Design, synthesis, characterization and computational docking studies of novel sulfonamide derivatives

Article abstract of DOI:10.17179/excli2017-886

This study reports three novel sulfonamide derivatives 4-Chloro-N-[(4-methylphenyl) sulphonyl]-N-propyl ben-zamide (1A), N-(2-hydroxyphenyl)-4-methyl benzene sulfonamide (1B) and 4-methyl-N-(2-nitrophenyl) benzene sulfonamide (1C). The compounds were synt

Full text of DOI:10.17179/excli2017-886

EXCLI Journal 2018;17:169-180 – ISSN 1611-2156
Received: October 17, 2017, accepted: January 29, 2017, published: February 01, 2018
Original article:
DESIGN, SYNTHESIS, CHARACTERIZATION AND
COMPUTATIONAL DOCKING STUDIES OF NOVEL SULFONAMIDE
DERIVATIVES
Hira Saleem1a, Arooma Maryam1a, Saleem Ahmed Bokhari1a, Ayesha Ashiq1,
Sadaf Abdul Rauf2, Rana Rehan Khalid1, Fahim Ashraf Qureshi1b, Abdul Rauf Siddiqi1
1
Department of Biosciences, COMSATS Institute of Information Technology, Islamabad,
Pakistan
2
Department of Computer Science, Fatima Jinnah Women University, The Mall,
Rawalpindi
Equal contributions, co-first authors
Shared correspondence: qureshifa@comsats.edu.pk
a
b
corresponding author: Abdul Rauf Siddiqi, Department of Biosciences, COMSATS
Institute of Information Technology, Park Road, Islamabad, Pakistan
E-mail: araufsiddiqi@comsats.edu.pk, abdulraufsher@gmail.com
http://dx.doi.org/10.17179/excli2017-886
This is an Open Access article distributed under the terms of the Creative Commons Attribution License
(http://creativecommons.org/licenses/by/4.0/).
ABSTRACT
This study reports three novel sulfonamide derivatives 4-Chloro-N-[(4-methylphenyl) sulphonyl]-N-propyl ben-
zamide (1A), N-(2-hydroxyphenyl)-4-methyl benzene sulfonamide (1B) and 4-methyl-N-(2-nitrophenyl) ben-
zene sulfonamide (1C). The compounds were synthesised from starting material 4-methylbenzenesulfonyl chlo-
1
ride and their structure was studied through H-NMR and 13C-NMR spectra. Computational docking was per-
formed to estimate their binding energy against bacterial p-amino benzoic acid (PABA) receptor, the dihydrop-
teroate synthase (DHPS). The derivatives were tested in vitro for their antimicrobial activity against Gram+ and
Gram- bacteria including E. coli, B. subtilis, B. licheniformis and B. linen. 1A was found active only against B.
linen; 1B was effective against E. coli, B. subtilis and B. linen whereas 1C showed activity against E. coli, B. li-
cheniformis and B. linen. 1C showed maximum activity with minimum inhibitory concentration (MIC) of 50,
100 and 150 µg/mL against E. coli, B. licheniformis and B. linen respectively. 1C exhibited maximum affinity to
DHPS with binding free energy of -8.1 kcal/mol. It enriched in the top 0.5 % of a library of 7663 compounds,
ranked in order of their binding affinity against DHPS. 1C was followed by 1B which showed a moderate to low
level MIC of 100, 250 and 150 µg/mL against E. coli, B. subtilis and B. linen respectively, whereas 1A showed a
moderate level MIC of 100 µg/mL but only against B. linen. These derivatives may thus serve as potential anti-
bacterial alternatives against resistant pathogens.
