Identification and molecular modeling of new quinolin-2-one thiosemicarbazide scaffold with antimicrobial urease inhibitory activity

Article abstract of DOI:10.1007/s11030-019-10021-0

Abstract: A new series of 6-substituted quinolin-2-one thiosemicarbazides 6a–j has been synthesized. The structure of the target compounds was proved by different spectroscopic and elemental analyses. All the designed final compounds were evaluated for their in vitro activity against the urease-producing R. mucilaginosa and Proteus mirabilis bacteria as fungal and bacterial pathogens, respectively. Moreover, all compounds were in vitro tested as potential urease inhibitors using the cup-plate diffusion method. Compounds 6a and 6b were the most active with (IC₅₀ = 0.58 ± 0.15 and 0.43 ± 0.09?μM), respectively, in comparison with lead compound I (IC₅₀ = 1.13 ± 0.00?μM). Also, the designed compounds were docked into urease proteins (ID: 3LA4 and ID: 4UBP) using Open Eye software to understand correctly about ligand–receptor interactions. The docking results revealed that the designed compounds can interact with the active site of the enzyme through multiple strong hydrogen bonds. Moreover, rapid overlay of chemical structures’ analysis was described to understand the 3D QSAR of synthesized compounds as urease inhibitors. The results emphasize the importance of polar thiosemicarbazide directly linked to 6-substituted quinolone moieties as promising antimicrobial urease inhibitors. Graphic abstract: [Figure not available: see fulltext.]

Full text of DOI:10.1007/s11030-019-10021-0

Molecular Diversity
https://doi.org/10.1007/s11030-019-10021-0
ORIGINAL ARTICLE
Identifcation and molecular modeling of new quinolin‑2‑one
thiosemicarbazide scafold with antimicrobial urease inhibitory
activity
Mohammed A. I. Elbastawesy1 · Yaseen A. M. M. El‑Shaier2 · Mohamed Ramadan1 · Alan B. Brown3 · Ashraf A. Aly4 ·
Gamal El‑Din A. Abuo‑Rahma5
Received: 10 August 2019 / Accepted: 29 November 2019
© Springer Nature Switzerland AG 2020
Abstract
A new series of 6-substituted quinolin-2-one thiosemicarbazides 6a–j has been synthesized. The structure of the target
compounds was proved by diferent spectroscopic and elemental analyses. All the designed fnal compounds were evaluated
for their in vitro activity against the urease-producing R. mucilaginosa and Proteus mirabilis bacteria as fungal and bacte-
rial pathogens, respectively. Moreover, all compounds were in vitro tested as potential urease inhibitors using the cup-plate
difusion method. Compounds 6a and 6b were the most active with (IC50 =0.58 0.15 and 0.43 0.09 µM), respectively,
in comparison with lead compound I (IC50 = 1.13 0.00 µM). Also, the designed compounds were docked into urease
proteins (ID: 3LA4 and ID: 4UBP) using Open Eye® software to understand correctly about ligand–receptor interactions.
The docking results revealed that the designed compounds can interact with the active site of the enzyme through multiple
strong hydrogen bonds. Moreover, rapid overlay of chemical structures’ analysis was described to understand the 3D QSAR
of synthesized compounds as urease inhibitors. The results emphasize the importance of polar thiosemicarbazide directly
linked to 6-substituted quinolone moieties as promising antimicrobial urease inhibitors.
* Ashraf A. Aly
ashrafaly63@yahoo.com
* Gamal El-Din A. Abuo-Rahma
gamal.aborahama@mu.edu.eg
1
Department of Pharmaceutical Organic Chemistry, Faculty
of Pharmacy, Al-Azhar University, Assiut 71524, Egypt
2
Department of Organic and Medicinal Chemistry, Faculty
of Pharmacy, University of Sadat City, Sadat-City, Menufa,
Egypt
3
Chemistry Department, Florida Institute of Technology,
Melbourne, FL 32901, USA
4
Department of Chemistry, Faculty of Science, Minia
University, El-Minia 61519, Egypt
5
Department of Medicinal Chemistry, Faculty of Pharmacy,
Minia University, El-Minia 61519, Egypt
Vol.:(0123456789)
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Molecular Diversity
Graphic abstract
left arm
N
right arm
NO2
right arm
liker
left arm
O2N
liker
S
S
ring enlargmnet
H
N
N
H
N
H
HN
N
N
H
O
I Reported compound
HN
IC50 = 1.13 0.00µM
O
II Reported compound
IC50 = 16.4 0.8µM
-Thiosemicarbazide
-Ring modification with keeping amid
-Aryl replacment
-Substituent on the aryl ring
R1
liker
Ar = Phenyl, benzyl, allyl
R1 = EDG, WEG
S
H
N
left arm
Ar
right arm
N
H
N
H
HN
O
Keywords Molecular docking · ROCS analysis · R. mucilaginosa · Proteus mirabilis · Hybridization
or acquired immunodefciency syndrome (AIDS) [6]. More-
over, Proteus mirabilis, a common cause of urinary tract
infections (UTIs) in individuals with functional or structural
abnormalities or with long-term catheterization, forms blad-
der and kidney stones as a consequence of urease-mediated
urea hydrolysis [7], in addition to high and constant increase
in antibiotic resistance [8, 9]. So, many researchers have
been aiming for more targeted and safer therapy to kill or at
least control these microbial infections for such complicated
medical situations.
Introduction
Nitrogen containing heterocycles are important structural
units in medicinal chemistry. Among various heterocyclic
compounds, quinolines have gained the largest attention.
Throughout the twentieth century [1], the chemistry and
biological applications of quinoline had been subjected to
intense studies from diferent research groups [2]. On the
other hand, urease (urea amidohydrolase, EC 3.5.1.5) is a
famous nickel-containing metalloenzyme, which catalyzes
the hydrolysis of urea into carbamate and ammonia [3]. Con-
sequently, these reactions cause signifcant alkalinity due to
the release of large quantities of ammonia. The increase in
pH is directly associated with the development of numerous
health complications in humans like kidney stone, hepatic
coma and pyelonephritis which depend on colonization site
by urease-producing microorganisms [4].
On a chemical front, thiosemicarbazides are a class of
compounds, which has been found to possess a wide spec-
trum of biological properties [10] such as antitubercular
[11], antiviral [12], herbicidal, antibacterial [13], antinocic-
eptive [14] and antioxidant properties [15]. Recently, many
studies have been reported on the efcacy of thiosemicar-
bazides and its hybrid derivatives to inhibit urease enzyme
activity [4] (Fig. 1).
For example, Rhodotorula species uses urease enzyme
as an essential factor for protection and spreading processes
[5]. The most prevalent species is R. mucilaginosa which
emerged as opportunistic pathogens with the ability to colo-
nize and infect susceptible patients: Nearly 90% of patients
with R. mucilaginosa infection have underlying solid or
hematologic malignancy, organ/bone marrow transplant, or
immunosuppression due to corticosteroid use, neutropenia
The application of chemical similarity analysis, either
topological (2D) or superposition shape similarity (3D), in
drug design is commonly used. It is a useful technique in
drug discovery and drug design approaches. Shape similarity
(3D) and electrostatic potential are considered as fundamen-
tal descriptors for computational drug discovery and under-
stand correctly when we thinking about the protein ligand
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Molecular Diversity
Fig. 1 Rationale for the design
of the target compounds 6a–j
left arm
N
right arm
NO2
right arm
liker
left arm
O2N
liker
S
S
ring enlargmnet
H
N
N
H
N
H
HN
N
N
H
O
I Reported compound
HN
IC50 = 1.13 0.00µM
O
II Reported compound
IC50 = 16.4 0.8µM
-Thiosemicarbazide
-Ring modification with keeping amid
-Aryl replacment
-Substituent on the aryl ring
R1
liker
Ar = Phenyl, benzyl, allyl
R1 = EDG, WEG
S
H
N
left arm
Ar
right arm
N
H
N
H
HN
O
binding. Shape similarity exhibits a good neighborhood
behavior that high similarity in shape behaves refective of
high similarity in biology, while high similarity in biology is
not refected in the similarity in structure [16]. Shape simi-
larity can be used in virtual screening [17], lead-hopping,
molecular alignment, pose generation and predictions [18].
