Synthesis of some N-aroyl-2-oxindole benzenesulfonamide conjugates with carbonic anhydrase inhibitory activity

Article abstract of DOI:10.1016/j.bioorg.2020.103635

Implication of carbonic anhydrases (CAs) in many physiological functions made them attractive therapeutic targets. Herein, we report the synthesis of three series of benzenesulfonamide-based compounds (5a-e, 9a-e and 10a-e) as potential ligands to four of

Full text of DOI:10.1016/j.bioorg.2020.103635

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Synthesis of some N-aroyl-2-oxindole benzenesulfonamide conjugates with
carbonic anhydrase inhibitory activity
Riham F. George, Silvia Bua, Claudiu T. Supuran, Fadi M. Awadallah
PII:
S0045-2068(19)32045-0
DOI:
https://doi.org/10.1016/j.bioorg.2020.103635
YBIOO 103635
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Bioorganic Chemistry
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28 January 2020
Please cite this article as: R.F. George, S. Bua, C.T. Supuran, F.M. Awadallah, Synthesis of some N-aroyl-2-
oxindole benzenesulfonamide conjugates with carbonic anhydrase inhibitory activity, Bioorganic Chemistry
(2020), doi: https://doi.org/10.1016/j.bioorg.2020.103635
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Synthesis of some N-aroyl-2-oxindole benzenesulfonamide conjugates
with carbonic anhydrase inhibitory activity
Riham F. Georgea,*, Silvia Buab,Claudiu T. Supuranb, **, Fadi M. Awadallaha,***
aPharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt.
bUniversity of Florence, Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical
Sciences, via Ugo Schiff 6, 50019, Sesto Fiorentino, Florence, Italy.
Declarations of interest: none
Abstract
Implication of carbonic anhydrases (CAs) in many physiological functions made
them attractive therapeutic targets. Herein, we report the synthesis of three series of
benzenesulfonamide-based compounds (5a-e, 9a-e and 10a-e) as potential ligands to four
of the human CA isoforms (hCA I, hCA II, hCA IX and hCA XII). All synthesized
compounds were evaluated for their CA inhibitory activity. Most of the compounds
preferentially inhibited the tumor-associated isoforms IX and XII. Series 9a-e and 10a-e
showed the highest activity. Of particular interest was compound 10a which demonstrated
the highest activity among all compounds with Ki of 68.3 and 21.5 nM against hCA IX and
hCA XII, respectively, in addition to its highest selectivity index. To get deep insight on
the interaction of compound 10a with CA, docking experiment was run to study the binding
interaction with key amino acids and zinc ion in the catalytic site of the four isoforms
studied.
Keywords: benzenesulfonamide; carbonic anhydrase inhibitors; synthesis; molecular
docking.
* Corresponding author
** Corresponding author
*** Corresponding author
e-mail addresses: riham.eskandar@pharma.cu.edu.eg (Riham F. George);
claudiu.supuran@unifi.it (Claudiu T. Supuran);
fadi.awadallah@pharma.cu.edu.eg (Fadi M. Awadallah).
1

1. Introduction
Carbonic anhydrases (CAs) constitute an important family of
metalloenzymes that catalyse the reversible CO2 hydration to
bicarbonate and protons which is a crucial reaction for pH regulatory
mechanisms [1-3]. The CAs are widespread in many living organisms
and accordingly they are classified into distinct genetic families, such
as: α-CAs that are present in vertebrates, protozoa, algae, corals, bacteria and green plants,
[1,4] the β-CAs have been identified in bacteria, fungi, Archaea, algae and chloroplasts of
both mono- and dicotyledons, [4-6] the γ-CAs are encoded in Archaea, bacteria and plants,
[7] the δ-CAs were found in marine phytoplankton, such as haptophytes, dinoflagellates,
diatoms and chlorophyte prasinophytes [8], whereas ζ-CAs seem to be present only in
marine diatoms [9]. A unique η-CA has been identified to date in the protozoa Plasmodium
falciparum [10]. Recently, θ-CAs were detected in the marine diatom Phaeodactylum
tricornutum [11] and the first iota-CA was identified in the marine diatom Thalassiosira
pseudonana [12].
The human carbonic anhydrases (hCAs) belonging to the α-
subfamily are subdivided into 16 diverse isoforms that have different
kinetic properties, cellular and tissue distribution. According to their
cellular distribution, they can be categorized as cytosolic (hCA I, hCA II,
hCA III, hCA VII, and hCA XIII), membrane-bound (hCA IV, hCA IX,
hCA XII, and hCA XIV), secreted (hCA VI), mitochondrial (hCA Va and hCA Vb), in
addition to the acatalytic isoforms also known as the CA related-proteins (CARP), hCA
VIII, hCA X and hCA XI which are located in the cytosol [1-3, 13, 14].
From a physiopathological aspect, CA isozymes are involved in many
2

medical conditions such as glaucoma (hCA II, hCA IV and hCA XII),
edema (hCA II, hCA IV, hCA XIV), central nervous system pathologies
(hCA VII and hCA XIV) and tumors (hCA IX and hCA XII), and therefore,
they are considered as significant therapeutic targets for a wide range
of disorders [15,16].
Primary sulfonamide group (RSO2NH2) is one of the most widely encountered
functionality of carbonic anhydrase inhibitors (CAIs) as it is responsible for coordination
to the enzyme’s zinc ion [17]. The group carrying the sulfonamide function is therefore
considered the scaffold of CAIs. Different approaches have been adopted to design
sulfonamide-based CAIs; of which the “tail approach" being the most efficient and
investigated one. It depends on attaching different molecular fragments (tails) to the
aromatic/heterocyclic ring bearing the sulfonamide scaffold, in order to modulate the
binding interaction with the active site cavity, which in turn affects potency and selectivity
(Figure 1A) [18,19].
r
e
c
Tail
a
N
O
p
s
R
Sc
(A)
(B)
3

Figure 1. (A) Schematization of the interaction between a generic sulfonamide and the
Zn2+ in the CA active site. (Sc = scaffold). (B) Illustration of an isatin/ benzene sulfonamide
hybrid incorporated in CA active site.
In this respect, benzene-sulfonamides are the most widely prominent scaffold of
CAIs that can be diversely substituted to achieve isozyme specificity. Isatin represents a
privileged molecular fragment in the design of biologically active agents. Recently, they
have been utilized as the tail moiety in several CAIs and many isatin/benzene sulfonamide
hybrid molecules have been reported (Figure 1B) [20]. The structure of these hybrids is
discriminated based on the attachment between the benzene sulfonamide scaffold and the
isatin tail, whether it is direct or through a spacer group. Also, these compounds vary in
the substitution observed on the isatin ring. Compounds I-IV are selected examples
illustrating the structure diversity of the isatin/benzenesulfonamide hybrids (Figure 2) [21-
24].
NH2
S O
NH2
S O
NH2
S O
O
O
O
N
O
N
NH
N
H3C
H3C
O
O
O
N
N
N
H
H
I
III
II
Ki= 1.0 nM (hCA IX)
Ki= 18.5 nM (hCA XII)
Ki= 4.0 nM (hCA IV)
Ki= 8.9 nM (hCA IX)
Ki= 9.2 nM (hCA XII)
H
N
O
O
S
O
NH
NH2
HN
N
O
NH2
O
S
O
NH
O
N
N
O
N
H
V
IV
H3C
Ki= 3.0 nM (hCA II)
Ki= 13.9 nM (hCA IX)
Ki= 4.7 nM (hCA IX)
Ki= 9.5 nM (hCA XII)
Figure2. Selected examples of isatin/benzene sulfonamide hybrids as CAIs.
4

