Muhammad Saadiq1, Ghias Uddin1, Abdul Latif2, Mumtaz Ali2, Nazia Akbar3, Sardar Ali2, Manzoor Ahmad2, Mohammad Zahoor4, Ajmal Khan5, Ahmed Al-Harrasi5. 1. Institute of Chemical Sciences, University of Peshawar, Peshawar, Khyber Pakhtunkhwa 25120, Pakistan. 2. Department of Chemistry, University of Malakand, Dir (Lower), Chakdara, Khyber Pakhtunkhwa 18800, Pakistan. 3. Department of Biotechnology & Genetic Engineering, Hazara University, Mansehra, Khyber Pakhtunkhwa, 21120, Pakistan. 4. Department of Biochemistry, University of Malakand, Dir (Lower), Chakdara, Khyber Pakhtunkhwa 18800, Pakistan. 5. UoN Chair of Oman's Medicinal Plants and Marine Natural Products, University of Nizwa, Nizwa 616, Sultanate of Oman.
Abstract
This research reports the synthesis of new benzimidazole-derived N-acylhydrazones (NAH), their characterization using various spectroscopic methods, and in vitro evaluation as potent carbonic anhydrase-II inhibitors. Among the target compounds (9-29), few showed higher inhibition than the standard acetazolamide (IC50: 18.6 ± 0.43 μM), for example, compound 9 (IC50: 13.3 ± 1.25 μM), 10 (IC50: 17.2 ± 1.24 μM), 12 (IC50: 14.6 ± 0.62 μM), and 15 (IC50: 14.5 ± 1.05 μM). Molecular docking was performed on the most active compounds, which revealed their binding interactions with the active site of the enzyme, thus supporting the experimental findings.
This research reports the synthesis of new benzimidazole-derived N-acylhydrazones (NAH), their characterization using various spectroscopic methods, and in vitro evaluation as potent carbonic anhydrase-II inhibitors. Among the target compounds (9-29), few showed higher inhibition than the standard acetazolamide (IC50: 18.6 ± 0.43 μM), for example, compound 9 (IC50: 13.3 ± 1.25 μM), 10 (IC50: 17.2 ± 1.24 μM), 12 (IC50: 14.6 ± 0.62 μM), and 15 (IC50: 14.5 ± 1.05 μM). Molecular docking was performed on the most active compounds, which revealed their binding interactions with the active site of the enzyme, thus supporting the experimental findings.
Carbonic anhydrases (CAs) are zinc-containing
enzymes that catalyze
the reversible hydration of carbon dioxide to bicarbonate ions and
protons. They are involved in a wide range of physiological processes,
such as pH regulation, gas exchange, ion transport, bone resorption,
fatty acid metabolism, and so forth. Their abnormal levels result
in glaucoma and edema. Many CA inhibitors (CAIs) mostly belong to
the sulfonamide class such as benzimidazole-6-sulfonamides, acetazolamide,
methazolamide, ethoxzolamide, dichlorophenamide, benzenesulfonamide,
and so forth.[1−4]However, numerous sulfonamides inhibit all CA isoforms non-specifically,
causing undesired side effects and reducing drug effectiveness owing
to off-target inhibition. Furthermore, due to sulfa allergy, a substantial
percentage of the general population cannot be treated with sulphonamides;
consequently, non-sulphonamide-based CAIs must be developed.[5]Benzimidazole is a privileged chemical
scaffold with tremendous
biological applications. Some of the benzimidazole-based market drugs
are omeprazole, pantoprazole (proton pump inhibitor), triclabendazole,
thiabendazole, albendazole (anthelmintic), benomyl, carbendazim, fuberidazole
(fungicide), candesertan, telmisartan (anti-hypertensive), mebendazole
(worm infestation), astemizole (antihistamine), bendamustine (anti-cancer),
afobazole (anxiolytic), casein kinase-1 inhibitors, pan RAF kinase
inhibitors, and so forth.[6−9]Benzimidazole-2-thiol (B2T) is an important
derivative of benzimidazole
with potential bioactivities. For example, a series of amide derivatives
based on B2T has been reported with antimicrobial activity against Candida albicans, Staphylococcus aureus, and Escherichia coli.[10] Another research study revealed high anti-convulsant