Based on the aforementioned information in the litera-
ture, and in continuation of our previous work in utilizing
molecular modeling in drug design approaches [19–22] and
in design of antibacterial urease inhibitors [23, 24], the aim
of this research is to connect two well-known biologically
active entities: quinolin-2-one with thiosemicarbazide scaf-
fold for the purpose synergistic improvement for antimi-
crobial and/or urease inhibition activity for such diferent
derivatives. The target compounds as depicted in Fig. 1 were
designed, synthesized and subjected to molecular docking
and ROCS technique [25] to calculate the shape similarity
for our compounds to the reported standards and applied
these descriptors to 3DQSAR study.
prepared by refluxing compounds 4a–e with hydrazine
hydrate for 12 h [22]. The fnal target thiosemicarbazides
6a–j were prepared by reaction of the hydrazine derivatives
5a–e and the appropriate isothiocyanate in dioxane under the
refux condition. The spectral and elemental data revealed
that all derivatives 6a–j underwent the reaction smoothly
to give the respective thiosemicarbazide hybrid structure in
1
good yield. The H NMR spectra experienced the disap-
pearance of NH2 signal and appearance of four singlet (NH)
signals at δH 7.89–11.24 ppm that augments the formation of
thiosemicarbazide hybrids. As a representative example, 1H
NMR of compound 6e showed singlet signals at δH 11.24,
9.99, 9.88, 9.24 ppm for four NH protons and also a char-
acteristic pattern for the additional fve phenyl protons at
7.16–7.42 ppm. Moreover, 13C NMR spectrum showed the
phenyl group: Four signals at δC 138.99, 127.90, 125.97 and
125.20 ppm represented mono-substituted phenyl. Further
structural confrmation also was provided from the analy-
1
sis of the H-15N HSQC spectrum of 6e, which showed a
broad singlet at δH 9.99, assigned as NH–Ph, and correlated
with attached nitrogen which appears at δN 125.6. Also,
1H NMR of compound 6i showed a ddt Jd= 17.0, 9.8 Hz,
Jt = 5.0 signal integrated with one proton at δ 5.35 ppm,
another doublet at 4.55 with J=11.0, in addition to another
signal at 3.63 ppm J=4.20 Hz, which was ascribed to the
allyl moiety. 13C NMR spectrum of the prepared fnal com-
pounds showed the characteristic thioxo and ring oxo car-
bonyl groups at ~ δ 181.00 and 162.00 ppm, respectively.
Furthermore, the mass spectra and elemental analyses data
confrmed the structural formula.
Results and discussion
Chemistry
The fnal target compounds 6a–j were prepared as shown in
Scheme 1. Compounds 2–5 were synthesized according to
reported methods, and their structures were confrmed by
matching their spectral data with the reported ones [26–28].
The key intermediates, hydrazine quinolones 5a–e, were
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Molecular Diversity
Scheme 1 Synthesis of target compounds 6a–j. Reagent and reaction conditions: (a) diethyl malonate, PPA, refux 3 h; (b) POCl3, refux 2 h; (c)
AcOH, refux 10 h; (d) NH2NH2·H2O (85%), EtOH, refux 8 h; (e) isothiocyanate derivatives, dioxane, refux 3–4 h
as a reference drug [29]. The results in Table 1 revealed that
R. mucilaginosa show that the tested compounds have mod-
erate-to-weak activity. Compounds 6d, 6f and 6g showed no
activity against the tested fungal strains. On the other hand,
compounds 6a, 6b, 6c, 6e, 6h, 6i and 6j showed approxi-
mate results of inhibition ranking from 48 to 56% from the
Biology
Antifungal activity
All synthesized compounds were tested against the urease-
producing R. mucilaginosa fungal strains using clotrimazole
Table 1 Urease inhibition IC50
Comp.
IC50 (µM) Urease
MIC (µM) P.
Activity against R. muci-
laginosa (inhibition zone
in mm)
(µM), anti-P. mirabilis MIC
(µM) and anti-R. mucilaginosa
activity (inhibition zone in mm)
of compounds 6a–j
mirabilis
6a
0.58 0.15
0.43 0.09
1.29 0.36
3.21 0.27
9.45 0.09
5.80 0.84
3.28 0.10
6.80 1.72
2.29 0.81
1.98 0.58
22.8 1.31
1.13 0.00
16.4 0.8
–
661.7
669.1
762.5
732.3
828.7
720.9
857.2
399.3
586.5
723
12
13
13
NA
13
NA
NA
14
13
13
–
6b
6c
6d
6e
6f
6g
6h
6i
6j
Thiourea
–
–
Lead compound I [4]
Lead compound II [4]
Ciprofoxacin
Clotrimazole
–
–
–
25
1.26
–
–
NA no inhibition
1 3

Molecular Diversity
activity of the reference clotrimazole. Compound 6h was
the most active one with 14-mm inhibition zone and better
in activity, especially to its analogs 6i and 6j. Based on this
fnding, the nature of quinolone 6-substituent has no efect
on the activity. Moreover, diferent substitutions on thiosem-
icarbazide moiety clearly changed the activity. Compounds
6a–e with a terminal phenyl part showed 48–52% inhibition.
However, compounds 6f and 6g with benzyl moiety showed
no activity, and compounds 6h, 6i and 6j with allyl terminal
part were the most active group, achieving 52–56% inhibi-
tory activity.
component to interfere with the enzymatic activity. A wide
variety of mechanisms including un-competitive, com-
petitive, non-competitive or even cooperative binding are
known to be involved in the interaction of an inhibitor with
an enzyme. Although the exact mechanism of urease inhibi-
tion by our test series 6a–j is not fully known or investigated,
but rather than the ordinary chelating mechanism (which
reported for thiourea on the enzyme Ni part), we believe that
the presence of quinolone part in our designed compounds
gives them opportunity to inhibit the enzyme in such dif-
ferent ways. Furthermore, since the usual average plasma
concentration of any drug is about 5 µg/mL [32], the anti-
urease target compounds are considered potential candidates
as a leading compound for further investigation.
Antibacterial screening
P. mirabilis strain was isolated from the urine of patients
sufering from urinary tract infection. The strain was nega-
tive for hemolysis and motile and was urease positive. The
test was done using the cup-plate difusion method [30]
(Table 1). The results indicated that the tested compounds
are, in general, weakly or moderately active. Only one com-
pound 6h, out of the ten compounds tested, showed signif-
cant antibacterial activity against P. mirabilis. Overall, this
compound proved to be the most active one. The fndings
also indicated that compounds 6a and 6i exhibited a promis-
ing antibacterial profle.
Molecular modeling
Docking study
Urease is secreted by a diverse of bacterial species, either
normal fora or pathogens. It is considered as a potent viru-
lence factor and in metabolism for some bacteria as Proteus
mirabilis and Helicobacter pylori [33]. Urease is necessary
for its colonization of the gastric mucosa [34]. All of the
target compounds have IC50% better than lead II, and com-
pounds 6a and 6b are better than lead I. Our hypothesis was
directed to examine the binding mode and the pharmaco-
phoric features of our designed scafold utilizing docking
and shape similarity studies using known compound I and
compound II [4], as shown in Fig. 1, as lead standards.