Considering the aforementioned facts, and in continuation of our project to develop
potent and selective CAIs as compounds V [25], it was thought worthwhile to design new
isatin-based benzene sulfonamide hybrids and explore their CA inhibitory activity. The
design of the new target compounds relies on two structural modifications. Firstly, N-
substitution of the isatin moiety with a benzoyl ring grafting groups of diverse size,
lipophilicity and electronic property (viz., H, F, Cl, Br, OCH3) was adopted to modulate
the interaction of the tail fragment with the CA active site. Secondly, the isatin ring was
merged with the benzene sulfonamide scaffold either through direct attachment
(compounds 4a-e) or via a hydrazinyl (compounds 9a-e) or hydrazinyl-2-oxoethylamino
spacers (compounds 10a-e) aiming to investigate the effect of this structure elongation on
the coordination of the tail fragment with the CA active site. Unexpectedly, compounds
4a-e were synthetically inaccessible, and the sulfonylbenzamides 5a-e were rather
obtained. Interestingly, these compounds can be regarded as the open isosteres of
compounds 4a-e which makes them significantly exceptional due to their high
conformational flexibility compared to the other target compounds, a feature which may
allow more efficient orientation of the tail moiety into the active site (Figure 3).
O
NH2
O S
O
S
O
NH2
HN
O
O
O
S
NH
O
NH
O
N
O
N
NH2
H
N
N
O
O
NH2
N
N
NH
S
N
O
O
O
O
O
O
R
R
4a-e
R
5a-e
9a-e
10a-e
R
a
b
c
d
e
R=H, R=F, R=Cl, R=Br, R=OCH3
Figure 3. General structures of the designed isatin/benzenesulfonamides 4a-e, 5a-e, 9a-e
and 10a-e.
2. Results and discussion
2.1. Chemistry
5

The synthetic pathways adopted for the preparation of the target compounds were
depicted in Schemes 1 and 2. Benzoylation of isatin (1) was carried out as reported using
different benzoyl chlorides in dry tetrahydrofuran (THF) in the presence of triethylamine
(TEA) affording N-aroyl-isatin derivatives 2a-e [26]. Synthesis of Schiff’s bases 4a-e
using the usual condensation reaction between 2a-e and sulfanilamide (3) in refluxing
glacial acetic acid failed to afford the expected products 4a-e and produced instead the
ring opened N-(2-(2-Oxo-2-((4-sulfamoylphenyl)amino)acetyl)phenyl)benzamides (5a-
e). Several trials were performed to obtain 4a-e through reacting 2a-e with sulfanilamide
(3) in glacial acetic acid, absolute ethanol or N,N-dimethylformamide at room temperature
or heating the reactants in absolute ethanol or methanol. However, all these trials failed to
produce the corresponding Schiff bases 4a-e, and the unreacted 2a-e were separated.
Opening of the pyrrole ring and formation of 5a-e could be explained on the basis of
increased basicity of the aromatic amino group of the sulfanilamide (3) in the presence of
glacial acetic acid which in turn attacked the carbonyl group at position 2 of the isatin ring
being the most electron deficient centre. This resulted in nucleophilic addition followed
by ring opening rather than the regular condensation with carbonyl at position 3 (Figure
1
4). The structure of 5a-e was confirmed by H NMR spectra that revealed three singlet
exchangeable signals at 7.30-7.31, 11.09-11.11 and 11.21-11.28 ppm assigned to NH2 and
2 NH protons along with increased number of aromatic protons due to the inserted
benzenesulfonamide moiety. Moreover, 13C NMR of 5a-e showed signals at 162.4-162.8,
165.2-166.2 and 190.2-190.8 ppm corresponding to the three carbonyl groups (Scheme
1).
6

O
O
S
NH2
N
O
O
O
(ii)
N
(i)
O
O
O
N
N
H
O
1
4a-e
R
R
O
H
2a-e
N
2a, 4a, 5a R= H
2b, 4b, 5b R= F
2c, 4c, 5c R= Cl
2d, 4d, 5d R= Br
O
NH2
NH
S
O
O
O
2e, 4e, 5e R= OCH3
R
5a-e
Reagents and reaction conditions: (i) appropriate benzoyl chloride, TEA, dry THF, RT,
6h; (ii) sulfanilamide (3), glacial acetic acid, 80oC, 3h.
Scheme 1. Synthetic pathway for compounds 5a-e.
O
O
S
O
HN
OH
O
O
NH2
H
N
O
Gl. acetic acid
N
O
NH2
O
H2N
N
NH
S
O
O
O
NH2
O
S
+
O
O
R
R
R
5a-e
3
2a-e
Figure 4. Proposed mechanism for formation of compounds 5a-e.
On the other hand, Schiff’s bases 9a-e and 10a-e were obtained via condensation of N-
aroyl-isatins 2a-e with hydrazinylbenzenesulfonamide hydrochloride (6) and 4-((2-
hydrazinyl-2-oxoethyl)amino)benzenesulfonamide (8), respectively. Reactants 6 and 8
were prepared according to the reported methods [27,28]. The reaction for compounds 9a-e
proceeded in methanol at room temperature, the acidity of the reactant 6 was sufficient to
7

catalyze the reaction. While for compounds 10a-e, two drops of HCl was required to render
the medium acidic to activate the hydrazinyl moiety (Scheme 2).
O
O
O
NH2
NH
O
(i)
(ii)
O
NH
O S
H2N
HCl
O S
H2N
NH2
O S
H2N
7
3
6
(iii)
(iv)
NH2
HN
O
O
O
S
NH2
O
NH
O S
H2N
8
N
NH
(v)
O
O
N
O
S
O
NH2
HN
O
R
9a-e
NH
N
O
9a, 10a R= H
9b, 10b R= F
9c, 10c R= Cl
9d, 10d R= Br
N
O
9e, 10e R= OCH3
10a-e
R
Reagents and reaction conditions: (i) NaNO2, dil. HCl, SnCl2; (ii) ethyl bromoacetate,
NaHCO3, aqueous ethanol, RT, overnight; (iii) NH2NH2.H2O, absolute ethanol, reflux,
3h; (iv) 2a-e, methanol, RT, 3h; (v) 2a-e, methanol, 2drops HCl, RT, 3h.
Scheme 2. Synthetic pathways of compounds 9a-e and 10a-e.
The structure of 9a-e was confirmed by 1H NMR which revealed two exchangeable singlet
signals at 7.28-7.29 and 12.39-12.46 ppm attributed to NH2 and NH protons, respectively,
in addition to increase in the integration of aromatic protons due to the incorporated
benzenesulfonamide fragment. Moreover, 13C NMR spectra of 9a-e displayed signals for
two carbonyl groups at 160.3-160.4 and 167.7-168.9 ppm. Regarding compounds 10a-e,
1H NMR spectra showed a singlet at 4.36-4.37 ppm corresponding to CH2 protons along
with three exchangeable singlet signals at 6.96-6.98, 8.32 and 11.57-11.61 ppm due to NH2
8