activity for B2T derivatives.[11] A pharmacophore
consisting of α-bromophenyallylidene on B2T imines has been
shown to enhance antimicrobial and antiproliferative activities.[12] A variety of structural forms based on B2T with
medicinal applications include acyclic nucleosides as antibacterial
agents,[13] aminoacetylenic-5-ethoxy-2-mercaptobenzimidazoles
as antibacterial and antifungal agents,[14] 2-MBI incorporated with thiazolidinone and isoxazole heterocycles
as potent anticonvulsant and anti-inflammatory/analgesic agents,[15] 2-MBI triazolylacetohydrazides as antimicrobial,
anti-inflammatory and analgesic agents,[16] afobazole as a potent anxiolytic drug,[17] and B2T oxadiazoles as antidiabetic agents.[18]Benzimidazole-2-thiol-based N-acylhydrazones
have
been reported as an antioxidant and α-glucosidase and cholinesterase
inhibitors.[19,20] These findings laid the base
to investigate the benzimidazole-derived N-acylhydrazones
for carbonic anhydrase inhibitory potential.Molecular docking
is a computational technique that attempts to
predict the binding of small molecules and large/macromolecules (receptor)
efficiently starting with their unbound structures. This procedure
is used not only to anticipate whether a ligand binds tightly to the
target but also to understand how it binds. To study the mechanism
of inhibition for carbonic anhydrase-II and the binding modes of acylhydrazones
(9–29), molecular docking studies were performed.
Bovine carbonic anhydrase-II (PDB ID: 1V9E) in complex with zinc metal was downloaded
from the Protein Data Bank and used for docking of compounds.[21,22] The active site of carbonic anhydrase-II where zinc metal is present
lies at the bottom of the deep cleft. The ligand–receptor interactions
and binding modes in the binding cavity of bovine carbonic anhydrase-II
in 2D and 3D forms were examined carefully by visual evaluation employing
GOLD. The docked orientation of compounds showed the direct interaction
of the zinc ion present in the active gorge and the ligand.
Results
and Discussion
Chemistry
A multi-step reaction
pathway leads to the
synthesis of N-acylhydrazones. In the first step,
benzimidazole-2-thiol (1) was alkylated with n-bromopropane (2) in absolute ethanol to yield
2-(propylthio)benzimidazole (3). Then, the N-alkylation of 2-(propylthio)benzimidazole was carried out using
chloroethylacetate (4) in DMF to get 2-(2-propylthio)benzimidazolyl)acetate
(5). In the third step, compound 5 was substituted
with hydrazine hydrate (6), resulting in the corresponding
acetohydrazide (7). Condensation of compound 7 with different aldehydes (8a,b) yielded a series of N-acylhydrazones (9–29). Purity of the
synthesized compounds was monitored by TLC in n-hexane
and ethyl acetate solvent systems and observed under UV light. The
structures of all compounds (Scheme ) were determined with the help of different spectroscopic
techniques such as 1H NMR, 13C NMR, and HR-MS(ESI). The main features of the final
products (9–29) in their 1H NMR spectra
included protons of the thiopropyl group (−SC3H7) at δ 0.95–3.30, methylene
protons (−NCH2CO−)
at δ 5.31–5.76, amide protons (−CO–NH−) at δ 11.47–12.09, imine protons
(−N=CH−) at δ 7.90–8.77
ppm, and aromatic protons of the benzimidazole nucleus and different
aromatic aldehydes in the aromatic region of the spectrum and other
substituents ,OH, CH3, OCH3, and N(CH2CH3), and so forth at the imine displaying varying chemical
shift values. The ESI-MS of the products displayed molecular ion peak
(M + H)+ characteristics of the compounds. After confirmation
of structures of the compounds, they were evaluated in vitro against
the bovine carbonic anhydrase-II enzyme. The inhibition profile is
presented in Table , and the probable mechanism of inhibition was studied through molecular
docking represented in Figures –6.
