
H(r)
ꢁ22.3
3.6
D
e
GðrÞ
D1
N1–H1/O6
1.742
2.736
2.710
2.476
0.301
2.767
ꢁ120.0
ꢁ9.1
ꢁ8.5
ꢁ13.3
1.23
0.72
0.76
0.74
14.4
1.1
1.0
1.6
D2
C12A–H121/N2
0.046
0.596
D4
C8–H83/O4
0.041
0.513
2.7
D5
C8–H81/N2
0.064
0.841
4.8
mediated dimer) with the structure of 1. The cell parameters of bonds of the type S/O and S/C interaction are weak in
and ILEREY structures are comparable and these two struc- strength compared to hydrogen bonds and S/S contact and the
2
tures share 3D isostructurality. This 3D isostructurality is dissociation energy for these interactions are the same. We also
further quantied using isostructurality index (P) proposed by noted that the strength of S/S contact is comparable to that of
65
F ´a bi ´a n and K ´a lm ´a n and the P value is found to be 0.02 for this one of the C–H/N (dimer D7) hydrogen bonds.
pair. Further, structures of 2 and OKUWEY show 0D SC (N–H/ In 2 (major disordered component), though all four inter-
mediated dimeric pair). However, no supramolecular molecular (N–H/O, C–H/N and C–H/O type) interactions
O
construct observed between 2 and ZAPQEO.
showing hydrogen bonding character based on KP-4 rule, one
of the hydrogen bonds (N–H/O) demonstrate intermediate
bonding character between shared and closed-shell interac-
tion as observed in 1. This conclusion has been made based on
Evaluation of intermolecular interactions using QTAIM
analysis
2
the positive value of Laplacian of electron density (V r > 0),
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
The topological parameters for the non-covalent interactions
observed in structures of 1 and 2 (major disordered compo-
nent) are summarized in Tables 3 and 4. The molecular graphs
exhibiting the non-covalent interactions in these dimers are
illustrated in Fig. S4 and S5.† In 1, there are three intermo-
lecular interactions of the type N–H/O (dimer D1) and
C–H/N (dimers D4 and D7) and all of these interactions
showing hydrogen bonding character according to the KP-4
rule. As mentioned in the previous section, dimer D2 stabi-
lizes with two interactions, namely C7–H71/Cg1(p) and
a chalcogen bond S2/C9. The topological analysis suggests
a bond path that established between H71 and N1 (pyrimidine
ring) atoms resulting in the formation of C–H/N interaction.
This interaction is found to be van der Waals in nature based
on KP-4 rule.
ꢁ
VðrÞ
.
1 and H(r) < 0. The remaining three hydrogen bonds
GðrÞ
2
display closed-shell character of bonding (based on (V r > 0),
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢁ
VðrÞ
\
1 and H(r) > 0). The dissociation energy for the
GðrÞ
ꢁ1
closed-shell interactions is in the range of 1.0–1.6 kcal mol
It should be important to note that the N–H/O hydrogen
bond is found be to stronger (D
to that of the corresponding hydrogen bond in 1. The distri-
bution of Laplacian of electron density and the total electronic
energy density (H(r)) for N–H/O hydrogen bond in 1 and 2 is
.
ꢁ1
e
¼ 14.4 kcal mol ) compared
It is of interest to note that the N–H/O hydrogen bond
exposes an intermediate bonding character between shared and
closed-shell interaction as concluded using the following
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢁ
VðrÞ
2
conditions: (i) V r > 0; (ii)
. 1 and (iii) H(r) < 0. Further,
GðrÞ
the remaining hydrogen bonds (C–H/N) belong to closed-shell
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢁ
VðrÞ
2
interaction categories as evident from (i) V r > 0; (ii)
\1
GðrÞ
Fig. 9 The distribution of the (a and b) Laplacian of the electron
density and (c and d) the total energy density showing the formation of
strong intermolecular N–H/O hydrogen bond in 1 and 2, respectively.
These diagrams were plotted in the plane comprising the atoms
involved in the hydrogen bond. Small green spheres indicate the bond
and (iii) H(r) > 0. The N–H/O hydrogen bond is calculated to be
strong among other intermolecular interactions in 1 and the
dissociation energy for this hydrogen bond is 13.0 kcal mol
ꢁ1
.