The docking studies for the synthesized compounds were
operated on the basis of crystal structures of urease pro-
teins (ID: 3LA4 and ID: 4UBP) using Open Eye® software
[35–37]. Open Eye Omega application was used to generate
diferent conformations of each ligand. Docking was con-
ducted using Fred, and the data were visualized by Veda
application. This software package generates consensus
scoring, which is a fltering process to obtain virtual binding
afnity; the lower consensus score means a better binding
afnity of the ligands toward the receptor. The compounds
are ranked according to their consensus score, as given in
Table 2. Interestingly, the consensus score values for the
tested compounds are almost in parallel with IC50 values.
Urease inhibition activity
The new synthetic quinolone–thiosemicarbazide hybrids
6a–j were further in vitro screened for their human urease
inhibitory potential, using thiourea as a standard inhibitor
[31]. The urease inhibitory activity and IC50 of the tested
compounds at different concentrations were evaluated
(Table 1). The results showed that all of the tested deriva-
tives exhibited potential urease inhibitory activities rank-
ing IC50 =0.43–9.45 µM, exceeding the reference thiourea.
Compounds 6a and 6b were the most active among the
tested series: They inhibited the activity of the enzyme at all
the tested concentrations achieving IC50 =0.58 and 0.43 µM,
respectively. Next to those, compounds 6e and 6h experi-
enced comparably weaker activity with IC50 = 9.45 and
6.80 µM, respectively. Moreover, compounds 6c, 6d, 6f–i
and 6j were found to exhibit varying degrees of inhibitory
efect at one or more tested concentrations. Overall, com-
pounds 6a and 6b with a thiosemicarbazide phenyl terminal
were proved to be the most potent inhibitors in the present
series, as they exhibited relatively much greater activity with
approximately 50-fold more potent than thiourea at a greater
number of tested concentrations.
Docking with 3LA4 Furthermore, docking of compound I
with 3LA4 [38] receptor revealed a consensus score of 79.
It forms diferent hydrogen bonding (HB) interactions (as
acceptor) with polar amino acids in the receptor cleft (as
donor). The left arm constitutes this compound bound to
Arg 609: A with HB (length 3.14 Å) through the nitrogen
of pyridine ring. The right arm forms HB with Met 737A
(length 2.37 Å) through the nitro group. The polar thiosemi-
carbazide linker interacts with the formation of two HBs
Ureases obtained from different sources contain (in
addition to the nickel metal) one to three protein subunits
present in varying stoichiometric ratios. A urease inhibitor
can, therefore, interact either with the metal or the protein
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Molecular Diversity
Table 2 Molecular modeling
consensus scores of compounds
6a, 6b and lead compounds I
and II
as compound II with the best consensus score of 65. Com-
pound 6b interacts through the formation of two HBs with
Lys: 169C A through the two terminals NHNH C=SNH to
form a cyclic form (Fig. 3c) (lengths 2.46 Å and 1.37 Å,
respectively). Also, the internal NH of thiosemicarbazide
functionality NHNH C=SNH forms HB with Meth: 367C
A (length 1.48 Å). The quinolone moiety, which represents
the right arm, adopted the receptor pocket and formed two
HBs with Hist: 323C A and Arg: 339 C A through the amide
functionality. The right arm lays in the receptor with hydro-
phobic–hydrophobic interactions (Fig. 3c). Compound 6a
interacts with the receptor with consensus score 96. It forms
two HBs with Asp: 224C A through the two terminals of
the linker NHNH C=SNH (lengths 1.93 Å and 1.91 Å). The
NH of quinolone moiety forms HB with Ala 366: A (length
2.12 Å), as shown in Fig. 3d. However, both compounds 6a
and 6b form HB with Ala: 366 A, but with a diferent pose
inside the receptor. This behavior emphasizes the role of
methyl substituent in quinolinyl moiety.
Compound
Consensus
score
3LA4 4UBP
Compound I
Compound II 80
6a
6b
79
97
95
96
65
84
45
with Arg 439 (length 3.20 Å and 3.02 Å) through the sulfur
atom (Fig. 2a). Compound II docked with consensus score
80. The NH of indole moiety (left arm) incorporated in HB
with His 593: A with the length of 2.30 Å. The linker forms
two HBs with Arg 439: A-alan 440: A through the sulfur
atom and NHNH C=S of the thiosemicarbazide functional-
ity with lengths of 3.19 Å and 1.83 Å, respectively (Fig. 2b).
Then, the study was directed to understand our compounds’
interaction. Compound 6b, the most potent among the syn-
thesized compounds, interacts with good interaction than
the lead I and lead II with consensus score 45 through the
formation of hydrophobic–hydrophobic interactions only
(no HBs formation) as shown in Fig. 2c. All of its pharma-
cophoric features (right arm, linker and left arm) occupy the
receptor clefts as lead compounds I and II and showed best
overlay to these leads (Fig. 2d).
ROCS analysis and 3DQSAR
3D shape-based superposition (ROCS) is a method that used
to predict similarity between compounds based on their three
dimensional. ROCS alignment requires: (a) query molecules
and those queries should be the standard or lead compounds,
here are compounds I and II, as given in Table 2 and (b) the
database molecules that our designed compounds. The out-
puts from ROC analysis are the overlay between the query
and database molecules as visualized by vROCS and VIDA
applications. The visualization of the query includes shape
counter, shape atoms and color atom labels. The color shape
of query compound I, illustrated in the following atoms,
labels 2 rings, 3 donors, and 5 acceptors (Fig. 4a). The color
shape of query compound II illustrated 3 rings, 5 donors, 4
acceptor and hydrophobic sites (Fig. 5a). Compounds 6a and
6b showed overlay with query I, as represented in Fig. 4b,
c, respectively. Even the query represented extra donor and
acceptor sites to the most active compounds 6a and 6b, and
compound 6b represented high similarity to color atom
of query I (Fig. 4c) than that obtained by 6a, as shown in
Fig. 4b, and compounds 6a and 6b adopted diferent shape
atoms to query I (Fig. 4c). This pattern is due to the presence
of methyl group in position 6 of quinolone ring.
Compound 6a docked with the target receptor with con-
sensus score 84 and with diferent poses because its left and
right arms bound the receptor clefts in a reverse pattern to
standards I and II and compound 6b (Fig. 2e). The carbonyl
of quinolone-one motif (left arm) forms two HBs with the
amino acid Arg: 439A (length 2.99 and 2.51 Å). This amino
acid interacted with polar linker in case of compounds I
and II. The internal nitrogen of the linker NHNH C=SNH
thiosemicarbazide functionality forms HB with CME 592:
A (length 2.29 Å).
Docking with 4UBP Docking was then carried out on
4UBP protein [39]. The receptor of this enzyme contains
two pockets linked together. Compound I docked with the
receptor (with consensus score 97) by formation of two HBs
with Ala: 366A through the NH of the polar linker NHNH
C=SNH as donor and HB with Gly 368C: A through the N of
pyridine moiety (left arm) as acceptor. The nitrophenyl moi-
ety (right arm) adopted the receptor pocket in a hydropho-
bic–hydrophobic interaction (Fig. 3a). Compound II docked
in the receptor in one pocket without interaction to other
sites with consensus score 95. It forms HB with Asp 224C:
A through the internal of NHNH C=SNH (length 1.54 Å) as
donor. Both the indole and phenyl moieties docked through
hydrophobic–hydrophobic interactions (Fig. 3b).