Scheme 1
Synthetic Route Leading
to Benzimidazole-Derived N-Acylhydrazones (9–29)
Table 1
In Vitro
Carbonic Anhydrase Inhibition
Potential of 9–29a,b
comp. no.
% inhibition
IC50 ± S.E.M (μM)
9
89.1
13.3 ± 1.25
10
83.0
17.2 ± 1.24
11
22.8
NA
12
91.7
14.6 ± 0.62
13
38.1
NA
14
20.8
NA
15
91.2
14.5 ± 1.05
16
5.6
NA
17
90.7
31.4 ± 2.29
18
81.2
22.7 ± 1.37
19
13.6
NA
20
67.7
45.5 ± 2.07
21
42.2
NA
22
90.1
24.7 ± 3.00
23
89.8
24.8 ± 1.24
24
84.3
162.3 ± 3.54
25
57.0
193.5 ± 3.24
26
67.8
166.0 ± 1.61
27
89.6
55.6 ± 4.25
28
67.6
42.1 ± 1.39
29
88.2
21.0 ± 0.74
acetazolamide
86.7
18.6 ± 0.43
S.E.M: standard error of mean.
NA: not active.
Figure 2
Close-up view of the top-scoring pose of acetazolamide (yellow
stick model) showing detailed ligand–enzyme interactions.
Figure 6
(A) Close-up view of
the top-scoring pose of compound 15 (cyan stick model)
showing detailed ligand–enzyme interactions;
(B) stereoview of ligand–enzyme interactions; (C) 2D view of
ligand–enzyme interactions; and (D) compound 15 (cyan stick model) superimposed on acetazolamide (yellow stick model),
the active site.
S.E.M: standard error of mean.NA: not active.
Carbonic Anhydrase
Inhibition Activity
In vitro carbonic
anhydrase inhibition activity of the target compounds (9–29) was evaluated using reported methods.[21] All the target compounds showed inhibition activity against bCA-II
except 11, 13, 14, 16, 19, and 21, which were found inactive
(Table ). Furthermore,
compounds 10, 12, 15, and 9 showed higher inhibitions than the standard acetazolamide (IC50: 18.6 ± 0.43 μM) where compound 9 was the most active inhibitor (IC50: 13.3 ±
1.25 μM) followed by 15 (IC50: 4.5 ±
1.05 μM), 12 (IC50: 14.6 ± 0.62
μM), and 10 (IC50: 17.2 ± 1.24
μM). However, compounds 23 (IC50: 24.8
± 1.24 μM), 22 (IC50: 24.7 ±
3.00 μM), 18 (IC50: 22.7 ± 1.37
μM), and 29 (IC50: 21.0 ± 0.74
μM) showed comparable inhibition to the standard, while compounds 17, 20, 24, 25, 26, 27, and 28 were found to be
the least active inhibitors of the enzyme.Figure displays
the most active inhibitors (9, 10, 12, and 15), highlighting the substituents (−2-OH,
3-OCH3, −Ph, −naphthalene, and −2,4-OCH3) on the benzylidene ring, which imparted them effective inhibition
ability. A comparison of the activity of compound 9 with
compounds 10, 12, and 15 reveals
the importance of 2-OH and 2-CH3 groups in the inhibition
potential against bCA-II. Similarly, the presence of −2,4-OCH3 groups on the benzene ring of compound 15 makes it a comparably
stronger inhibitor of CA. The present study reports non-sulfonamide
carbonic anhydrase II inhibitors by incorporating the benzimidazole
and N-acylhydrazone scaffolds in a single nucleus.
Figure 1
Structures
of the most active inhibitors 9, 10, 12, and 15.
Structures
of the most active inhibitors 9, 10, 12, and 15.