and 2 NH protons, respectively. Furthermore, their 13C NMR spectra exhibited a signal at
44.8-45.0 ppm due to the methylene carbon in addition to three signals at the range of
160.4- 169.0 ppm corresponding to three C=O carbons. It was noteworthy that the 1H and
13C NMR spectra of the flouro-containing compounds 5b, 9b and 10b showed multiplet
1
signals as expected due to H-19F and 13C-19F coupling, 19F being the main isotope,
therefore, the splitting are clearly visible in both spectra.
2.2.Carbonic anhydrase inhibition.
The CA inhibitory activity of all the newly synthesized compounds 5a-e, 9a-e and 10a-e
was evaluated against hCA I, hCA II (cytosolic) as well as hCA IX and hCA XII
(transmembrane, tumor-associated isoforms) using the stopped-flow CO2 hydrase assay
[29-33]. The inhibitory activities were compared to acetazolamide (AAZ) (Table 1). The
following SAR was deduced:
(i)
Activity against hCA I is the least among all the other isoforms, lying in the
micromolar range (Ki =1555.8-8429.2 nM). The benzamide derivatives 5a-e,
with relatively flexible geometry, were more potent than the other isatin-based
compounds. Moreover, the isatin hybrids with shorter hydrazine spacer 9a-e
were more potent than compounds 10a-e which have the longer hydrazinyl-2-
oxoethylamino spacer. Concerning the effect of the substitution on the benzoyl
group on activity, it was observed that electron withdrawing substitution of
suitable size, -Cl, (5c, 9c), an exception was observed in the fluorine derivative
10b, was associated with the highest activity followed by the unsubstituted
derivatives (5a, 9a and 10a). The compounds with the large -Br group, or
electron donating substitution, -OCH3, were the least in potency.
(ii)
Regarding the activity against hCA II, the tested compounds demonstrated a
slightly better overall potency; Ki values ranged from 89.2 to 634.1 nM. Based
on average potencies, the benzamide series, 5a-e, showed the highest inhibitory
activity followed by compounds 10a-e then compounds 9a-e. Interestingly, it
was noticed that hybrids with the benzoyl moiety substituted with the electron
donating –OCH3 group (5e, 9e and 10e) revealed the highest potency in all
series. Derivatives with the unsubstituted benzoyl or chloro/fluorobenzoyl group
9

came next in activity, while the bromobenzoyl compounds were the least in
activity.
(iii) As per the activity of the compounds against hCA IX, a gradual shift in
selectivity started to be noticed where the activity ranged from 68.3-421.3 nM.
Unlike their activity towards hCA I and hCA II, derivatives 5a-e revealed the
least potency against hCA IX. The hybrids with the hydrazinyl-2-oxoethylamino
spacer 10a-e were the most potent followed by the hybrids with the shorter
hydrazino spacer 9a-e. Among the latter series 9a-e and 10a-e, the unsubstituted
benzoyl derivatives 9a and 10a were the most potent followed by the
chlorobenzoyl compounds 9c and 10c. The fluorobenzoyl and methoxybenzoyl
hybrids were of moderate potency while the bromobenzoylisatins 9d and 10d
were the least potent. The compound possessing the highest inhibitory activity
against hCA IX was the unsubstituted benzoyl isatin derivative 10a.
(iv)
Finally, a significant shift in selectivity toward the inhibition of hCA XII was
observed by all the tested compounds. Ki values spanned in the range of 21.5-
175.1 nM. The hydrazinoisatin derivatives 9a-e and the hydrazinyl-2-
oxoethylamino derivatives 10a-e displayed the highest potency compared to the
benzamide derivatives 5a-e. Regarding the influence of the substitution on the
benzoyl moiety on activity, the order of activity was -OCH3 >H >Cl> F > Br in
series 5a-e and 9a-e, while in series 10a-e, OCH3 and unsubstituted benzoyl
isatins 10e and 10a, respectively, were almost equipotent and preceded the
halogenated benzoyl derivatives. The most active compounds against hCA XII
belonged to the hydrazinyl-2-oxoethylamino isatins bearing the unsubstitued
benzoyl and methoxybenzoyl groups, 10a and 10e, possessing Ki values of 21.5
and 22.3 nM, respectively.
(v)
In summary, the tested compounds showed moderate selectivity to the human
isoform IX but high selectivity toward the isoform XII with significantly low
potency against hCA I. This selectivity profile suggested that the designed
compounds might be potentially useful in cancer treatment. Focusing on the
activity on hCA XII, being the highest inhibited isoform, the isatin derivatives,
9a-e and 10a-e were more efficient in the enzyme inhibition than their non-cyclic
10

benzamide bioisosteres 5a-e. Also, the derivatives with the longer hydrazinyl-2-
oxoethylamino spacer 10a-e were more potent than their shorter hydrazine
congeners 9a-e. Furthermore, the unsubstituted benzoyl and methoxybenzoyl
hybrids 10a and 10e, respectively, were almost equipotent and the most potent
of all tested compounds.
(vi)
Since this investigation is a continuation of the previous work on developing
isatin-based carbonic anhydrase derivatives (compounds V, Figure 1) [25], it
seems essentially useful to outline the progress of our findings. In the previous
study, where the compounds possessed N-unsubstituted isatins or N-substituted
derivatives bearing small alkyl or benzyl groups, there was no consistent relation
between the activity against a specific isoform and the size of N-substitution.
Concerning the effect of the spacer group on activity, the longer hydrazinyl-2-
oxoethylamino linker shifted selectivity towards the tumor associated isoform
hCA IX but not hCA XII. In the current investigation, a more informative and
consistent SAR was developed in terms of the effect of the benzoyl substitution
on potency which can be attributed to the fact that the carbonyl group of the
benzoyl moiety might be involved in steric hindrance with the carbonyl group at
position 2 of the isatin ring leading to a restricted rotation of the benzoyl group
and thus locking the bioactive conformation of the molecule. On the other hand,
and in accordance with the previous study, the increase in the length of the spacer
group shifted selectivity towards the tumor-associated isoform hCA IX and
additionally to hCA XII.
11

Table 1. Inhibition data of human CA isoforms hCA I, II, IX and XII with compounds 5a-e,
9a-e, 10a-e and the standard inhibitor acetazolamide (AAZ) by a stopped flow CO2 hydrase
assay [29].
O
NH2
O
S
O
S
O
NH2
HN
O
NH
N
NH
O
O
N
H
N
O
O
NH2
N
N
NH
S
O
O
O
O
O
R
R
R
10a-e
5a-e
9a-e
Compd.
ID
R
Ki* (nM)
hCAII hCAIX hCAXII I/IX
Selectivity ratio
hCAI
II/IX
I/XII
II/XII
5a
5b
5c
5d
5e
9a
9b
9c
H
F
Cl
1891.8
1962.5
1555.8
2024.6
2456.7
3447.1
3604.3
3417.7
5926.1
150.6
163.1
192.4
332.0
89.2
418.4
458.2
390.2
634.1
185.6
254.3
340.9
309.6
549.7
171.5
12
362.9
421.3
274.3
417.2
221.8
84.9
172.4
145.7
265.1
192.2
68.3
142.9
93.2
197.1
164.8
25
88.6
164.4
140.9
175.1
60.4
32.9
48.2
42.4
88.9
31.4
21.5
79.1
86.2
130.2
22.3
5.7
5.21
4.66
5.67
4.85
0.41
0.39
0.70
0.79
21.35
11.94
11.04
11.56
40.67
1.70
0.99
1.36
1.90
1.48
Br
OCH3
H
11.08 0.40
40.60 4.93
20.91 2.66
23.46 2.68
22.35 2.39
27.46 0.96
93.90 3.72
43.20 2.38
68.77 3.32
42.77 2.79
47.93 1.04
104.77 12.72
F
Cl
Br
74.78
80.61
66.66
168.07 5.91
298.28 11.83
78.05
74.35
64.74
354.20 7.69
43.86 2.10
9.51
9.20
7.13
9d
9e
OCH3 5277.3
H
F
Cl
Br
10a
10b
10c
10d
10e
AAZ
6413.1
6173.9
6409.4
8429.2
4.31
3.59
4.22
OCH3 7898.6
------ 250
10
0.48
* Mean from 3 different assays, by a stopped flow technique (errors were in the range of  5-10 % of the
reported values).
2.3. Molecular docking study
In order to rationalize the obtained CA inhibition results and the relative selectivity towards
CA IX and CA XII isoforms, compound 10a, which revealed the highest activity and
selectivity for these isoforms, was selected for docking into the active pocket of CA I
(PDBID: 3W6H), CA II (PDBID: 3HS4), CA IX (PDB ID: 3IAI) and CA XII (PDB ID:
1JD0) co-crystallized with acetazolamide (AAZ) [34]. The molecular docking was
12