In consideration of lead II as a query, both compounds
6a and 6b adopt high overlay to color atoms of the left atom
(indole moiety) and polar linker (thiosemicarbazide func-
tionality). The two compounds fail to adopt color atom of
the left arm of query II (Fig. 5b), while both compounds 6a
and 6b exhibited similar alignment in shape atoms to query
II (Fig. 5c).
Compound 6b, the most potent among the synthesized
compounds, binds the receptor in one pocket of receptor
1 3

Molecular Diversity
Fig. 2 Visual representation for a standard I; b standard II; c com-
pound 6b; and d overlay of the binding modes of 6b and standards I
and II docked with PDB ID: 3LA4; e compound 6a forms HB with
essential amino acids. These compounds illustrated HB (dashed green
lines) and hydrophobic–hydrophobic interaction toward urease-bind-
ing site (PDB ID: 3LA4). (Color fgure online)
Finally, we subjected the most active compounds 6b to
ROCS as a query. Compound 6b showed atoms labels: 3
rings, 4 donors and 2 acceptors (Fig. 6a).
The second output of ROCs analysis is the score. Score
represents various aspects of that alignment. The two core
scoring methods are Shape Tanimoto (Tanimoto coefcient)
and Color Tanimoto. Tanimoto Combo is the sum of those
1 3

Molecular Diversity
Fig. 3 Visual representation for a standard I, b standard II, c com-
pound 6b, d compound 6a forms HB with essential amino acids in a
diferent pose. These compounds illustrated HB (dashed green lines)
and hydrophobic–hydrophobic interaction toward urease-binding site
(PDB ID: 4UBP). (Color fgure online)
two independent components (Shape and Color Tanimoto).
Shape Tanimoto represents the shared volume and mismatch
volume and has scale from 0 to 1. Color Tanimoto is the
distribution of chemical features in 3D (also scale from 0
to 1) (Table 3). The scores are computed, and the process is
repeated to each conformation of the query molecules (I and
II) and each conformation for the database molecules 6a–e
(Table 3). All compounds showed higher score in Tanimoto
combo to lead II (as query) in the range from 1.24 to 1.01
rather than the lead I (as query) in the range from 1.05 to
0.92.
query, the Tanimoto colors similarity of compounds was
6c>6a=6b>6i>6g=lead II. This ranking indicating the
right arm is essential to be aryl directly attached to the polar
thiosemicarbazide linker.
From previous data, the synthesized compounds ranked
best which need not to be structurally similar (in a 2-D
sense) to the queries. In this study, our designed com-
pounds are more similar to lead II as shown in number
of atom labels (Fig. 6a), and shape similarity using Tani-
moto Color is a good descriptor in the expected 3DQSAR
determination. In order to understand the 3D pharma-
cophoric feature of our compounds and figure out their
3DQSAR, ROCS was operated with compound 6f, and
we can find from the figure that the compound does not
exhibit complete overlay with query II. The benzyl arm
adopted perpendicular position of the phenyl group in
By studying the Tanimoto scores values, we found that
compounds score Tanimoto Color descriptor is best-matched
with compounds’ activity rather than the summation descrip-
tor (Tanimoto Combo). Considering lead II as query, com-
pounds were 6c>6d=6b=6a>6e. Regarding lead I as a
1 3

Molecular Diversity
Fig. 4 a Representation of
shape and color atoms of com-
pound I as query by vROCS
application; b overlay and
alignment of 6a on compound I
shape; c overlay and alignment
of 6b on compound I shape.
Both compounds 6a and 6b
show dissimilarity in quinolone
ring to query I
lead II, and its quinolone moiety does not overlay with
the indole moiety (Fig. 5a–c). According to these find-
ings, the presence of phenyl group in the thiosemicar-
bazide terminal is also important. The cyclic amide in
quinolone system participates in formation of HB with
essential amino acids inside the receptor. Also, 2D struc-
ture is not essential and 3D is more accurate which is rep-
resented by Tanimoto Color. These findings will guide us
in the future, to elaborate new urease inhibitors originated
from different scaffold systems by keeping the essential
pharmacophoric features.
Conclusion
A new series of quinolin-2-one thiosemicarbazide deriva-
tives 6a–j have been synthesized and characterized by
diferent spectroscopic and elemental analysis techniques
1
including H NMR, 13C NMR, 2D NMR, MS and ele-
mental microanalyses. In vitro screening of antimicrobial
activity was carried out for all the synthesized compounds
against the urease-producing R. mucilaginosa and Pro-
teus mirabilis strains. Results revealed that most of the
tested compounds showed moderate-to-good activity
1 3

Molecular Diversity
Fig. 5 a Representation of shape and color atoms of compound II as query by vROCS application; b overlay and alignment of 6a and 6b on
compound II shape; c both compounds 6a and 6b show similarity in color and shape to lead II
against R. mucilaginosa, with 12–14 mm zone of inhibi-
tion compared to clotrimazole (25 mm). Compound 6h
experienced the highest anti-P. mirabilis activity achiev-
ing MIC = 399.3 µM which represents about 300 times
less activity than the reference ciprofloxacin. Moreo-
ver, all the prepared compounds were in vitro tested as
potential urease inhibitors. Among the tested compounds,
6a and 6b were the most active, showing a potent ure-
ase inhibition activity on diferent tested concentrations
(IC50 = 0.58 0.15 and 0.43 0.09 µM) and proved that
they could be potential candidates for further investiga-
tion to treat certain clinical conditions caused by micro-
bial ureases. Molecular docking showed the importance of
thiosemicarbazide as a rich donor and acceptor. Quinolone
system contains amide part (donor and acceptor also) to
from HB. The use of ROCS led to the identifcation of a
new inhibitor with diverse scafolds presenting synthetic
opportunities. The scafolds should contain polar linker
rich with donor and acceptor pharmacophore and linked
directly with two aryl systems; the aryl should contain 1
or 2 rings and contain donor and acceptor pharmacophore
parts. To the best of our knowledge, this is the frst exam-
ple of inhibition of this enzyme by quinolone-derived thio-
semicarbazides. The present study provides a knowledge
that encourages researchers for further modifcation of this
scafold to be more active antibacterial and/antifungal ure-
ase inhibitors.
Experimental
Chemistry
Reagent and materials
Unless otherwise noted, all materials were obtained from
commercial suppliers and used without further purifcation.
Reactions were monitored by TLC (Kieselgel 60 F254 pre-
coated plates, E-Merck, Germany); the spots were detected
by exposure to UV lamp at 254 nm. Melting points were
determined on an electrothermal melting point apparatus
(Stuart Scientifc Co.) and were uncorrected. NMR spectra
1 3

Molecular Diversity
Fig. 6 a Representation of shape and color atoms of compound 6b as query by vROCS application; b 3D visual representation of compound 6f;
c 3D visual representation of lead II; D) visual representation of compound 6f and lead II and showed dissimilarity
Table 3 Tanimoto scores for
Compd.