Molecular Docking
To examine the interaction of the
ligand with the active site of the receptor, four most active compounds
(9, 10, 12, and 15) were modeled. For comparison, the standard acetazolamide (yellow
stick model) was also docked (GOLD fitness score of 48.2) in the Zn+2 bound cavity of 1V9E (Figure ). Important interactions observed
were of metal–acceptor (Zn), H-bonding (His95, His93, His63,
His118, Thr198, Thr197, and Gln91), and Pi–sulfur (His63, His93,
and His95).Close-up view of the top-scoring pose of acetazolamide (yellow
stick model) showing detailed ligand–enzyme interactions.Compound 9 was found to be the most
active, showing
interactions with different amino acid residues and having a GOLD
fitness score of 52.5. The aromatic ring was predicted to have π–π
T-shaped, π–sigma, and π–alkyl interactions
with His93, leu98, and Val120, respectively. The thiopropyl chain
showed π–alkyl, π–sigma, and π–π
T-shaped interactions with His2 and His63. Metal–acceptor interactions
with ZN260, carbon–hydrogen bonding with Pro200, and hydrogen
bonding were also witnessed with Thr198 (Figure ).
Figure 3
(A) Close-up view of the top-scoring pose of
compound 9 (green stick model) showing detailed ligand–enzyme
interactions;
(B) stereoview of ligand–enzyme interactions; (C) 2D view of
ligand–enzyme interactions; and (D) compound 9 (green stick model) superimposed on acetazolamide (yellow stick
model), the active site.
(A) Close-up view of the top-scoring pose of
compound 9 (green stick model) showing detailed ligand–enzyme
interactions;
(B) stereoview of ligand–enzyme interactions; (C) 2D view of
ligand–enzyme interactions; and (D) compound 9 (green stick model) superimposed on acetazolamide (yellow stick
model), the active site.Compound 10, another active compound among the series,
displayed interactions with amino acid residues of the active site,
having a GOLD score of 51.7. The important amino acid residues involved
in these interactions are Thr198, Thr197, Leu196, Val141, Val120,
His93, His63, and Val59. The interactions predicted for the aromatic
ring include π–alkyl with Val120 and Val121, π–sigma
with Leu196, π–π T-shaped with His93, π–donor
hydrogen bond with Thr197, and π–cation with ZN260. Thr198
exhibited H-bonding with the nitrogen atom of the imine functional
group. Val59 displayed alkyl interactions with the CH3 group
of the thiopropyl chain. Aromatic rings of the mercaptobenzimidazole
nucleus were predicted to involve π–sigma and π–π
T-shaped interactions with His63 (Figure ).
Figure 4
(A) Close-up view of the top-scoring pose of
compound 10 (blue stick model) showing detailed ligand–enzyme
interactions;
(B) stereoview of ligand–enzyme interactions; (C) 2D view of
ligand–enzyme interactions; and (D) compound 10 (blue stick model) superimposed on acetazolamide (yellow stick model),
the active site.
(A) Close-up view of the top-scoring pose of
compound 10 (blue stick model) showing detailed ligand–enzyme
interactions;
(B) stereoview of ligand–enzyme interactions; (C) 2D view of
ligand–enzyme interactions; and (D) compound 10 (blue stick model) superimposed on acetazolamide (yellow stick model),
the active site.Compound 12 with a GOLD fitness score of 52.1 occupied
the active gorge of 1V9E with a pose similar to that of acetazolamide.
Among important interactions of the aromatic rings, π–donor
H-bonding with TRp4 and Thr197 residues is included. His93, Val120,
Leu196, Thr197, Pro200, and ZN260 displayed π–π
T-shaped, π–alkyl, π–sigma, π–donor
H-bonding, π–alkyl, and π–cation interactions
with aromatic rings. His2 demonstrated π–alkyl interactions
with the alkyl group (Figure ).
Figure 5
(A) Close-up view of the top-scoring pose of compound 12 (brown stick model) showing detailed ligand–enzyme interactions;
(B) stereoview of ligand–enzyme interactions; (C) 2D view of
ligand–enzyme interactions; and (D) compound 12 (brown stick model) superimposed on acetazolamide (yellow stick
model), the active site.