Keywords: Sulfonamide, derivatives, synthesis, antimicrobial, activity, structure
INTRODUCTION
are posing substantial economic and health
threats globally (Sengupta et al., 2013;
Lushniak, 2014). Microbes have evolved
various intrinsic mechanisms enabling them
to develop antibiotic resistance specific to
structural and functional features of
Antibiotic resistance is an inevitable evo-
lutionary phenomenon which renders antimi-
crobial products ineffective against infec-
tions. Antibiotic resistant microbial strains
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Received: October 17, 2017, accepted: January 29, 2017, published: February 01, 2018
antibiotics (Sengupta et al., 2013). They ac- considered as first best option (Sławiński et
quire resistance against active drugs through al., 2013). Growing concern associated with
spontaneous mutations and horizontal gene antibiotic resistance has spurred further re-
transfer. Overuse of antibiotics gradually search for more selective and efficacious an-
eliminates drug-sensitive strains leaving be- timicrobial solutions. To that effect, a rela-
hind drug resistant species to survive and re- tively direct and cost effective strategy for
produce as a consequence of natural selec- drug discovery is ligand based design, which
tion (Randall et al., 2013).
involves designing new therapeutic mole-
Sulfonamides have long been in use as cules based on structural and functional
effective therapeutic agents against both properties of already known drugs. The nov-
Gram+ and Gram- bacterial strains associat- el derivatives improve basic structural and
ed with a range of infectious diseases (Nasr functional therapeutic attributes while decoy-
et al., 2016). These broad spectrum synthetic ing pathogen’s resistance mechanism.
drug molecules compete with and inhibit the
Here we report three novel sulfonamide
binding of p-amino benzoic acid (PABA) in derivatives, their mode of synthesis, physico-
binding site of dihydropteroate synthase chemical properties, structure, binding affini-
(DHPS) enzyme thereby interfering with the ties with DHPS, activity and Minimum In-
vital bacterial dihydrofolic acid synthesis hibitory Concentration (MIC) against a set of
pathway (Seydel, 1968; Argyropoulou et al., Gram- and Gram+ bacteria. These novel de-
2009). In bacteria, folic acid is an essential rivatives are listed below (Table 1).
component required for DNA and RNA syn-
thesis. By disrupting folic acid synthesis
pathway in bacterial cell, sulfonamides com-
promise the microbes’ ability to divide and
reproduce. In addition to being antibacterial,
sulfonamides and their derivatives are wide-
ly prescribed as insulin release inducers, an-
tiviral, antifungal, anti-cancer and anti-
inflammatory agents (Bano et al., 2011;
Zoumpoulakis et al., 2012; Sławiński et al.,
2013).
However, bacteria have developed re-
sistance against popular sulfonamide based
drugs such as co-trimoxazol and sulfameth-
oxazole etc. Owing to the rise of resistance
against sulfonamides in a number of bacteri-
al pathogens, the sulfonamides are hardly
MATERIALS AND METHODS
Structure of DHPS
Structure of dihydropteroate synthase
(DHPS) enzyme of Escherichia Coli, de-
termined through X-Ray Crystallography,
solved at 2.00Å resolution (PDB: 1AJ0) al-
ready bound with a sulfonamide ligand
(C6H8N2O2S) was selected as target and re-
trieved
from RCSB’s PDB database
(Achari et al., 1997). DHPS sulfonamide
pocket is configured by H bond forming
Ser219, Arg220, and Arg63 and aromatic
Pro64, Phe190, Phe157 and Pro232 residues
(Figure 1).
Table 1: Sulfonamide derivatives synthesized in this study
IUPAC Name
Code
Chemical Group
4-chloro-N-[(4-methylphenyl)sulfonyl]-N-propyl benzamide
1A
Sulfonamide
N-(2-hydroxyphenyl)-4-methyl benzenesulfonamide
4-methyl-N-(2-nitrophenyl) benzenesulfonamide
1B
1C
Sulfonamide
Sulfonamide
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Figure 1: (a) Structure of Escherichia coli Dihydropteroate Synthase (DHPS), PDB: 1AJ0 (8). A sul-
fonamide molecule (C6 H8 N2 O2 S) molecule is bound inside the binding pocket. (b) Zoomed in bind-
ing pocket of DHPS shown in transparent surface, the sidechains of the residues configuring the bind-
ing pocket and imparting the polar and nonpolar interactions on sulfonamide molecule are labelled,
three green dashed lines show hydrogen bonds with Arg 63, Ser219 and Arg 220.