Tanimoto Combo (Stand I as query)
Tanimoto Combo (Stand II as query)
compounds 6a–j and lead
compounds I and II as query
Shape Tanimoto
Color Tanimoto
Shape Tanimoto
Color Tanimoto
6c
1.02
0.98
0.93
0.94
1.03
0.96
1.02
0.93
0.92
1.05
0.92
2
0.72
0.71
0.72
0.68
0.78
0.71
0.78
0.69
0.68
0.7
0.30
0.27
0.27
0.26
0.25
0.25
0.24
0.24
0.24
0.21
0.20
1
1.24
1.17
1.21
1.03
1.07
2.00
1.21
1.01
1.00
1.08
1.19
1.01
0.83
0.77
0.81
0.83
0.75
1
0.81
0.73
0.72
0.76
0.81
0.72
0.41
0.39
0.39
0.30
0.31
1
0.39
0.28
0.28
0.33
0.37
0.28
6a
6b
6i
6g
Lead II
6d
6j
6h
6f
6e
0.72
1
Lead I
1 3

Molecular Diversity
were measured on a Bruker AV-400 spectrometer (Bruker
153.43, 151.38, 139.04, 133.48, 127.87, 125.95, 125.16,
119.33, 116.58, 112.63, 105.40, 94.07, 55.63. GS MS: m/z
calcd: 340.10, found: 340.41. Anal. Calcd for C17H16N4O2S
(340.10): C, 59.98; H, 4.74; N, 16.46. Found: C, 59.70; H,
4.56; N, 16.73.
1
BioSpin Corp., Billerica, MA, USA) (400 MHz for H,
101 MHz for 13C and 40.55 MHz for 15N) at Florida Insti-
tute of Technology, USA. The 1H and 13C-NMR chemical
shifts are given relative to internal standard TMS=0; 15
N
shifts are reported versus external neat nitromethane = 0.
Vario EL III German CHN Elemental analyzer model was
used for elemental analysis. Preparation and analytical data
of compounds 2–5 were as reported [22].
2‑(6‑Chloro‑2‑oxo‑1,2‑dihydroquinolin‑4‑yl)‑N‑phenylhy‑
drazinecarbothioamide (6d) Yield: 0.28 gm, (81%; mp:
224–226 °C, 1H NMR (400 MHz, DMSO-d6) δ ppm 11.26
(s, 1H, –CO–NH), 9.99 (s, 1H, Ar–NH), 9.90 (s, 1H, quin-
NH), 9.29 (s, 1H, NNH), 8.04 (s, 1H, quin-Ar–H), 7.55
(d, J=7.1, 1H, quin-Ar–H), 7.42 (d, J=6.9, 2H, Ar–H),
7.32 (t, J=7.2 Hz, 2H, Ar–H), 7.28 (d, J=9.1, 1H, quin-
Ar–H), 7.16 (t, J=7.1, 1H, Ar–H), 5.54 (s, 1H, CH). GS
MS: m/z calcd: 344.05, found: 344.23. Anal. Calcd for
C16H13ClN4OS (344.05):C, 55.73; H, 3.80;N, 16.25. Found:
C, 55.92; H, 3.57; N, 16.49.
General procedure for the synthesis of compounds 6a–j
To a suspension of hydrazinoquinoline 5 (1 mmol) in diox-
ane (25 mL), the appropriate isothiocyanate derivatives
(1 mmol) were added and the mixture was heated at refux
on a boiling water bath for 3–4 h. The mixture was then left
to cool, and the precipitate so formed was collected by fltra-
tion, washed with methanol and recrystallized by ethanol to
give the target compounds.
2‑(6‑Bromo‑2‑oxo‑1,2‑dihydroquinolin‑4‑yl)‑N‑phenyl‑
hydrazinecarbothioamide (6e) Yield: 0.32 g (82%); mp:
230–232 °C, 1H NMR (400 MHz, DMSO-d6) δ ppm 11.24
(s, 1H, –CO–NH), 9.99 (s, 1H, Ar–NH), 9.88 (s, 1H, quin-
NH), 9.28 (s, 1H, NNH), 8.17 (s, 1H, quin-Ar–H), 7.65 (dd,
J=8.8, 2.0, 1H, quin-Ar–H), 7.42 (d, J=7.7, 2H, Ar–H),
7.32 (t, J=7.8, 2H, Ar–H), 7.22 (d, J=8.8, 1H, quin-Ar–H),
7.16 (t, J=7.3, 1H, Ar–H), 5.53 (s, 1H,,=CH).13C NMR
(101.0 MHz, DMSO-d6) δ ppm 181.02, 162.57, 150.72,
138.99, 138.13, 132.98, 127.90, 125.97, 125.60, 125.20,
117.43, 113.97, 112.47, 94.21. GS MS: m/z calcd: 388.00,
found: 388.22. Anal. Calcd for C16H13BrN4OS (388.00):
C, 49.37; H, 3.37; N, 14.39. Found: C, 49.40; H, 3.31; N,
14.46.
2‑(2‑Oxo‑1,2‑dihydroquinolin‑4‑yl)‑N‑phenylhydrazinecar‑
bothioamide (6a) Yield: 0.23 g (74%); mp: 185–187 °C,
1H NMR (400 MHz, DMSO-d6) δ ppm 11.00 (s, 1H, –CO–
NH), 9.92 (s, 1H, Ar–NH), 9.84 (s, 1H, quin-NH), 9.15 (s,
1H, NNH), 7.77 (d, J=8.0 Hz, 1H, quin-Ar–H), 7.46–7.41
(m, 3H, quin-Ar–H), 7.30–7.14 (m, 5H, Ar–H), 5.51 (s, 1H,
C=CH). GS MS: m/z calcd: 310.09, found: 310.20. Anal.
Calcd for C16H14N4OS (310.09): C, 61.92; H, 4.55; N, 18.0.
Found: C, 61.79; H, 4.35; N, 17.90.
2‑(6‑Methyl‑2‑oxo‑1,2‑dihydroquinolin‑4‑yl)‑N‑phenyl‑
hydrazinecarbothioamide (6b) Yield: 0.29 g (91%); mp:
215–217 °C, 1H NMR (400 MHz, DMSO-d6) δ ppm 11.03
(s, 1H, –CO–NH), 9.94 (s, 1H, Ar–NH), 9.86 (s, 1H, quin-
NH), 9.15 (s, 1H, NNH), 7.77 (s, 1H, quin-Ar–H), 7.44 (d,
J=7.6 Hz, 2H, Ar–H), 7.33 (d, J=7.8 Hz, 1H, quin-Ar–H),
7.32 (t, J=7.9 Hz, 2H, Ar–H), 7.17 (d, J=8.4 Hz, 1H, quin-
Ar–H), 7.16 (t, J=7.3 Hz, 1H, Ar–H), 5.50 (s, 1H,=CH),
2.35 (s, 3H, CH3).13C NMR (101.0 MHz, DMSO-d6) δ ppm
181.07, 162.73, 151.46, 139.06, 137.03, 131.47, 129.29,
127.85, 125.88, 125.10, 122.63, 115.26, 112.14, 93.70,
20.65. GS MS: m/z calcd: 324.10, found: 324.86. Anal.
Calcd for C17H16N4OS (324.10): C, 62.94; H, 4.97; N,
17.27. Found: C, 62.53; H, 4.74; N, 17.03.
N‑Benzyl‑2‑(6‑methyl‑2‑oxo‑1,2‑dihydroquinolin‑4‑yl)
hydrazinecarbothioamide (6f) Yield: 0.26 g (77%); mp:
239–240 °C, 1H NMR (400 MHz, DMSO-d6) δ ppm
11.00 (s, 1H, –CO–NH), 9.61 (s, 1H, CH2-NH), 9.03 (s,
1H, quin-NH), 8.83 (s, 1H, NNH), 7.74 (s, 1H, quin-Ar–
H), 7.27–7.20 (m, 5H, Ar–H), 7.17–7.13 (m, 2H, Ar–H),
5.46 (s, 1H,=CH), 4.72 (s, 2H, benzylic-CH2), 2.32 (s, 3H,
CH3).13C NMR (101.0 MHz, DMSO-d6) δ ppm 181.53,
162.32, 150.95, 138.97, 136.57, 131.00, 128.89, 127.52,
126.63, 126.11, 121.91, 114.85, 111.60, 93.01, 46.10, 20.16.