(A) Close-up view of the top-scoring pose of compound 12 (brown stick model) showing detailed ligand–enzyme interactions;
(B) stereoview of ligand–enzyme interactions; (C) 2D view of
ligand–enzyme interactions; and (D) compound 12 (brown stick model) superimposed on acetazolamide (yellow stick
model), the active site.The GOLD score of compound 15 was calculated as 53.0,
showing a very good fit in the binding cavity of the enzyme having
a Zn+2 ion. Upon visual inspection, some important interactions
of the ligand and amino acid residues can be seen. Zn260, Thr197,
and His95 were witnessed for their metal–acceptor and hydrogen
bonding interactions with compound 15. The π–sigma
interaction was predicted for Thr198 and His93 with the aromatic ring
and methoxy group. Similarly, the phenyl ring showed π–alkyl
interactions with Leu196. His2 and Trp4 exhibited π–π
T-shaped and π–donor H-bonding with the aromatic ring
of the mercaptobenzimidazole nucleus (Figure ).(A) Close-up view of
the top-scoring pose of compound 15 (cyan stick model)
showing detailed ligand–enzyme interactions;
(B) stereoview of ligand–enzyme interactions; (C) 2D view of
ligand–enzyme interactions; and (D) compound 15 (cyan stick model) superimposed on acetazolamide (yellow stick model),
the active site.
Experimental Section
Chemicals were purchased from BDH, Daejung,
Alfa Aesar, Merck, and Aldrich. Melting points were determined on
Gallenkamp digital melting point equipment MGB-595-010 M. Silica gel
plates (Aldrich) were employed for TLC. The 1H NMR and 13C NMR spectra were recorded on a Bruker AVANCE spectrometer
(600 and 150 MHz, made in Germany)/DMSO with TMS as an internal standard.
The HR-MS(ESI) was recorded on a JEOL JMS600. The chemical synthesis
given below was performed according to the reported methods.[19,20]
Synthesis of 2-(Propylthio)-1H-benzo[d]imidazole (3)
A total of 133 mmol
(20 g) 2-MBI (1) was taken in an RB flask in 40 mL of
ethanol, to which 133 mmol (7.5 g) KOH was added and heated over a
magnetic hotplate stirrer. Then, 133 mmol (12 mL) bromopropane (2) was added. After completion, the reaction mixture was filtered
and dried to get white needle-like crystals of the product.
Synthesis
of Ethyl 2-(2-(Propylthio)-1H-benzo[d]imidazol-1-yl)acetate (5)
A total
of 80 mmol 2-propylthiobenzimidazole (15.45 g) (3) was
taken in an RB flask in DMF, to which 80 mmol K2CO3 (11.05 g) was added. Then, 80 mmol chloroethylacetate (4) (9.8 mL) was added dropwise and refluxed at 100 °C
for 12 h. After completion, the product was extracted in an ethyl
acetate–water system and dried.
Synthesis of 2-(2-(Propylthio)-1H-benzo[d]imidazol-1-yl)acetohydrazide
(7)
In an RB flask, 60 mmol ethyl-2-(2-(propylthio)benzimidazolyl)acetate
(14.88 g) (5) was taken in methanol and stirred for 5
min. Then, 80 mmol (4 g, 4 mL) N2H4·H2O (6) was added and refluxed for 12 h. After
completion, the mixture was decanted into distilled ice water to get
the precipitated product (7). The product was filtered,
washed with water, and dried. White amorphous solid, mp 95–97
°C (yield 82%). 1H NMR (600 MHz, DMSO): δ (ppm) = 7.12–7.53
m, (4H, Ar–H), 4.74 s, (2H, −NCH2), 3.46–4.45
m, (3H, −CONHNH2), 0.95–3.30 m, (7H, SCH2CH2CH3).