Structure and physical properties of Sul-
fonamide derivatives
Synthesis and structure of 4-Chloro-N-[(4-
methylphenyl) sulfonyl]- N-propyl ben-
zamide (1A)
The structures of newly synthesized
compounds were determined through NMR
1A was obtained by reacting propan-1-
spectroscopy and mass spectrometry. The
amine with 4-methylbenzenesulfonyl chlo-
spectra were recorded on a Bruker DPX-400
ride at first followed by reaction with 3-
NMR spectrometer (Billerica, USA) (400
chlorobenzoyl chloride (Figure 2). Briefly,
2.5 M solution of the propylamine (propan-
1-amine) was prepared in distilled water. The
solution was added to 0.44 M p-toluene sul-
fonyl chloride (4-methylbenzenesulfonyl
chloride). The mixture was stirred slowly for
1
MHz for H and 100 MHz for 13C-NMR),
using CDCl3 as the solvent. The physical
properties were also determined and charac-
terized by FT-IR and Elemental analysis
(CHNS).
2-3 hours while maintaining pH during the
reaction between 6-10 with 3 % Na2CO3. N-
Synthesis of Sulfonamide derivatives
In view of already known structure activ-
propyl benzenesulfonamide thus formed was
ity relationship of sulfonamide derivatives,
further reacted with 3-chlorobenzoyl chlo-
three derivatives of sulfonamide were pre-
ride to obtain precipitates of 4-chloro-N-[(4-
pared through substitution reactions with p-
toluene sulfonyl chloride as detailed below.
methylphenyl) sulfonyl]-N-propyl ben-
zamide. The precipitates were then filtered
and washed with cold water. TLC was per-
formed using the mixture of ethyl acetate
and n-hexane (1:4) as mobile phase.
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Figure 2: (a) Reaction of
propan-1-amine with 4-
methylbenzenesulfonyl
chloride to produce 4-
methyl-N-propylbenzene-
sulfonamide, (b) 4-methyl-
N-propylbenzenesulfona-
mide was further reacted
with 3-chlorobenzoyl chlo-
ride to obtain 4-chloro-N-
[(4-methylphenyl)
sulfo-
nyl]-N-propylbenzamide.
Crystalline form of compound 1A as off
white powder (93 % yield) was obtained
with following physical properties: molecu-
lar weight (351.85), molar refractivity
(92.25±0.4 cm3), molar volume (275.6±3.0
cm3), parachor (724.3±6.0 cm3), index of re-
fraction (1.58±0.02), surface tension
(47.6±3.0 dyne/cm), density (1.276±0.06g/
cm3) and polarizability (36.57±0.5 10-24
cm3). NMR data of compound 1A showed
1H-NMR signals at δ 7.821(d, J=2.12, 1H,
H-3, H-5), 7.809 (d, J=2.2, 1H, H-3′, H-5′),
7.735 (d, J=2.1, 1H, H-2, H-6), 7.351 (d,
J=2.29, 1H, H-2′, H-6′), 4.207 (t, J=7, 2H, H-
8) and 13C-NMR found signals at δ/ppm:
128.8, 128.8, 135.7, 165.7, 144.3, 56.9, 21.3,
129.7, 129.7, 45.5, 127.5, 127.5, 135.1,
128.9, 128.9, 133.7, 11.1. Elemental analysis
of compound 1A found C (58.06 %), H
(5.16 %), N (3.985), O (13.64 %), S (9.11 %)
and Cl (10.08 %).
Synthesis and structure of N-(2-
hydroxyphenyl)-4-methyl benzenesulfona-
mide (1B)
1B was synthesized by reacting 2-
aminophenol with 4-methylbenzenesulfonyl
chloride, TLC was performed and the precip-
itates were filtered and washed with distilled
cold water in a procedure similar to de-
scribed earlier (Figure 3). Physical properties
of white crystalline solid 1B (yield: 91 %)
were: molecular weight (263.12), melting
point (76 °C), molar refractivity (70.08±0.4
cm3), molar volume (193.2±3.0 cm3), para-
chor (538.8±6.0 cm3), index of refraction
(1.64±0.02), surface tension (60.4±3.0
dyne/cm), density (1.36±0.06 g/cm3) and po-
larizability (27.78±0.5 10-24 cm3); 1H-NMR
signals at δ 7.86 (d, J=8.4, 1H, H-2, H-6),
7.57 (t, J=, 1H, H-3, H-5), 7.55 (dd, J=1.8,
7.3, 1H, H-4), 7.46 (d, J=7.5, 1H, H-2′, H-
6′), 7.19 (d, J=7.5, 1H, H-3′, H-5′), 2.36 (s,
13
J); C-NMR (CDCl3, 100 MHz) signals at
δ/ppm: 136.0, 113.7, 117.3, 127.5, 127.5,
144.3, 147.2, 129.7, 129.7, 21.3, 125.3,
131.2, 127.7. Elemental analysis of com-
pound 1B showed C (59.30 %), H (4.98 %),
N (5.32 %), O (18.23 %) and S (12.18 %).