GS MS: m/z calcd: 338.12, found: 338.39. Anal. Calcd for
C18H18N4OS (324.10): C, 63.88; H, 5.36; N, 16.56. Found:
C, 64.19; H, 5.20; N, 16.18.
2‑(6‑Methoxy‑2‑oxo‑1,2‑dihydroquinolin‑4‑yl)‑N‑phenyl‑
hydrazine‑carbothioamide (6c) Yield: 0.28 g (83%); mp:
200–202 °C, 1H NMR (400 MHz, DMSO-d6) δ ppm 11.00
(s, 1H, –CO–NH), 9.95 (s, 1H, Ar–NH), 9.88 (s, 1H, quin-
NH), 9.15 (s, 1H, NNH), 7.47 (s, 1H, quin-Ar–H), 7.41 (d,
J=7.4 Hz, 2H, Ar–H), 7.31 (m, 2H, quin-Ar–H), 7.21–7.14
(m, 3H, Ar–H), 5.50 (s, 1H,=CH), 3.79 (s, 3H, OCH3).13C
NMR (101.0 MHz, DMSO-d6) δ ppm 181.11, 162.46,
N‑Benzyl‑2‑(6‑bromo‑2‑oxo‑1,2‑dihydroquinolin‑4‑yl)
hydrazinecarbothioamide (6g) Yield: 0.31 g (78%); mp:
243–245 °C, 1H NMR (400 MHz, DMSO-d6) δ ppm 11.20
(s, 1H, –CO–NH), 9.64 (s, 1H, CH2NH), 9.14 (s, 1H, quin-
NH), 8.89 (s, 1H, NNH), 8.12 (s, 1H, quin-Ar–H), 7.64 (dd,
J=8.8, 1.1 Hz, 1H, quin-Ar–H), 7.29–7.23 (m, 4H, Ar–H),
1 3

Molecular Diversity
7.21–7.19 (m, 2H, Ar–H), 5.48 (s, 1H, C=CH), 4.71 (s, 2H,
benzylic-CH2).13C NMR (101.0 MHz, DMSO-d6) δ ppm
181.10, 162.08, 150.16, 138.88, 137.67, 132.51, 127.54,
126.57, 126.14, 124.85, 117.00, 113.42, 112.02, 93.53,
46.09. GS MS: m/z calcd: 402.01, found: 402.47. Anal.
Calcd for C17H15BrN4OS (402.01): C, 50.63; H, 3.75; N,
13.89. Found: C, 50.81; H, 3.67; N, 14.26.
for C13H13BrN4OS (352.00): C, 44.20; H, 3.71; N, 15.86.
Found: C, 44.25; H, 3.42; N, 15.59.
Biology
Antifungal activity
N‑Allyl‑2‑(2‑oxo‑1,2‑dihydroquinolin‑4‑yl)hydrazinecar‑
bothioamide (6h) Yield: 0.22 g (79%); mp: 191–189 °C,
1H NMR (400 MHz, DMSO-d6) δ ppm 11.06 (s, 1H, –
CO–NH), 9.55 (s, 1H, NNH), 9.07 (s, 1H, quin-NH), 8.46
(s, 1H, Allyl-NH), 7.90 (d, J=8.0 Hz, 1H, Ar–H), 7.48 (t,
J=7.3 Hz, 1H, Ar–H), 7.28 (d, J=8.0 Hz, 1H, Ar–H), 7.15
(dd, J=7.8, 7.3 Hz, 1H, Ar–H), 5.82 (ddt, Jd=17.4, 10.1 Hz,
Jt =5.1; 1H, CH2 =Allyl), 5.43 (s, 1H, quin-C=CH), 5.07
(d, J=17.2 Hz, 1H, CH=Allyl), 5.02 (d, J=10.5 Hz, 1H,
CH=Allyl), 4.09 (d, J=4.6 Hz, 2H, CH2-Allyl).13C NMR
(101.0 MHz, DMSO-d6) δ ppm 181.10, 162.35, 151.09,
138.60, 134.58, 129.92, 122.28, 120.06, 114.90, 114.62,
111.70, 92.79, 45.19. GS MS: m/z calcd: 274.09, found:
274.80. Anal. Calcd for C13H14N4OS (274.09): C, 56.91; H,
5.14; N, 20.42. Found: C, 56.69; H, 5.38; N, 19.92.
Sabouraud agar (SA) media were prepared in the Myco-
logical Center (AUMC), Assiut University, Assiut. The
antifungal activity of tested compounds was determined
according to the agar disk difusion method [29]. Rho-
dotorula mucilaginosa AUMC 8795 was used to test the
antifungal activity of the target compounds.
A suspension from spores in sterile distilled water was
prepared: The spores were taken from 2- to 5-day-old cul-
ture of the test fungi growing on Sabouraud agar (SA)
medium [29]. The fnal spore concentration was nearly
5 × 104 spores/mL. Approximately 15 mL of growth
medium was then introduced on sterilized Petri dishes of
9 cm diameter and inoculated with 1 mL of spore sus-
pension. Plates were shaken gently to homogenize the
inocula. Antifungal activity of the tested compounds 6a–j
was performed by the standard agar disk difusion method
as follows:
N‑Allyl‑2‑(6‑methyl‑2‑oxo‑1,2‑dihydroquinolin‑4‑yl)
hydrazinecarbothioamide (6i) Yield: 0.25 g (87%); mp:
196–198 °C, 1H NMR (400 MHz, DMSO-d6) δ ppm 10.99
(s, 1H, –CO–NH), 9.53 (s, 1H, NNH), 8.97 (s, 1H, quin-
NH), 8.43 (s, 1H, Allyl-NH), 7.72 (s, 1H, Ar–H), 7.31 (d,
J=7.2 Hz, 1H, Ar–H), 7.16 (d, J=8.0 Hz, 1H, Ar–H), 5.81
(ddt, Jd=17.0, 9.8, Jt =5.0 Hz; 1H, Allyl=CH), 5.40 (s,
1H, quin-C=CH), 5.06 (d, J=17 Hz, 1H, CH=Allyl), 5.01
(d, J=11.0 Hz, 1H, CH=Allyl), 4.09 (d, J=4.2 Hz, 2H,
N-CH2), 2.33 (s, 3H, CH3).13C NMR (101.0 MHz, DMSO-
d6) δ ppm 181.11, 162.27, 150.90, 136.56, 134.58, 130.92,
128.86, 121.92, 114.82, 114.62, 111.57, 92.92, 45.18, 20.16.
GS MS: m/z calcd: 288.10, found: 288.26. Anal. Calcd for
C14H16N4OS (288.10): C, 58.31; H, 5.59; N, 19.43. Found:
C, 58.45; H, 5.21; N, 19.07.
Sterile 5-mM flter paper disk (Whatman) was saturated
with 10 µL solutions of the test compound or clotrimazole
(40 µmol/mL in DMSO). In addition, as a negative control,
other disks were impregnated with the solvent (DMSO) and
served. The disks were then dried for 1 h and placed in the
center of each plate. The seeded plates were incubated at
28 2 °C for 7 days. The radii of inhibition zones (in mM)
of triplicate sets were measured at successive intervals dur-
ing the incubation period, and the results are presented in
Table 1.