performed using Molecular Operating Environment (MOE, 2015.10) and the results were
presented in Figure 5 and Figures 1-6 in the supplementary materials.
(i)
It was observed that the high activity and selectivity of compound 10a to CA
IX compared to the other isoforms resulted from its binding to the active site of
the crystal structure of the enzyme through most of the fundamental binding
interactions of the co-crystallized ligand, AAZ. Thus, it interacted through Zn2+
metal coordination with sulfonamide anion (S-O-, S=NH), hydrogen bonding
with Thr199 (similar to AAZ) and additionally to His94 through arene-arene
interaction. (Figure 5C, Figures 1C, 4 and 6C in supplementary materials).
Regarding its interaction with CA XII, compound 10a revealed binding mode
through the same hot spots of AAZ, i.e. Zn2+, Thr199, Thr200 and Leu198 via
metal coordination and hydrogen bondings, respectively (Figure 5D, Figure 1D,
5 and 6D in supplementary materials). In addition to these fundamental
interactions, three additional hydrogen bonds were observed between C=O of
isatin core, C=O of benzoyl group and NH=N with Lys67, Asn69 and Gln92,
respectively.
(ii)
(iii) As per the interaction with the crystal structure of CA I, compound 10a showed
only Zn2+coordination and hydrogen bonding with his200 explaining its mild
inhibitory activity in the enzyme assay (Figure 5A, Figures 1A, 2 and 6A in
supplementary materials).
(iv)
Similarly, compound 10a interacted with the binding site of CA II only via
Zn2+coordinate bond and hydrogen bond with leu198 (Figure 5B, Figures 1B,
3 and 6B in supplementary materials).
(v)
Accordingly, the observed binding mode of compound 10a to the crystal
structures of CA I, CA II, CA IX and CA XII, were consistent and explicit to
its activity and selectivity profile.
13

(B)
(A)
(D)
(C)
Figure 5. 2D diagram of compound 10a showing its interaction with the CA I (A), CA II (B), CA
IX (C) & CA XII (D) binding site.
3. Conclusion
Three series of benzenesulfonamide-based carbonic anhydrase inhibitors were synthesized.
The design of the new compounds involved a hybrid approach combining the
benzenesulfonamide zinc binding fragment to the privileged isatin fragment as the tail
portion. Linking groups were either the shorter hydrazinyl linker (9a-e) or the longer
hydrazinyl-2-oxoethylamino linker (10a-e). These compounds were synthesized by
14

condensation of the N-benzoylisatins 2a-e with either hydrazinylbenzenesulfonamide 6, or
4-((2-hydrazinyl-2-oxoethyl)amino)benzenesulfonamide 8. Direct attachment of the
pharmacophoric fragments via reaction of the N-benzoylisatins and benzenesulfonamide
was synthetically inaccessible and instead open chain benzenesulfonamide isosteres (5a-e)
were obtained. All compounds were subjected to enzyme inhibitory assay against four
human CA isoforms (I, II, IX and XII). The most susceptible isoforms were IX and XII.
Series 9a-e and 10a-e showed potent inhibitory activity preferentially against hCA IX, and
selectively against hCA XII. Compounds 10a-e were generally more potent than 9a-e
against these isoforms. Compounds 10a and 10e were the highest in potency against hCA
XII (Ki = 21.5 and 22.3 nM, respectively). Interestingly, compound 10a combined the
highest activity against both tumor-associated isoforms IX and XII, together with the
highest selectivity index. Concerning the substitution on the N-benzoyl moiety, it was
observed that highest activity was associated with the absence of any substitution or with
the presence of Cl and OCH3 groups. To have a deep insight on the interaction with the
four tested CA isoforms, compound 10a was selected to perform docking experiments with
the crystal structures of the four isoforms. A consistent correlation was observed between
potency of the compound in the enzyme assay and its binding modes. Interactions with
isoform XII, to which 10a is highly potent, included the zinc ion, Thr199, Thr200, Leu198,
Lys67, Asn69 and Gln92. Fewer interactions were observed with isoform IX, including the
zinc ion, Thr199 and His94. The poor activity of 10a against isoforms I and II was
consistent with poor interactions where 10a only interacted with zinc ion and His200 in
isoform I, and in isoform II with zinc ion and Leu198.
4. Experimental
4.1. Chemistry
Melting Points are uncorrected and were carried out by open capillary tube method using
Stuart SMP3 Melting Point apparatus. Infrared spectra were recorded on Shimadzu
Infrared spectrometer IR Affinity-1 (FTIR- 8400S-Kyoto-Japan), and expressed in wave
number (cm-1). 1H NMR and 13C NMR Spectra were recorded on Bruker High Performance
Digital FT-NMR Spectrometer Avance III 400 MHz, 13C, 100 MHz NMR spectrometer.
Chemical shifts were expressed in δ units and were related to that of the solvents. Mass
15

Spectra were recorded using ISQLT Thermo Scientific Mass spectrometer at The Regional
Center for Mycology and Biotechnology, Al-Azhar University. Elemental Microanalyses
were carried out at the Regional Center for Mycology and Biotechnology, Al-Azhar
University. All the reactions were monitored by TLC using silica gel F254 plates (Sigma-
Aldrich), using chloroform: methanol 9.5:0.5 as eluting system and were visualized by UV-
lamp. Compounds 2a-e [26], 6 [27], 7 and 8 [28] were prepared according to their reported
methods.
4.1.1. General procedure for preparation of compounds 5a-e
A mixture of equimolar amounts of the appropriate 1-benzoylisatin derivative (2a-e) and
sulfanilamide (3) (10 mmol) in glacial acetic acid (5 mL) was heated at 80oC for 3h. The
obtained solid was filtered while hot, washed with ethanol and dried to obtain 5a-e in a
pure form.
4.1.1.1.
N-(2-(2-Oxo-2-((4-sulfamoylphenyl)amino)acetyl)phenyl)benzamide (5a)
Yellow crystals, yield 89%, m.p. 250-252oC (decomposition); IR (KBr, ʋ cm-1): 3389,
3314, 3277, 3111 (2NH and NH2), 3069-3032 (CH aromatic), 1697, 1663 (3C=O), 1628
1
(bending NH), 1599-1522 (C=C), 1346, 1163 (SO2); H NMR (DMSO-d6, 400 MHz): δ
7.31 (s, 2H, NH2, D2O exchangeable), 7.37 (t, J = 7.60 Hz, 1H, aromatic H), 7.53 (t, J =
7.64 Hz, 2H, aromatic H), 7.61 (t, J = 7.12 Hz, 1H, aromatic H), 7.74-7.79 (m, 3H, aromatic
H), 7.85-7.88 (m, 3H, aromatic H), 7.93 (d, J = 7.56 Hz, 2H, aromatic H), 8.09 (d, J = 8.24
Hz, 1H, aromatic H), 11.11 (s, 1H, NH, D2O exchangeable), 11.28 (s, 1H, NH, D2O
13
exchangeable); C NMR (DMSO-d6, 100 MHz): δ 120.3, 122.8, 124.6, 124.7, 127.1,
127.9, 129.2, 132.4, 132.7, 134.2, 135.0, 139.2, 139.9, 141.2 (aromatic carbons), 162.6
(C=O), 166.2 (C=O), 190.6 (C=O); MS, m/z [%]: 423 [M+, 22], 77 [100]; Anal. Calcd. for
C21H17N3O5S (423.44): C, 59.57; H, 4.05; N, 9.92. Found: C, 59.31; H, 4.28; N, 10.14.
4.1.1.2.
4-Fluoro-N-(2-(2-oxo-2-((4-sulfamoylphenyl)amino)acetyl)phenyl)
benzamide (5b)
16