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Figure 3: Reaction of 2-aminophenol with 4-methylbenzenesulfonyl chloride producing N-(2-
hydroxyphenyl)-4-methyl benzenesulfonamide (1B).
dicated C (53.42 %), H (4.14 %), N
Synthesis and structure of 4-methyl-N-(2-
(9.58 %), O (21.89 %) and S (10.97 %), in
the compound.
nitrophenyl) benzenesulfonamide (1C)
In a procedure similar to that described
earlier, 1C was synthesized by reacting 2-
nitroaniline with 4-methylbenzenesulfonyl
chloride (Figure 4), separated by TLC, crys-
In silico screening of sulfonamide
derivatives seeded compound library
Before undertaking activity assays, we
talized, washed and dried as off-white crys-
decided to screen a representative set of
talline solid (yield 93 %). Its physical prop-
compounds against DHPS to see their rela-
erties were determined as: molecular weight
tive binding affinity with the target.
(293.31), molar refractivity (74.58±0.4 cm3),
molar volume (206.6±3.0 cm3), parachor Development of compound library
(580.7±6.0 cm3), index of refraction
A diverse library of 6990 selected com-
(1.64±0.02), surface tension (62.3±3.0 pounds was built from a number of open
dyne/cm), density (1.41±0.06 g/cm3), polar- source compound libraries including com-
izability (29.56±0.5 10-24 cm3) and melting pounds comparable in size, structure, physi-
1
point (167 °C); H-NMR showed signals at cal and chemical properties to our sulfona-
δ 7.821 (d, J=2.12, 1H, H-3, H-5), 7.80 (d, mide derivatives. Structure files for sulfona-
J=2.2, 1H, H-3′, H-5′), 7.735 (d, J=2.1, 1H, mides 1A, 1B & 1C were written in .mol2
H-2, H-6), 7.351 (d, J=2.29, 1H, H-2′, H-6′), format and were subjected to Multiconf-
4.207 (t, J=7, 2H, H-8); 13C-NMR δ/ppm Dock software (Sauton et al., 2008) to gen-
was: 117.3, 144.3, 127.7, 129.7, 129.7, erate different conformers of the synthesized
127.5, 127.5, 140.5, 117.3, 140.5, 127.7, sulfonamide derivatives. The conformers
136.0, 21.3. Elemental analysis (CNHS) in-
Figure 4: 2-nitroaniline was reacting with 4-methylbenzenesulfonyl chloride to synthesize 4-methyl-N-
(2- nitrophenyl) benzenesulfonamide, 1C.
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showed a maximum Root Mean Square De- polar hydrogen, removal of water molecules
viation (RMSD) of 2Å and free energy devi- and energy minimization. Once the receptor
ation of 10 KJ/mol from the parent structures. protein was ready, site finder tool was ap-
Thus 672 conformers of 1A, 1B & 1C were plied to find active site in 1AJ0 structure and
generated. These conformers along with an electrostatic surface map was created
DHPS bound sulfonamide ligand (4-amino- around it to define the docking site. Later
benzenesulfonamide, C6 H8 N2 O2 S) as in sulfonamide derivatives containing ligand
1AJ0 PDB file were also seeded in the com- database was docked within the defined
pound library of 6990 compounds to make docking site of 1AJ0. This tool uses triangu-
up a total of 7663 compounds in .mol2 for- lar matcher algorithm as a default ligand
mat.
placement methods to find 1000 best con-
formations of subject ligands within the
binding pockets of the target protein
(Lengauer and Rarey, 1996). These 1000
poses were rescored through London dG
scoring function to select top 10 confor-
mations per molecule. For each confor-
mation, final binding energy, S-score and
RMSD values were calculated by General-
ized Born Solvation Model by keeping the
active pocket residues rigid. To validate
docking protocol of MOE, a test run was ac-
complished using the co-crystallized sulfon-
amide ligand bound in 1AJ0 as control.