Synthesis of N-Acylhydrazones (9–29)
The acetohydrazide
(7) obtained in the previous
step was refluxed for 3–4 h with different aldehydes (3 mmol)
(8), which yielded the respective N-acylhydrazones
(9–29). The reaction mixture was decanted into
distilled cold water. The product precipitated was filtered, washed,
and dried. The structures of all the compounds (9–29) were found consistent with their HR-MS(ESI), 1H NMR,
and 13C NMR spectra. Their spectral data and physical properties
are given below.
In this assay,
colorless 4-nitrophenyl acetate (4-NPA) is hydrolyzed to yellow 4-nitrophenol.[23] The assay was carried out at 25 °C in 20
mM HEPES-tris buffer of pH 7.4 in a 96-well plate. Each well of the
96-well plate comprised 140 μL of HEPES-tris buffer solution,
20 μL of fresh enzyme solution (0.1 mg/mL in buffer) of purified
bovine erythrocyte CA II, and 20 μL of the test compound in
DMSO (10% final concentration). The mixture of the enzyme and inhibitor
was pre-incubated for 15 min at room temperature to allow the formation
of the EI complex. After incubation, the reaction was initiated by
adding 20 μL of substrate 4-NPA (0.7 mM). For kinetic studies,
0.8, 0.4, 0.2, and 0.1 mM substrate was used. It was followed by continuous
measurement of the amount of the product formed at λ = 400 nm
for 30 min at 1 min intervals in 96-well flat-bottom plates, using
an ELISA Reader x MARK Microplate spectrophotometer, BIORAD (USA).
The activity of control (in the absence of the inhibitor) was taken
as 100%. The measurements were taken in triplicate at each used concentration.[21]The % inhibition was calculated using
the following formulaTwo-dimensional (2D) structures of
compounds 9–29 were drawn in ChemDraw and then
altered to 3D structures, which were then minimized using Chimera.
Docking simulations were carried out using GOLD software. For ligand
molecules, the GOLD score was selected as a fitness function.[24] Different docking poses were made/generated
using the GOLD program, and for each compound, the best-docked pose
was selected, which is based on two criteria: (i) fitness function
scores and (ii) the binding position of the ligand.[25] Carbonic anhydrase-II (PDB ID: 1V9E) was used as receptor proteins. The PDB
structure was taken from the Protein Data Bank and updated, arranged
using the GOLD program by carrying out different steps, that is, optimization
of hydrogen bonds by flipping amino side chains, the addition of hydrogens,
minimization of the protein complex, charge correction, and assigning
of bond orders. All the ligands (bound), H2O molecules,
and cofactors were excluded from the proteins.[26] The interactions of synthesized docked compounds with various
amino acids can be seen inside the selected binding pocket. Discovery
Studio Visualizer software for visualization of 2D and 3D structures
was used, and then, they were processed.
Conclusions
In
conclusion, we were able to synthesize a new series of non-sulfonamide
acylhydrazones and to test the new products for their potential against
carbonic anhydrase enzyme. The in vitro carbonic anhydrase-II inhibition
potential of the compounds displayed excellent results. Among the
synthesized compounds, 9, 10, 12, and 15 showed the highest inhibition,
even greater than that of the standard acetazolamide. The molecular
docking results indicated a competitive inhibiting behavior of the
synthesized compounds by recording metal–acceptor and π–cation
interactions with Zn2+ ions. These findings are interesting
in that non-sulfonamide compounds might also be considered in the
drug development process against carbonic anhydrases.
Authors: Nicolino Pala; Laura Micheletto; Mario Sechi; Mayank Aggarwal; Fabrizio Carta; Robert McKenna; Claudiu T Supuran Journal: ACS Med Chem Lett Date: 2014-06-07 Impact factor: 4.345
Authors: Joachim Bischof; Johann Leban; Mirko Zaja; Arnhild Grothey; Barbara Radunsky; Olaf Othersen; Stefan Strobl; Daniel Vitt; Uwe Knippschild Journal: Amino Acids Date: 2012-02-14 Impact factor: 3.520