Yellow crystals, yield 68%, m.p. 246-248oC; IR (KBr, ʋ cm-1): 3319, 3252, 3238,
3119 (2NH and NH2), 3060 (CH aromatic), 1693, 1672 (3C=O), 1624 (bending NH), 1599-
1526 (C=C), 1340, 1157 (SO2); 1H NMR (DMSO-d6, 400 MHz): δ 7.31 (s, 2H, NH2, D2O
exchangeable), 7.34-7.39 (m, 3H, aromatic H), 7.75-7.79 (m, 3H, aromatic H), 7.84-7.87
(m, 3H, aromatic H), 7.99-8.02 (m, 3H, aromatic H), 11.09 (s, 1H, NH, D2O exchangeable),
13
11.21 (s, 1H, NH, D2O exchangeable); C NMR (DMSO-d6, 100 MHz): δ 116.0, 116.3,
120.3, 123.1, 124.9, 125.3, 127.1, 130.7, 130.8, 132.2, 134.8, 138.9, 139.9, 141.2, 163.6,
166.1 (aromatic carbons), 162.5 (C=O), 165.2 (C=O), 190.3 (C=O); MS, m/z [%]: 441 [M+,
5], 442 [(M+ + 1), 28], 443 [(M++ 2), 12], 123 [100]; Anal. Calcd. for C21H16FN3O5S
(441.43): C, 57.14; H, 3.65; N, 9.52. Found: C, 57.35; H, 3.83; N, 9.78.
4.1.1.3.
4-Chloro-N-(2-(2-oxo-2-((4-sulfamoylphenyl)amino)acetyl)phenyl)benzamide
(5c)
Off white crystals, yield 77%, m.p. 264-266oC (decomposition); IR (KBr, ʋ cm-1):
3337, 3294, 3252, 3190 (2NH and NH2), 3081 (CH aromatic), 1678 (3C=O), 1636 (bending
NH), 1593-1531 (C=C), 1335, 1161 (SO2); 1H NMR (DMSO-d6, 400 MHz): δ 7.30 (s, 2H,
NH2, D2O exchangeable), 7.38 (t, J = 7.60 Hz, 1H, aromatic H), 7.61 (d, J = 8.44 Hz, 2H,
aromatic H), 7.73 (d, J = 8.12 Hz, 1H, aromatic H), 7.78 (d, J = 8.88 Hz, 2H, aromatic H),
7.85 (t, J = 8.82 Hz, 3H, aromatic H), 7.94 (d, J = 8.48 Hz, 2H, aromatic H), 7.99 (d, J =
8.20 Hz, 1H, aromatic H), 11.09 (s, 1H, NH, D2O exchangeable), 11.24 (s, 1H, NH, D2O
13
exchangeable); C NMR (DMSO-d6, 100 MHz): δ 120.3, 123.1, 124.9, 125.3, 127.1,
129.2, 129.8, 132.2, 133.0, 134.8, 137.6, 138.7, 140.0, 141.2 (aromatic carbons), 162.4
(C=O), 165.2 (C=O), 190.3 (C=O); MS, m/z [%]: 457 [M+, 2], 458 [(M++ 1), 7], 459 [(M+
+ 2), 2], 139 [100]; Anal. Calcd. for C21H16ClN3O5S (457.89): C, 55.09; H, 3.52; N, 9.18.
Found: C, 55.32; H, 3.66; N, 9.40.
4.1.1.4.
4-Bromo-N-(2-(2-oxo-2-((4-sulfamoylphenyl)amino)acetyl)phenyl)benzamide
(5d)
17

Off white crystals, yield 46%, m.p. 256-258oC (decomposition); IR (KBr, ʋ cm-1):
3300, 3294, 3260, 3190 (2NH and NH2), 3078 (CH aromatic), 1678 (3C=O), 1636 (bending
NH), 1589, 1531 (C=C), 1331, 1161 (SO2); 1H NMR (DMSO-d6, 400 MHz): δ 7.30 (s, 2H,
NH2, D2O exchangeable), 7.38 (t, J = 7.56 Hz, 1H, aromatic H), 7.73-7.80 (m, 5H, aromatic
H), 7.83-7.88 (m, 5H, aromatic H), 8.00 (d, J = 8.20 Hz, 1H, aromatic H), 11.09 (s, 1H,
NH, D2O exchangeable), 11.24 (s, 1H, NH, D2O exchangeable); 13C NMR (DMSO-d6, 100
MHz): δ 120.3, 123.0, 124.9, 125.3, 126.5, 127.1, 130.0, 132.2, 133.4, 134.8, 138.7, 140.0,
141.2 (aromatic carbons), 162.4 (C=O), 165.3 (C=O), 190.2 (C=O); MS, m/z [%]: 502 [M+,
8], 381 [100]; Anal. Calcd. for C21H16BrN3O5S (502.34): C, 50.21; H, 3.21; N, 8.37. Found:
C, 50.49; H, 3.48; N, 8.61.
4.1.1.5. 4-Methoxy-N-(2-(2-oxo-2-((4-sulfamoylphenyl)amino)acetyl)phenyl)benzamide
(5e)
Yellow crystals, yield 47%, m.p. 221-223oC; IR (KBr, ʋ cm-1): 3321, 3252 (2NH
and NH2), 3098-3009 (CH aromatic), 2963-2916 (CH aliphatic), 1682 (3C=O), 1628
1
(bending NH), 1585, 1531 (C=C), 1327, 1157 (SO2); H NMR (DMSO-d6, 400 MHz): δ
3.84 (s, 3H, OCH3), 7.07 (d, J = 8.76 Hz, 2H, aromatic H), 7.30 (s, 2H, NH2, D2O
exchangeable), 7.33 (t, J = 7.64 Hz, 1H, aromatic H), 7.73-7.79 (m, 3H, aromatic H), 7.84-
7.87 (m, 3H, aromatic H), 7.93 (d, J = 8.76 Hz, 2H, aromatic H), 8.14 (d, J = 8.28 Hz, 1H,
aromatic H), 11.11 (s, 1H, NH, D2O exchangeable), 11.23 (s, 1H, NH, D2O exchangeable);
13C NMR (DMSO-d6, 100 MHz): δ 55.9 (OCH3), 114.4, 120.3, 122.5, 124.0, 124.3, 126.3,
127.1, 129.9, 132.5, 135.2, 139.7, 139.9, 141.2, 162.9 (aromatic carbons), 162.8 (C=O),
165.5 (C=O), 190.8 (C=O); MS, m/z [%]: 453 [M+, 23], 119 [100]; Anal. Calcd. for
C22H19N3O6S (453.47): C, 58.27; H, 4.22; N, 9.27. Found: C, 58.50; H, 4.45; N, 9.13.
4.1.2. General procedure for preparation of 9a-e
A mixture of the appropriate 1-benzoylisatin derivative (2a-e) (10 mmol) and 4-
hydrazinylbenzenesulfonamide hydrochloride (6) (0.22 g, 11 mmol) in methanol (5 mL)
18