ADMET of compound library
Absorption, Distribution, Metabolism,
Excretion and Toxicity (ADMET) values of
compounds were estimated based on struc-
tural characteristics or structural alerts. The
compounds were rated in three categories
which included: 1) those derivatives that
were present in accepted range which ful-
filled the physiochemical filter, 2) the com-
pounds that lied in intermediate range i.e.
showing low or very few structural alerts and
3) the compounds present in the rejected list
showing high structural alerts. The last, be-
ing not suitable drug candidates, were delet-
ed. Drug likeliness of the compounds was
measured on the basis of Lipinski’s rule of
five (RO5).
Procedure for determining antibacterial
activity
Both Gram-, Escherica coli (E. coli), and
Gram+ bacteria, Bacillus subtilis (B. sub-
tilis), Bacillus licheniformis (B. licheniform-
is) and Brevibacterium linens (B. linens),
were used to determine the activity. Inocula
of the microbes were prepared in sterilized
LB media following standard set of proto-
cols. Sterilized petri dishes of agar medium
were prepared and sterilized. The activity
was measured by well diffusion and disc dif-
fusion method as detailed below.
Molecular docking against DHPS
Molecular docking studies against 1AJ0
were carried out in Molecular Operating En-
vironment (MOE) software (Chemical
Computing Group ULC, 2013). Being more
accurate and faster, MOE is widely used to
undertake in silico ligand screening and to
predict binding affinities between small mol-
ecules and receptor protein targets. Screened
library of 7663 compounds including 672
conformers of 1A, 1B and 1C were opti-
mized in MOE. Ligand optimization includ-
ed addition of partial charges through Proto-
nate3D tools and subsequent energy minimi-
zation of these hits by applying MMFF94X
force field. Afterwards optimized ligands
were added to the MOE ligand database in-
dividually for docking purpose. Similarly
PDB file of E. coli DHPS (1AJ0) was also
prepared for docking by addition of non-
Well diffusion method
100 µl of inoculum of each of the mi-
crobes mentioned above was spread over the
media layer of the petri dishes in triplicate
with a sterile cotton swab, and were put to
incubate for an hour to dry. Wells 7 mm in
diameter, 20 mm apart, were casted by a
sterilized pipette cut near the tip. Solution of
each of the compounds 1A, 1B and 1C were
prepared at a concentration of 300 µg/mL. A
300 µg/mL solution of sulfamethoxazole and
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nutrient broth were also prepared to serve as
RESULTS AND DISCUSSION
positive and negative control respectively.
100 µl of each of the solutions were added in
wells of aforementioned culture plated petri
dishes for each of the four microbe cultures
in triplicate and incubated for 24 hours at
36±1 °C (Table 2).
Structural and physicochemical characteri-
zation of Sulfonamide derivatives
The structures of newly synthesized
compounds were determined through spec-
troscopic data of IR, 1H NMR, 13C NMR and
mass spectra; the physical properties were
also determined and characterized by FT-IR
Disc diffusion method
The well diffusion experiment was also and elemental analysis (CHNS) as given in
repeated in disc diffusion assay. In this assay Materials and Methods. Drug likeliness of
instead of wells 7 mm wide Whatman filter the derivatives was evaluated on the basis of
paper discs were used. The discs were Lipinski’s RO5 in which is regarded as a rule
soaked with 2 mL of each sample solution, of thumb to distinguish between drug and
ensuring the final dry amount of the 1A, 1B non-drug like compounds. It predicts the
and 1C to remain same as much as poured in probability of success of prospective drug
wells in solution form; the discs were left at likeliness for the subject compound on the
room temperature until complete evapora- basis of its molecular mass (≤ 500 Dalton),
tion. Discs were then placed over the surface hydrogen bond donors (≤ 5), hydrogen bond
of agar and results were recorded.
acceptors (≤10), lipophilicity (expressed as
LogP ≤ 5) and molar refractivity (between 1-
40). In order to qualify as a prospective drug,
a compound should meet at least two or
more aforementioned thresholds. All of our
sulfonamide derivatives 1A, 1B and 1C qual-
ified the ADMET and Lipinski’s rule (RO5)
criteria for their drug likeliness.