Antibacterial activity and MIC determination
The antibacterial activity against P. mirabilis was tested
using the cup-plate difusion method [30]. Briefy, 0.5 ml of
1×108 CFU/ml (0.5 McFarland turbidity) P. mirabilis was
plated in sterile Petri dish; then, 20 mL of Muller-Hinton
agar (oxoid) was poured in the plates. After solidifcation of
the media, four equidistant cups were made in the agar. Four
diferent concentrations of the tested compounds were pre-
pared by twofold serial dilutions in DEMSO; then, 100 μL
of each concentration is applied to the cups separately. Com-
pounds allowed difusing into the Mullet-Hinton agar, and
then, plates were incubated overnight at 35 °C. The inhibi-
tion zones of the bacteria around the cups were measured,
and the MIC values were calculated by plotting the natural
logarithm of the tested concentrations against squares of the
N‑Allyl‑2‑(6‑bromo‑2‑oxo‑1,2‑dihydroquinolin‑4‑yl)
hydrazinecarbothioamide (6j) Yield: 0.28 g (80%); mp:
190–192 °C, 1H NMR (400 MHz, DMSO-d6) δ ppm 11.20
(s, 1H, –CO–NH), 9.56 (s, 1H, NNH), 9.10 (s, 1H, quin-
NH), 8.52 (s, 1H, Allyl-NH), 8.13 (bs, 1H, Ar–H), 7.63
(d, J = 9.2 Hz, 1H, Ar–H), 7.21 (d, J = 8.4 Hz, 1H, Ar–H),
5.80 (ddt, Jd= 17.0, 10.5, Jt = 5.3 Hz; 1H, CH = Allyl), 5.42
(s, 1H, quin-C=CH), 5.06 (d, J = 18.0, 1H, CH = Allyl),
5.02 (d, J = 11.1 Hz, 1H, CH = Allyl), 4.08 (d, J = 5.0 Hz,
2H, CH2-Allyl).13C NMR (101.0 MHz, DMSO-d6) δ
ppm 181.05, 162.09, 150.16, 137.66, 134.52, 132.51,
124.90, 116.99, 114.65, 113.41, 112.02, 93.41, 45.20.
GS MS: m/z calcd: 352.00, found: 352.69. Anal. Calcd
1 3

Molecular Diversity
inhibition zone. The MIC value is the antilogarithm of the
intercept on the logarithm of concentration axis.
Shape alignment and ROCS The basic method to represent
shape and color features in ROCS is using ROC application
of OpenEye Scientifc Software [35–37]. Compounds I and
II [4] were selected as query molecules. Compounds library
was adopted as the database fle. Both query and data-
base fles were energy-minimized by Omega applications.
ROCS runs were employed by personal PC in very fast
using vROCS interface. vROCS was employed to run and
analyze/visualize the results. ROCS application searched
the database with the query to fnd molecules with similar
shape and colors. Compound conformers were scored based
upon the Gaussian overlap to the query, and the best-scoring
parameters is Tanimoto Combo scores (shape+color); the
highest score is best-matched with the query compound.
Urease inhibitory activity In vitro screening and inhibitory
studies on urease (Jack bean urease) were determined using
colored Berthelot phenols method, which measures the lib-
eration of ammonia from the reaction [40]. Briefy, the assay
mixture, containing 1 unit of enzyme, was added to 650 µL
of bufer solution (50 mMol phosphate bufer pH 6.7,
400 mMol sodium salicylate, 10 mMol sodium nitroprus-
side and 2 mMol EDTA/L) and mixed with 10 µL of dif-
ferent concentrations 0.1–100 mM of the tested compounds
in DMF as a solvent. DMF was tested alone and showed no
inhibitory efect on the enzyme. After 15 min of incubation
at room temperature, 10 µL of 50 mg/L urea solution was
add. The mixture was incubated for 0.5 h in water bath at
37 °C to allow the hydrolysis process.
Acknowledgements Yaseen Elshaier acknowledges the OpenEye Sci-
entifc Software Inc. (Santa Fe, NM, USA) for providing the academic
license that helped in performing the docking and ROCS studies. The
NMR spectrometer at Florida Institute of Technology was purchased
with the assistance of the US National Science Foundation (CHE 03
42251).
After complete urea hydrolysis and ammonia liberation,
the reaction was stopped by adding 200 µL of the hypochlo-
rite reagent (150 mmol/L sodium hydroxide, 140 mm/L
sodium hypochlorite). The ammonia liberated was allowed
to complex with the hypochlorite and salicylate for 25 min at
30 °C. The absorbance was measured at 578 nm using UV/
VIS Spectrophotometer (Optizen POP, 5U4608, Korea), and
experiments were performed in triplicate in a fnal volume of
1 mL. All results were compared with thiourea, a standard
inhibitor of urease. The percentage inhibition was calcu-
lated as the diference of absorbance values with and with-
out the test compounds, and the concentration that provokes
an inhibition halfway between the minimum and maximum
responses of each compound (relative IC50) was determined
by monitoring the inhibition efect of various concentrations
of compounds in the assay.
Compliance with ethical standards
Conflict of interest The authors declare that there is no confict of in-
terest regarding the publication of this article.
References
1. Prajapati SM, Patel KD, Vekariya RH, Panchal SN, Patel HD
(2014) Recent advances in the synthesis of quinolines: a review.
RSC Adv 4:24463–24476
2. Navneetha O, Deepthi K, Rao AM, Jyostna TS (2017) A review
on chemotherapeutic activities of quinoline. Int J Pharm Chem
Biol Sci 7:364–372
3. Saeed A, Zaib S, Pervez A, Mumtaz A, Shahid M, Iqbal J (2013)
Synthesis, molecular docking studies, and in vitro screening of
sulfanilamide-thiourea hybrids as antimicrobial and urease inhibi-
tors. Med Chem Res 22:3653–3662
Molecular modeling
Molecular docking study The docking studies were per-
formed using the OpenEye Modeling software [35–37].
A virtual library of target compounds was used, and their
energies were minimized using the MMFF94 force feld,
followed by the generation of multi-conformers using the
OMEGA application. The whole library of minimized
energy values was docked appropriate target. The receptor
PDB fles were downloaded from the Protein Data Bank
(PDB) (PDB ID: 3LA4) [38] and (PDB ID: 4UBP) [39].
Both the ligand input fle and the receptor input fle were
passed into FRED to perform the molecular docking simula-
tions. Multiple scoring functions were employed to predict
energy profle of the ligand–receptor complex. The Vida
application was employed as a visualization tool to show
the ligands pose and the potential binding interactions of the
ligands to the receptor of interest.
4. Ali B, Khan KM, Hussain S, Hussain S, Ashraf M, Riaz M,
Wadood A, Perveen S (2018) Synthetic nicotinic/isonicotinic thio-
semicarbazides: in vitro urease inhibitory activities and molecular
docking studies. Bioorg Chem 79:34–45
5. Sen K, Komagata K (1979) Distribution of urease and extracel-
lular DNase in yeast species. J Gener Appl Microbiol 25:127–135
6. Wirth F, Goldani LZ (2012) Epidemiology of Rhodotorula: an
emerging pathogen. Interdiscip Perspect Infect Dis 2012:1–7
7. Burall LS, Harro JM, Li X, Lockatell CV, Himpsl SD, Hebel JR,
Johnson DE, Mobley HL (2004) Proteus mirabilis genes that con-
tribute to pathogenesis of urinary tract infection: identifcation of
25 signature-tagged mutants attenuated at least 100-fold. Infect
Immun 72:2922–2938
8. Cernohorska L, Chvilova E (2011) Proteus mirabilis isolated from
urine, resistance to antibiotics and bioflm formation. Klinicka
mikrobiologie a infekcni lekarstvi 17:81–85
9. Tumbarello M, Trecarichi EM, Fiori B, Losito AR, D’Inzeo T,
Campana L, Ruggeri A, Di Meco E, Liberto E, Fadda G (2012)
Multidrug-resistant Proteus mirabilis bloodstream infections:
1 3

Molecular Diversity
24. Abdullah MA, El-Baky RMA, Hassan HA, Abdelhafez E-SM,
Abuo-Rahma GE-DA (2016) Fluoroquinolones as urease inhibi-
tors: anti-Proteus mirabilis activity and molecular docking studies.