was stirred at room temperature for 3h. The obtained precipitate was filtered, washed with
ethanol, dried and recrystallized from ethanol.
4.1.2.1. 4-(2-(1-Benzoyl-2-oxoindolin-3-ylidene)hydrazinyl)benzenesulfonamide (9a)
Yellow crystals, yield 50%, m.p. 254-256oC (decomposition); IR (KBr, ʋ cm-1):
3418, 3372, 3306 (NH and NH2), 3086-3059 (CH aromatic), 1747, 1690 (2C=O), 1597
1
(bending NH), 1570, 1508 (C=C), 1331, 1150 (SO2); H NMR (DMSO-d6, 400 MHz): δ
7.28 (s, 2H, NH2, D2O exchangeable), 7.35 (t, J = 7.52 Hz, 1H, aromatic H), 7.46 (t, J =
7.78 Hz, 1H, aromatic H), 7.54 (t, J = 7.60 Hz, 2H, aromatic H), 7.66 (d, J = 7.40 Hz, 1H,
aromatic H), 7.70 (d, J = 8.84 Hz, 2H, aromatic H), 7.78-7.82 (m, 3H, aromatic H), 7.86-
13
7.89 (m, 3H, aromatic H), 12.41 (s, 1H, NH, D2O exchangeable); C NMR (DMSO-d6,
100 MHz): δ 115.0, 115.5, 119.4, 122.8, 125.5, 127.7, 128.6, 129.5, 129.9, 133.1, 134.8,
138.7, 138.8, 145.6, (aromatic carbons), 160.3 (C=O), 168.9 (C=O); MS, m/z [%]: 420
[M+, 100], 421[(M++ 1), 16], 422 [(M++ 2), 2]; Anal. Calcd. for C21H16N4O4S (420.44): C,
59.99; H, 3.84; N, 13.33. Found: C, 60.13; H, 3.96; N, 13.59.
4.1.2.2.
4-(2-(1-(4-Fluorobenzoyl)-2-oxoindolin-3-ylidene)hydrazinyl)benzene-
sulfonamide (9b)
Yellow crystals, yield 45%, m.p. 284-286oC (decomposition); IR (KBr, ʋ cm-1):
3414, 3298, 3252 (NH and NH2), 3074 (CH aromatic), 1709, 1686 (2C=O), 1601 (bending
NH), 1570, 1504 (C=C), 1331, 1150 (SO2); 1H NMR (DMSO-d6, 400 MHz): δ 7.29 (s, 2H,
NH2, D2O exchangeable), 7.33-7.40 (m, 3H, aromatic H), 7.46 (t, J = 7.74Hz, 1H, aromatic
H), 7.71 (d, J = 8.72 Hz, 2H, aromatic H), 7.80 (d, J = 8.40 Hz, 3H, aromatic H), 7.86 (d,
J = 8.08 Hz, 1H, aromatic H), 7.97-8.00 (m, 2H, aromatic H), 12.40 (s, 1H, NH, D2O
13
exchangeable); C NMR (DMSO-d6, 100 MHz): δ 115.0, 115.5, 115.6, 115.8, 119.4,
122.8, 125.5, 127.6, 127.8, 129.5, 131.2, 131.3, 132.9, 133.0, 138.7, 138.8, 145.6, 163.9,
166.4 (aromatic carbons), 160.3 (C=O), 167.7 (C=O); MS, m/z [%]: 438 [M+, 28], 440
[(M++ 2), 21], 167 [100]; Anal. Calcd. for C21H15FN4O4S (438.43): C, 57.53; H, 3.45; N,
12.78. Found: C, 57.80; H, 3.67; N, 12.62.
19

4.1.2.3.
4-(2-(1-(4-Chlorobenzoyl)-2-oxoindolin-3-ylidene)hydrazinyl)benzene-
sulfonamide (9c)
Yellow crystals, yield 58%, m.p. 288-290oC (decomposition); IR (KBr, ʋ cm-1):
3445 (NH and NH2), 3050 (CH aromatic), 1732, 1697 (2C=O), 1639 (bending NH), 1597-
1516 (C=C), 1350, 1153 (SO2); 1H NMR (DMSO-d6, 400 MHz): δ 7.28 (s, 2H, NH2, D2O
exchangeable), 7.36 (t, J = 7.54 Hz, 1H, aromatic H), 7.47 (t, J = 7.82 Hz, 1H, aromatic
H), 7.61 (d, J = 8.36 Hz, 2H, aromatic H), 7.71 (d, J = 8.72 Hz, 2H, aromatic H), 7.78-7.82
(m, 3H, aromatic H), 7.89-7.91 (m, 3H, aromatic H), 12.39 (s, 1H, NH, D2O exchangeable);
13C NMR (DMSO-d6, 100 MHz): δ 115.0, 115.6, 119.4, 122.8, 125.6, 127.6, 127.8, 128.7,
129.6, 131.7, 133.7, 137.8, 138.6, 138.7, 145.6 (aromatic carbons), 160.3 (C=O), 167.9
(C=O); MS, m/z [%]: 454 [M+, 100], 455 [(M++ 1), 32], 456 [(M++ 2), 47]; Anal. Calcd.
for C21H15ClN4O4S (454.89): C, 55.45; H, 3.32; N, 12.32. Found: C, 55.62; H, 3.54; N,
12.60.
4.1.2.4.
4-(2-(1-(4-Bromobenzoyl)-2-oxoindolin-3-ylidene)hydrazinyl)benzene-
sulfonamide (9d)
Yellow crystals, yield 60%, m.p.> 300oC (decomposition); IR (KBr, ʋ cm-1): 3375,
3263 (NH and NH2), 3086 (CH aromatic), 1724, 1674 (2C=O), 1597 (bending NH), 1566-
1520 (C=C), 1327, 1146 (SO2); 1H NMR (DMSO-d6, 400 MHz): δ 7.28 (s, 2H, NH2, D2O
exchangeable), 7.36 (t, J = 7.54 Hz, 1H, aromatic H), 7.47 (t, J = 7.78 Hz, 1H, aromatic
H), 7.71 (d, J = 8.76 Hz, 2H, aromatic H), 7.75 (d, J = 8.52 Hz, 2H, aromatic H), 7.79-7.83
(m, 4H, aromatic H), 7.85-7.88 (m, 1H, aromatic H), 7.91 (d, J = 8.12 Hz, 1H, aromatic
13
H), 12.39 (s, 1H, NH, D2O exchangeable); C NMR (DMSO-d6, 100 MHz): δ 115.0,
115.4, 116.7, 119.4, 122.8, 125.6, 127.4, 127.7, 129.5, 131.6, 131.8, 133.5, 134.1, 138.6,
138.8, 145.6 (aromatic carbons), 160.3 (C=O), 168.0 (C=O); MS, m/z [%]: 499 [M+, 27],
285 [100]; Anal. Calcd. for C21H15BrN4O4S (499.34): C, 50.51; H, 3.03; N, 11.22. Found:
C, 50.43; H, 3.19; N, 11.43.
20