Procedure for determining MIC
Minimum inhibitory concentration (MIC)
was estimated through micro-dilution meth-
od. The nutrient broth solution was prepared
and incubated for 48 hours. 100 mg of each
of the sample compounds was solubilized.
Dilutions of 0.5, 1.0, 1.5, 2.0, 2.5 and 3.0
mg/mL were prepared. 0.7 mL of media (nu-
trient broth) and 100 µl each of the afore-
mentioned diluted solutions were added in
different test tubes along with 200 µl each of
the inoculum culture. Thus the final concen-
trations of 50, 100, 150, 200, 250 and
300 µg/ mL were achieved in each of the
tubes. The conditions were kept same for
positive and negative control. The tubes
were incubated for eighteen hours. Using
this methodology, lowest concentration in
µg/mL units of each derivative showing in-
hibition in growth was estimated.
Activity of 1A, 1B and 1C against microbes
Antimicrobial activity of the sulfonamide
derivatives 1A, 1B and 1C against a set of
Gram+ and Gram- bacteria including E. coli,
B. subtilis, B. licheniformis and B. linens was
also determined using sulfamethoxazole as a
reference. 1A was found active against B.
linens, whereas 1B was active against E.
coli, B. subtilis and B. linens. 1C was effec-
tive against E. coli, B. licheniformis and B.
linens (Table 2).
Table 2: Activity of Sulfonamide derivatives 1A, 1B and 1C against bacterial pathogens E. coli, B. sub-
tilis, B. licheniformis and B. linen
Compounds
E. coli
-
B. subtilis
B. licheniformis
B. linens
Active
1A
1B
-
-
-
Active
Active
Active
1C
Active
-
Active
---
-
Active
Active
-
Active
Active
---
Active
Nutrient Broth (Negative Control)
Sulfamethoxazole (Positive Control)
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1A showed moderate level of activity same conformation showing 0Å RMSD to
with Minimum Inhibitory Concentration the co-crystallized structure (1AJ0). Ligand
(MIC) of 100 µg/mL but only against B. lin- conformations were same with focused
ens. 1B was active against 3 of the 4 bacteri- docking, (when receptor binding pocket di-
al species used in this study, namely E. coli, mensions and coordinates were defined
B. subtilis, and B. linens. However, its MIC through 3D grid) and with blind docking
values of 100, 250 and 150 µg/mL indicated (when binding pocket was not defined and
a range of moderate to low level of activity. the whole receptor structure was targeted for
On the other hand, 1C showed maximum ac- docking). Thus, DHPS binding pocket was
tivity with MIC of 50, 100 and 150 µg/mL found perfectly selective for sulfonamides.
against E. coli, B. licheniformis and B. lin-
ens, respectively (Table 3).
In the second instance, an exhaustive
docking protocol was followed, which in-
volved both blind and focused docking of
our selected library of 7663 compounds
Molecular docking
The newly synthesized sulfonamide de- seeded with 672 conformers of 1A, 1B and
rivatives showed promising activity against 1C and also the native sulfonamide ligand
Gram+ and Gram- bacteria particularly bound with DHPS. The docked compounds
against E. coli, the Gram- bacterium, with were later ranked on the basis of their bind-
the exception of 1A, which was found effec- ing affinity. Interestingly, derivative 1C
tive only against B. linens. Most effective of ranked in top 40 compounds both in focused
these derivatives was 1C with best activity and blind docking out of a library of com-
(MIC 50 µg/ml) against E. coli. This is im- pounds which included popular sulfonamide
portant because E. coli is known to develop drugs such as sulfacetamide, sulfadiazine,
resistance rapidly against antibacterial drugs. sulfisoxazole, sulfisomidine, sulfaisodimi-
Addition of 1C in the list of drugs effective dine, sulfadoxine and sulfamethoxazole with
against this bacterium is quite significant. a binding affinity of -8.1 kcal/mol (Figure 5).
Against B. subtilis however, 1C showed no
activity.