The corresponding value for C–H/N hydrogen bonds is in the
ꢁ
1
range of 1.0–1.3 kcal mol . As noted earlier, the chalcogen critical points.
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ꢁ1
Table 5 The glide XP docking scores (in kcal mol ) for the title bonding interaction with the active site residues. Specically,
compounds 1 and 2 and control inhibitor
the amine group in compound 1 is involved in a hydrogen bond
with the backbone carbonyl group of the Val 115 residue of H.s
DHFR. In contrast, the carbonyl group of 1 has participated in
Glide XP docking score
DHFR
a hydrogen bond with the backbone amine group of Ala 7 of S.a
DHFR enzyme. Similarly, the carbonyl group of 2 makes
a hydrogen bond with the amine group of the conserved Ala 9
residue of H.s DHFR. In contrast, the carbonyl group of 2
involves a hydrogen bond with amine group of conserved Ala 7
of S.a DHFR.
S.
aureus
Compound
H. sapiens
1
2
ꢁ6.5
ꢁ5.4
ꢁ6.0
ꢁ6.9
ꢁ7.5
ꢁ7.3
Trimethoprim (control inhibitor)
Conclusions
depicted in Fig. 9. As can be seen from this gure that the total
electronic energy density (H(r)) has uninterrupted regions of
negative values represent the intermediate bonding character.
In the present investigation, we explored role of various types of
non-covalent interactions present in the crystal structures of
two pyrimidine-5-carbonitrile derivatives. The X-ray analysis
revealed that the molecular conformation is locked by an
intramolecular C–H/C interaction which is one of the
common interaction observed in nitrile containing organic
Molecular docking
In the present study, we explored the anticancer and antibac-
terial activities of the title compounds against dihydrofolate
reductase (DHFR) enzymes from two different species, namely
Homo sapiens and Staphylococcus aureus, respectively employing
in silico molecular docking approach. The glide XP docking
scores of the title compounds are compared with the control
inhibitors trimethoprim (Table 5). The result suggests that the
glide XP scores for the title compounds are comparable with
trimethoprim for both targets. Both title compounds make at
least one hydrogen bond with the active residue of the DHFR
enzymes. The predicted binding pose of the title compounds at
the active site of the H.s DHFR and S.a DHFR and hydrogen
bond interaction formed between ligand and protein is illus-
trated in Fig. 10. In all cases, either donor or acceptor group of
the pyrimidine moiety has participated in the hydrogen
nd
compounds. If aliphatic group is present at the 2 position of
the pyrimidine ring, this intramolecular interaction is not
existing. Both structures 1 and 2 show common 3D topology of
the energy frameworks and these features suggesting that they
have similar bending properties. The molecular electrostatic
potential surface revealed potential sites which are involved in
non-covalent interactions and donating and accepting tenden-
cies of different donor and acceptors sites present in these
compounds. The Hirshfeld surface analysis suggested that the
chalcogen bond is only preferred in thiophene containing
derivative. This result is in good agreement with the PIXEL
energy analysis. This chalcogen bond (formed between thio-
phene S and cyano carbon) is one of the rare non-covalent
interactions as revealed by CSD analysis. The strong dimer in
both compounds formed by highly directional N–H/O
hydrogen bond. The topological analysis indicated that this
hydrogen bond showed intermediate bonding character
between shared and closed-shell interaction. All other interac-
tions observed in both structures are of closed-shell type of
interactions. The common packing motifs observed in the title
compounds and their closely related structures are discussed. A
detailed investigation of molecular docking analysis was per-
formed to probe the inhibitory activities of the title compounds
against DHFR enzyme from two different species (human and
Staphylococcus aureus). The docking results are compared with
known DHFR inhibitor trimethoprim. This in silico docking
analysis suggested that the title compounds have comparable
inhibitory potential against these targets.
Conflicts of interest
The authors declare that they have no competing interests.
Acknowledgements
This work was funded by the Deanship of Scientic Research at
Princess Nourah bint Abdulrahman University through the
Research Groups Program (Grant No. RGP-1442-0010(4)).
Fig. 10 Predicted binding poses of the compounds 1 (a and b) and 2 (c
and d) at the active site of (a and c) H.s DHFR (b and d) S.a DHFR.
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