4.1.2.5.
4-(2-(1-(4-Methoxybenzoyl)-2-oxoindolin-3-ylidene)hydrazinyl)benzene-
sulfonamide (9e)
Yellow crystals, yield 45%, m.p. 220-222oC; IR (KBr, ʋ cm-1): 3406, 3317, 3240
(NH and NH2), 3050 (CH aromatic), 2936 (CH aliphatic), 1674, 1655 (2C=O), 1605
1
(bending NH), 1560-1508 (C=C), 1327, 1149 (SO2); H NMR (DMSO-d6, 400 MHz): δ
3.88 (s, 3H, OCH3), 7.07 (d, J = 8.64 Hz, 2H, aromatic H),7.29 (s, 2H, NH2, D2O
exchangeable), 7.32 (t, J = 7.68 Hz, 1H, aromatic H), 7.44 (t, J = 7.74 Hz, 1H, aromatic
H), 7.68-7.71 (m, 3H, aromatic H), 7.78-7.81 (m, 3H, aromatic H), 7.91 (d, J = 8.64 Hz,
2H, aromatic H), 12.46 (s, 1H, NH, D2O exchangeable); 13C NMR (DMSO-d6, 100 MHz):
δ 56.1 (OCH3), 114.1, 114.9, 115.1, 119.4, 122.5, 125.1, 126.3, 127.8, 127.9, 129.5, 132.9,
138.7, 139.1, 145.6, 163.8 (aromatic carbons), 160.4 (C=O), 167.9 (C=O); MS, m/z [%]:
450 [M+, 9], 451 [(M++1), 3], 77 [100]; Anal. Calcd. for C22H18N4O5S (450.47): C, 58.66;
H, 4.03; N, 12.44. Found: C, 58.74; H, 4.21; N, 12.69.
4.1.3. General procedure for preparation of compounds 10a-e
To a mixture of the appropriate 1-benzoylisatin derivative (2a-e) (10 mmol), 4-((2-
hydrazinyl-2-oxoethyl)amino)benzenesulfonamide (8) (0.27 g, 11 mmol) in methanol
(5mL) was added 2 drops of conc. hydrochloric acid. The reaction mixture was stirred at
room temperature for 3h, the obtained precipitate was filtered, washed with ethanol, dried
and recrystallized from ethanol to give 10a-e in a pure form.
4.1.3.1.
4-((2-(2-(1-Benzoyl-2-oxoindolin-3-ylidene)hydrazinyl)-2-oxoethyl)amino)
benzenesulfonamide (10a)
Yellow crystals, yield 55%, m.p.244-246oC (decomposition); IR (KBr, ʋ cm-1):
3383, 3240, 3105 (2NH and NH2), 3067 (CH aromatic), 2916 (CH aliphatic), 1751, 1697
21

1
(3C=O), 1601 (bending NH), 1516 (C=C), 1346, 1150 (SO2); H NMR (DMSO-d6, 400
MHz): δ 4.36 (s, 2H, CH2), 6.70 (d, J = 8.56 Hz, 2H, aromatic H), 6.96 (s, 2H, NH2, D2O
exchangeable), 7.37 (t, J = 7.60 Hz, 1H, aromatic H), 7.51-7.56 (m, 5H, aromatic H), 7.61
(t, J = 7.84 Hz, 1H, aromatic H), 7.67 (t, J = 6.80 Hz, 1H, aromatic H), 7.84-7.91 (m, 3H,
aromatic H), 8.32 (s, 1H, NH, D2O exchangeable), 11.59 (s, 1H, NH, D2O exchangeable);
13C NMR (DMSO-d6, 100 MHz): δ 44.9 (CH2), 112.0, 115.4, 115.7, 117.2, 121.1, 121.5,
125.1, 125.7, 127.8, 128.6, 128.7, 130.0, 131.5, 131.9, 132.8, 133.4, 134.6, 141.1, 151.4,
162.8 (aromatic carbons), 160.4 (C=O), 168.5 (C=O), 169.0 (C=O); MS, m/z [%]: 477 [M+,
7], 478 [(M++1), 2], 105 [100]; Anal. Calcd. for C23H19N5O5S (477.50): C, 57.85; H, 4.01;
N, 14.67. Found: C, 58.11; H, 4.27; N, 14.58.
4.1.3.2.
4-((2-(2-(1-(4-Fluorobenzoyl)-2-oxoindolin-3-ylidene)hydrazinyl)-2-oxoethyl)
amino)benzenesulfonamide (10b)
Yellow crystals, yield 45%, m.p. 259-261oC (decomposition); IR (KBr, ʋ cm-1):
3379, 3263, 3171, 3121 (2NH and NH2), 3078, 3013 (CH aromatic), 2909 (CH aliphatic),
1
1744, 1693 (3C=O), 1601 (bending NH), 1508 (C=C), 1342, 1150 (SO2); H NMR
(DMSO-d6, 400 MHz): δ 4.37 (s, 2H, CH2), 6.70 (d, J = 8.44 Hz, 2H, aromatic H), 6.96
(s, 2H, NH2, D2O exchangeable), 7.34-7.39 (m, 3H, aromatic H), 7.53-7.56 (m, 3H,
aromatic H), 7.61 (t, J = 7.86 Hz, 1H, aromatic H), 7.89 (d, J = 8.16 Hz, 1H, aromatic H),
7.94-7.98 (m, 2H, aromatic H), 8.32 (s, 1H, NH, D2O exchangeable), 11.59 (s, 1H, NH,
D2O exchangeable); 13C NMR (DMSO-d6, 100 MHz): δ 44.9 (CH2), 112.0, 115.5, 115.6,
115.7, 115.8, 115.9, 117.3,121.0, 121.5, 125.1, 125.7, 126.2, 127.8, 130.7, 131.9, 133.0,
133.2, 133.3, 141.0, 141.5, 151.4, 164.0, 164.2, 166.6, 166.7 (aromatic carbons), 160.4
(C=O), 167.3 (C=O), 167.8 (C=O); MS, m/z [%]: 495 [M+, 12], 497 [(M++2), 2], 76 [100];
Anal. Calcd. for C23H18FN5O5S (495.49): C, 55.75; H, 3.66; N, 14.13. Found: C, 55.97; H,
3.39; N, 14.29.
4.1.3.3.
4-((2-(2-(1-(4-Chlorobenzoyl)-2-oxoindolin-3-ylidene)hydrazinyl)-2-oxoethyl)
amino)benzenesulfonamide (10c)
22