Figure 6 shows the binding pose of 1C in
the pocket of DHPS. 1C exhibited strong hy-
Prior to the activity assays, computation- drogen bonds with binding pocket residues
al studies involving molecular docking were Arg63 and Ser219 involving nucleophilic
undertaken to investigate structural and func- oxygen of the sulfonyl group and nitrogen of
tional basis of antibacterial activity of our the amino group. Whereas, strong hydropho-
newly synthesized sulfonamide derivatives bic interaction was also exhibited by other
by estimating in silico binding affinities and residues of the binding pocket which include
binding conformations. Firstly, the native Ile20, Pro64, Ile117, Phe 190, Lys221,
sulfonamide ligand was docked against Ser219, Gly227 and His257.
DHPS structure at MOE. The ligand occu-
pied the DHPS binding pocket in exactly
Table 3: Minimum Inhibitory Concentration (MIC) of 1A, 1B, and 1C against various bacterial strains
Minimum Inhibitory Concentration (MIC) µg/ml
Compounds
Bacterial strains
E. coli
--
B. subtilis
--
B. licheniformis
--
B. linens
100
1A
1B
1C
100
50
50
250
--
50
--
100
50
150
150
50
Sulfamethazole (Positive Control)
Nutrient Broth (Negative Control)
--
--
--
--
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Figure 5: Ranges of binding energy exhibited by the compounds in the library. Each histogram repre-
sents fraction of the compound library in percent (%) exhibiting the corresponding range of binding
energy at the x-axis; the values are shown in positive. 1C with a binding energy of 8.1 kcal/mol was
found in the most favorable range (8.1-8.5 kcal/mol) enriching in the top 0.57 % of the library.
Figure 6: 1C bound in DHPS binding pocket. A: DHPS residues exhibiting multiple interactions with
1C, inhibiting its PABA binding pocket. Green dotted lines represent hydrogen bonds between Arg63
and oxygen of sulfonyl group, and between Ser219 and -NH group of 1C. B: 2D representation of
DHPS in complex with 1C. Residues are represented in three letter code with their position. Arrows in
green dotted lines represent hydrogen bonds with donor at the base and acceptor at the arrow head.
Polar and hydrophobic residues are shown with purple and green interiors respectively; the basic resi-
dues are shown in blue rings. Differences in solvent accessible surface area for 1C atoms and DHPS
residues are plotted as blue smudge and turquoise halo, respectively.
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EXCLI Journal 2018;17:169-180 – ISSN 1611-2156
Received: October 17, 2017, accepted: January 29, 2017, published: February 01, 2018
1B also exhibited appreciable interaction
This study reports three novel sulfona-
to the binding pocket of DHPS. Strong hy- mide derivatives which showed activity
drogen bond between Arg255 and the oxy- against both Gram+ and Gram- bacterial
gen of sulfonyl group was observed. In addi- pathogens. 1A showed moderate level activi-
tion to this, residue Arg63 exhibited arene- ty against B. linens. 1B was active against E.
cation interaction with the methyl benzene- coli, B. subtilis and B. linens showing mod-
sulfonamide group of 1B (Figure 7). Binding erate to low level activity. 1C was the most
score of 1B with binding pocket of DHPS active sulfonamide derivative with a high
was observed to be -5.4 kcal/mol. Other level activity against E. coli and moderate
binding pocket residues Ile20, Asn22, Glu60, level activity against B. licheniformis and B.
Ser61, Thr62, Asp96, Phe190, Ser219, linens (Tables 1&2). The derivatives have
Lys221, Asp220, Ser222 and Arg235 were demonstrated appreciable structural and
also found interacting with 1B.
functional properties to inhibit the PABA
1A exhibited arene-hydrogen bond inter- binding pocket of bacterial DHPS with opti-
action with binding pocket residue, His257, mum values of binding energy (Figures 6-8).
while its binding energy was found to be -4.2 Of a particular importance is 1C which en-
kcal/mol. His257 being a basic residue usu- riched in top 0.57 % of the compound library
ally participates in hydrogen bonding by ac- ranked in order of the binding energy when
cepting protons. Other binding pocket resi- docked against DHPS (Figure 5). Surprising-
dues exhibiting hydrophobic interactions ly, 1C did not show any activity against B.
were Ile20, Asn22, Ser27, His43, Arg63, subtilis.