Am J Microbiol Res 4:81–84
risk factors and outcomes. Antimicrob Agents Chemother
56:3224–3231
10. Singhal S, Arora S, Agarwal S, Sharma R, Singhal N (2013) A
review on potential biological activities of thiosemicarbazides.
World J Pharm Pharm Sci 2:4661–4681
25. Toolkit, OEChem (2012) OpenEye Scientifc Software, Santa Fe,
NM, (USA)
11. Pitucha M, Karczmarzyk Z, Swatko-Ossor M, Wysocki W, Wos
M, Chudzik K, Ginalska G, Fruzinski A (2019) Synthesis, in vitro
screening and docking studies of new thiosemicarbazide deriva-
tives as antitubercular agents. Molecules 24:251–267
26. Abass M (2000) Chemistry of substituted quinolinones. Part II
synthesis of novel 4-pyrazolylquinolinone derivatives. Synth
Commun 30:2735–2757
27. Ismail M, Abass M, Hassan M (2000) Chemistry of substituted
quinolinones. Part VI. Synthesis and nucleophilic reactions of
4-chloro-8-methylquinolin-2 (1H)-one and its thione analogue.
Molecules 5:1224–1239
12. Cihan-Üstündağ G, Gürsoy E, Naesens L, Ulusoy-Güzeldemirci
N, Çapan G (2016) Synthesis and antiviral properties of novel
indole-based thiosemicarbazides and 4-thiazolidinones. Bioorg
Med Chem 24:240–246
28. Ismail M, Abdel-Megid M, Hassan M (2004) Some reactions of
2-and 4-substituted 8-methylquinolin-2 (1H)-ones and their thio
analogues. Chem P-Slovak Acad Sci 58:117–125
13. Umadevi P, Deepti K, Srinath I, Vijayalakshmi G, Tarakaramji
M (2012) Synthesis and in vitro antibacterial activity of some
new urea, thiourea and thiosemicarbazide derivatives. Int J Pharm
Pharm Sci 4:383
29. William H (1977) Microbiological assay. An introduction to quan-
titative principles and evaluation. Academic Press, New York
30. Miller RE, Rose SB (1941) Studies with the agar cup-plate
method: IV. A correlation of agar cup-plate data with antiseptic
dilution data. Am J Clin Pathol 11:414–424
14. Wujec M, Kędzierska E, Kuśmierz E, Plech T, Wróbel A, Paneth
A, Orzelska J, Fidecka S, Paneth P (2014) Pharmacological and
structure-activity relationship evaluation of 4-aryl-1-diphenyla-
cetyl (thio) semicarbazides. Molecules 19:4745–4759
15. Šarkanj B, Molnar M, Čačić M, Gille L (2013) 4-Methyl-7-hy-
droxycoumarin antifungal and antioxidant activity enhancement
by substitution with thiosemicarbazide and thiazolidinone moie-
ties. Food Chem 139:488–495
31. Pervez H, Iqbal MS, Tahir MY, F-u-H Nasim, Choudhary MI,
Khan KM (2008) In vitro cytotoxic, antibacterial, antifungal and
urease inhibitory activities of some N 4-substituted isatin-3-thio-
semicarbazones. J Enzyme Inhib Med Chem 23:848–854
32. Schulz M, Iwersen-Bergmann S, Andresen H, Schmoldt A (2012)
Therapeutic and toxic blood concentrations of nearly 1000 drugs
and other xenobiotics. Crit Care 16:136–140
16. Masek BB, Merchant A, Matthew JB (1993) Molecular shape
comparison of angiotensin II receptor antagonists. J Med Chem
36:1230–1238
33. Sujoy B, Aparna A (2013) Potential clinical signifcance of urease
enzyme. Eur Sci J 9:94–102
17. Hawkins PC, Skillman AG, Nicholls A (2007) Comparison of
shape-matching and docking as virtual screening tools. J Med
Chem 50:74–82
34. Mobley H, Island MD, Hausinger RP (1995) Molecular biology
of microbial ureases. Microbiol Mol Biol Rev 59:451–480
35. Fast Rigid Exhaustive Docking (FRED) Receptor, version 2.2.5;
OpenEye Scientifc Software, Santa Fe, NM (USA); http://www.
eyesopen.com
18. Rush TS, Grant JA, Mosyak L, Nicholls A (2005) A shape-based
3-D scafold hopping method and its application to a bacterial
protein–protein interaction. J Med Chem 48:1489–1495
19. Khodair AI, Attia AM, Gendy EA, Elshaier YA, El-Magd MA
(2019) Discovery of new S-glycosides and N-glycosides of pyr-
idine-biphenyl system with antiviral activity and induction of
apoptosis in MCF 7 cells. J Heterocycl Chem 56:1733–1747
20. Abdellatif KR, Fadaly WA, Kamel GM, Elshaier YA, El-Magd
MA (2019) Design, synthesis, modeling studies and biological
evaluation of thiazolidine derivatives containing pyrazole core
as potential anti-diabetic PPAR-γ agonists and anti-infammatory
COX-2 selective inhibitors. Bioorg Chem 82:86–99
36. OMEGA, version 2.5.1.4; OpenEye Scientifc Software, Santa Fe,
NM (USA); http://www.eyesopen.com
37. VIDA, version 4.1.2; OpenEye Scientifc Software, Santa Fe, NM
(USA); http://www.eyesopen.com
38. Balasubramanian A, Ponnuraj K (2010) Crystal structure of the
frst plant urease from jack bean: 83 years of journey from its frst
crystal to molecular structure. J Mol Biol 400:274–283
39. Benini S, Rypniewski WR, Wilson KS, Miletti S, Ciurli S, Man-
gani S (2000) The complex of Bacillus pasteurii urease with ace-
tohydroxamate anion from X-ray data at 1.55 Å resolution. J Biol
Inorg Chem 5:110–118
21. Adel MA, Ahmed IK, Eman AG, Mohammed AE-M, Yaseen
AMME (2019) New 2-oxopyridine/2-thiopyridine derivatives
tethered to a benzotriazole with cytotoxicity on MCF7 cell lines
and with antiviral activities. Lett Drug Des Discov 16:1–14
22. Elbastawesy MAI, Aly AA, Ramadan M, Elshaier YAMM,
Youssif BGM, Brown AB, Abuo-Rahma E-DAG (2019) Novel
pyrazoloquinolin-2-ones: design, synthesis, docking studies, and
biological evaluation as antiproliferative EGFR- TK inhibitors.
Bioorg Chem 90:103045–103061
40. Weatherburn M (1967) Phenol-hypochlorite reaction for determi-
nation of ammonia. Anal Chem 39:971–974
Publisher’s Note Springer Nature remains neutral with regard to
jurisdictional claims in published maps and institutional afliations.
23. Abdullah MA, Abuo-Rahma GE-DA, Abdelhafez E-SM, Hassan
HA, El-Baky RMA (2017) Design, synthesis, molecular dock-
ing, anti-Proteus mirabilis and urease inhibition of new fuoro-
quinolone carboxylic acid derivatives. Bioorg Chem 70:1–11
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