Yellow crystals, yield 50%, m.p. 250-252oC (decomposition); IR (KBr, ʋ cm-1):
3379, 3260, 3167, 3113 (2NH and NH2), 3071, 3013 (CH aromatic), 2909 (CH aliphatic),
1
1747, 1693 (3C=O), 1597 (bending NH), 1520 (C=C), 1342, 1150 (SO2); H NMR
(DMSO-d6, 400 MHz): δ 4.36 (s, 2H, CH2), 6.70 (d, J = 8.36 Hz, 2H, aromatic H), 6.97
(s, 2H, NH2, D2O exchangeable), 7.37 (t, J = 7.58 Hz, 1H, aromatic H), 7.55 (d, J = 8.60
Hz, 2H, aromatic H), 7.59-7.61 (m, 3H, aromatic H), 7.83-7.89 (m, 3H, aromatic H), 7.94
(d, J = 8.16 Hz 1H, aromatic H), 8.32 (s, 1H, NH, D2O exchangeable), 11.61 (s, 1H, NH,
D2O exchangeable); 13C NMR (DMSO-d6, 100 MHz): δ 44.8 (CH2), 112.0, 115.8, 115.9,
117.3,121.0, 121.5, 125.8, 127.8, 128.8, 129.2,131.6, 131.9, 133.1, 138.3, 140.9, 151.3,
(aromatic carbons), 160.4 (C=O), 166.9 (C=O), 167.4 (C=O); MS, m/z [%]: 511 [M+, 11],
438 [100]; Anal. Calcd. for C23H18ClN5O5S (511.94): C, 53.96; H, 3.54; N, 13.68. Found:
C, 54.12; H, 3.71; N, 13.87.
4.1.3.4.
4-((2-(2-(1-(4-Bromobenzoyl)-2-oxoindolin-3-ylidene)hydrazinyl)-2-oxoethyl)
amino)benzenesulfonamide (10d)
Yellow crystals, yield 50%, m.p. 245-247oC (decomposition); IR (KBr, ʋ cm-1):
3379, 3352, 3256 (2NH and NH2), 3094 (CH aromatic), 2905 (CH aliphatic), 1763, 1693
1
(3C=O), 1601 (bending NH), 1516 (C=C), 1346, 1150 (SO2); H NMR (DMSO-d6, 400
MHz): δ 4.37 (s, 2H, CH2), 6.68-6.72 (m, 2H, aromatic H), 6.98 (s, 2H, NH2, D2O
exchangeable), 7.37 (t, J = 7.54 Hz, 1H, aromatic H), 7.54-7.57 (m, 2H, aromatic H), 7.61
(t, J = 8.04 Hz, 1H, aromatic H), 7.70-7.83 (m, 5H, aromatic H), 7.94 (d, J = 8.12 Hz 1H,
aromatic H), 8.32 (s, 1H, NH, D2O exchangeable), 11.60 (s, 1H, NH, D2O exchangeable);
13C NMR (DMSO-d6, 100 MHz): δ 45.0 (CH2), 112.0, 115.6, 115.8, 117.3, 121.0, 121.5,
125.9, 127.8, 129.8, 130.4, 131.5, 131.9, 132.8, 133.4, 133.9, 140.9, 141.3, 151.3 (aromatic
carbons), 160.4 (C=O), 167.1 (C=O), 168.1 (C=O); MS, m/z [%]: 555 [M+, 2], 50 [100];
Anal. Calcd. for C23H18BrN5O5S (556.39): C, 49.56; H, 3.26; N, 12.59. Found: C, 49.81;
H, 3.43; N, 12.62.
23

4.1.3.5. 4-((2-(2-(1-(4-Methoxybenzoyl)-2-oxoindolin-3-ylidene)hydrazinyl)-2-oxoethyl)
amino)benzenesulfonamide (10e)
Yellow crystals, yield 55%, m.p. 242-244oC (decomposition); IR (KBr, ʋ cm-1): 3387,
3352, 3233 (2NH and NH2), 3097 (CH aromatic), 2970-2905 (CH aliphatic), 1743, 1693
1
(3C=O), 1601 (bending NH), 1516 (C=C), 1342, 1150 (SO2); H NMR (DMSO-d6, 400
MHz): δ 3.89 (s, 3H,OCH3), 4.37 (s, 2H, CH2), 6.71 (d, J = 8.36 Hz, 2H, aromatic H), 6.97
(s, 2H, NH2, D2O exchangeable), 7.06 (d, J = 8.68 Hz, 2H, aromatic H), 7.33 (t, J = 7.60
Hz, 1H, aromatic H), 7.54-7.60 (m, 4H, aromatic H), 7.72 (d, J = 8.12 Hz, 1H, aromatic
H), 7.89 (d, J = 8.84 Hz, 2H, aromatic H), 8.32 (s, 1H, NH, D2O exchangeable), 11.57 (s,
1H, NH, D2O exchangeable); 13C NMR (DMSO-d6, 100 MHz): δ 44.8 (CH2), 56.1 (OCH3),
111.8, 114.1, 115.1, 117.0, 121.1, 124.8, 125.4, 125.7, 126.1, 126.2, 127.8, 131.8, 133.1,
141.8, 151.4, 164.1 (aromatic carbons), 160.4 (C=O), 167.4 (C=O), 168.0 (C=O); MS, m/z
[%]: 507 [M+, 20], 64 [100]; Anal. Calcd. for C24H21N5O6S (507.52): C, 56.80; H, 4.17; N,
13.80. Found: C, 56.63; H, 4.41; N, 13.57.
4.2.
Carbonic anhydrase inhibition.
An Applied Photophysics stopped-flow instrument has been used for assaying the
CA catalysed CO2 hydration activity [29-33]. Phenol red (at a concentration of 0.2 mM)
has been used as a pH indicator, working at the absorbance maximum of 557 nm, with 20
mM Hepes (pH 7.5) as the buffer, and 20 mM Na2SO4 (for maintaining constant the ionic
strength), following the initial rates of the CA-catalyzed CO2 hydration reaction for a
period of 10-100 s at 25°C [29]. The CO2 concentrations ranged from 1.7 to 17 mM for the
determination of the kinetic parameters and inhibition constants. For each inhibitor, at least
six traces of the initial 5-10% of the reaction have been used for determining the initial
velocity. The uncatalyzed rates were determined in the same manner and subtracted from
the total observed rates. Stock solutions of inhibitor (0.1 mM) were prepared in distilled-
deionized water and dilutions up to 0.01 nM were done thereafter with the assay buffer.
Inhibitor and enzyme solutions were preincubated together for 15 min at room temperature
prior to assay, in order to allow for the formation of the E-I complex. The inhibition
constants were obtained by non-linear least-squares methods using PRISM 3 and the
24

Cheng-Prusoff equation, as reported earlier [29-33], and represent the mean from at least
three different determinations. All hCA isoforms were recombinant ones obtained in-house
as reported earlier [1].
4.3. Molecular modeling.
All the molecular modeling studies were carried out using Molecular Operating
Environment (MOE, 2015.10) software. All minimizations were performed with MOE
until an RMSD gradient of 0.05 kcal∙mol−1Å−1 with MMFF94x force field and the partial
charges were automatically calculated. The X-ray crystallographic structure of human
carbonic anhydrase isoforms I, II, IX and XII co-crystalized with acetazolamide (PDB ID:
3W6H, 3HS4, 3IAI and 1JD0, respectively) were downloaded from the protein data bank
[34]. Water molecules which are not involved in the binding were removed. The protein
was prepared for the docking study using Protonate 3D protocol in MOE with default
options. The 3D structures of the compounds were drawn by using the MOE of (Chemical
Computing Group software, Canada) drawing tool bar. The Lowest energy conformer of
the compounds (global-minima) was docked into the active site. All structures were drawn
with deprotonation of their sulfonamide moiety and the negative charge was localized
automatically by the program on S-O–. The co-crystalized ligand (acetazolamide) was used
to define the binding site for docking. Triangle Matcher placement method and London dG
scoring function were used for docking. Docking setup was first validated by self-docking
of the co-crystallized ligand (acetazolamide) in the vicinity of the binding site of the
enzyme and by the ability of the docking pose to reproduce all the key interactions
accomplished by the co-crystallized ligand with the hot spots in the active site. The
validated setup was then used in predicting the ligand-receptor interactions at the binding
site for the compounds of interest.
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