Arg220 and Asp258 (Figure 8).
Figure 7: 1B bound in DHPS in binding pocket. A: DHPS residues exhibiting multiple interactions with
1B. Green dotted lines represent hydrogen bond between Arg255 and oxygen of sulfonyl group of 1B
and arene-cation interaction between Arg63 and aromatic ring of methyl benzenesulfonamide group.
B: 2D representation of DHPS in complex with 1B. Residues are represented in three letter code with
their position. Arrows in green dotted lines represent hydrogen bonds with donor at the base and ac-
ceptor at the arrow head. Polar and hydrophobic residues are shown with purple and green interiors
respectively; the acidic and basic residues are differentiated by red and blue rings respectively. Differ-
ences in solvent accessible surface area for 1B atoms and DHPS residues are plotted as blue smudge
and turquoise halo respectively.
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EXCLI Journal 2018;17:169-180 – ISSN 1611-2156
Received: October 17, 2017, accepted: January 29, 2017, published: February 01, 2018
Figure 8: 1A bound in binding pocket of DHPS. A: Green dotted lines represent arene-hydrogen bond
between His257 and 1A. B: 2D representation of DHPS in complex with 1A. Residues are represent-
ed in three letter code with their position. Arrows in green dotted lines represent hydrogen bonds with
donor at the base and acceptor at the arrow head. Polar and hydrophobic residues are shown with
purple and green interiors respectively; the acidic and basic residues are differentiated by red and blue
rings respectively. Differences in solvent accessible surface area for 1A atoms and DHPS residues
are represented as blue smudge and turquoise halo respectively.
Owing to their prolonged usage, bacteria structural and functional affinities and their
have developed resistance against reputed MIC values against a set for Gram+ and
sulfonamide drugs. Thus their capacity to in- Gram- bacteria. To the best of our
hibit microbial pathways has been gradually knowledge, these derivatives, their synthesis
compromised (Sköld, 2000). Ligand based and physico-chemical properties along with
strategies have been widely employed to dis- computational docking investigations and in
cover active sulfonamide derivatives. A vitro antimicrobial studies against the subject
number of research studies have sought to bacterial species have not been reported be-
develop novel sulfonamide derivatives fore. The reported derivatives exhibited sig-
through structure aided optimization of al- nificant antimicrobial properties against bac-
ready known sulfonamide scaffolds to teria. 4-methyl-N-(2-nitrophenyl) benzene-
achieve maximum biological activity and sulfonamide (1C) was found highly active
minimum microbial resistance (Ezabadi et against E. coli along with B. licheniformis
al., 2008; Kamel et al., 2010; Zoumpoulakis and B. linens as indicated by its high MIC
et al., 2012; Mondal et al., 2015). Thus new and binding energy values. This was fol-
sulfonamide derivatives may inhibit the tar- lowed by N-(2-hydroxyphenyl)-4-methyl
get enzymes as well as decoy the bacterial benzenesulfonamide (1B) which showed
resistance mechanisms. Designed through moderate to low activity against E. coli, B.
ligand based approach, three novel sulfona- subtilis and B. linens; whereas 4-chloro-N-
mide derivatives (1A, 1B and 1C) with sub- [(4-methylphenyl) sulfonyl]- N-propyl ben-
stantial drug potential are presented for fur- zamide (1A) was found moderately active
ther in vivo and clinical verification.
against B. linens. Thus 1C was found most
active derivative and it may serve as an ef-
fective drug particularly against E. coli relat-
ed pathogenesis.
CONCLUSION
This study describes synthesis, structure
and physico-chemical properties of three
novel sulfonamide derivatives with their
179

EXCLI Journal 2018;17:169-180 – ISSN 1611-2156
Received: October 17, 2017, accepted: January 29, 2017, published: February 01, 2018
Nasr T, Bondock S, Eid S. Design, synthesis, antimi-
crobial evaluation and molecular docking studies of
some new 2, 3-dihydrothiazoles and 4-thiazolidinones
containing sulfisoxazole. J Enzyme Inhib Med Chem.
2016;31:236-46.
Conflict of interest
The authors declare that they have no
conflict of interest.
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