Synthesis, pharmacological activity evaluation and molecular modeling of new polynuclear heterocyclic compounds containing benzimidazole derivatives

Article abstract of DOI:10.1007/s12272-012-1204-6

Novel heterocyclic compounds containing benzimidazole derivatives were synthesized from 2-(1Hbenzimidazol-2-yl) acetonitrile (1) and arylhydrazononitrile derivative 2 was obtained via coupling of 1 with 4-methyl phenyldiazonium salt, which was then reacted with hydroxylamine hydrochloride to give amidooxime derivative 3. This product was cyclized into the corresponding oxadiazole derivative 4 upon reflux in acetic anhydride. Compound 4 was refluxed in DMF in the presence of triethylamine to give the corresponding 5-(1H-benzimidazol-2-yl)-2-p-tolyl-2H-1,2,3-triazol-4-amine 6. Treatment of compound 6 with ethyl chloroformate afforded 2,6-dihydro-2-(4-methylphenyl)-1,2, 3-triazolo[4″,5″-4′,5′]pyrimido[1,6-a] benzimidazole-5(4H)-one (8). 1,2-bis(2-cyanomethyl-1H-benzimidazol-1-yl)ethane- 1,2-dione (10) was synthesized via the condensation reaction of 2-(1H-benzimidazol-2-yl) acetonitrile (1) and diethyloxalate. The reactivity of compound 10 towards some diamine reagents was studied. The in vitro antimicrobial activity of the synthesized compounds was investigated against several pathogenic bacterial strains such as Escherichia coli O157, Salmonella typhimurium, E. coli O119, S. paratyphi, Pseudomonas aeruginosa, Staphylococcus aureus, Listeria monocytogenes and Bacillus cereus. The results of MIC revealed that compounds 12a-c showed the most effective antimicrobial activity against tested strains. On the other hand, compounds 12a, b exhibited high activity against rotavirus Wa strain while compounds 12b, c exhibited high activity against adenovirus type 7. In silico target prediction, docking and validation of the compounds 12a-c were performed. The dialkylglycine decarboxylase bacterial enzyme was predicted as a potential bacterial target receptor using pharmacophorebased correspondence with previous leads; giving the highest normalized scores and a high correlation docking score with mean inhibition concentrations. A novel binding mechanism was predicted after docking using the MOE software and its validation.

Full text of DOI:10.1007/s12272-012-1204-6

Arch Pharm Res Vol 35, No 12, 2063-2075, 2012
DOI 10.1007/s12272-012-1204-6
Synthesis, Pharmacological Activity Evaluation and Molecular Modeling
of New Polynuclear Heterocyclic Compounds Containing Benzimida-
zole Derivatives
Fatma A. Bassyouni1, Tamer S. Saleh2, Mahmoud M. ElHefnawi3, Sherein I. Abd El-Moez4,
Waled M. El-Senousy5, and Mohamed E. Abdel-Rehim6
1Chemistry of Natural and Microbial Products Department and Pharmaceutical Research Department, Center of Excel-
2
lence for Advanced Sciences, National Research Centre, 12622, Cairo, Egypt, Green Chemistry Department and Phar-
maceutical Research Department, Center of Excellence for Advanced Sciences, National Research Centre, 12622, Cairo,
3
Egypt, Informatics and Systems Department and Biomedical Informatics and Chemo Informatics Group, Division of
Engineering Research and Centre of Excellence for Advanced Sciences, National Research Centre, 12622, Cairo, Egypt,
5
4Microbiology and Immunology Department, National Research Centre, 12622, Cairo, Egypt, Water Pollution Research
Department, Environmental Research Division and Food-Borne Viruses Group, Center of Excellence for Advanced Sci-
6
ences, National Research Centre, 12622, Cairo, Egypt, and Department of Analytical Chemistry, Stockholm University,
10691 Stockholm, Sweden
(Received July 1, 2011/Revised August 19, 2011/Accepted September 15, 2011)
Novel heterocyclic compounds containing benzimidazole derivatives were synthesized from 2-(1
benzimidazol-2-yl) acetonitrile ( ) and arylhydrazononitrile derivative was obtained via cou-
pling of with 4-methyl phenyldiazonium salt, which was then reacted with hydroxylamine
hydrochloride to give amidooxime derivative . This product was cyclized into the corresponding
oxadiazole derivative upon reflux in acetic anhydride. Compound was refluxed in DMF in the
presence of triethylamine to give the corresponding 5-(1 -benzimidazol-2-yl)-2- -tolyl-2 -1,2,3-
triazol-4-amine . Treatment of compound with ethyl chloroformate afforded 2,6-dihydro-2-(4-
methylphenyl)-1,2,3-triazolo[4'',5''-4',5']pyrimido[1,6-a]benzimidazole-5(4 )-one ( ). 1,2-bis(2-cya-
nomethyl-1 -benzimidazol-1-yl)ethane-1,2-dione (10) was synthesized via the condensation reac-
tion of 2-(1 -benzimidazol-2-yl) acetonitrile ( ) and diethyloxalate. The reactivity of compound 10
H-
1
2
1
3
4
4
H
p
H
6
6
H
8
H
H
1
towards some diamine reagents was studied. The in vitro antimicrobial activity of the synthesized
compounds was investigated against several pathogenic bacterial strains such as Escherichia coli
O157, Salmonella typhimurium, E. coli O119, S. paratyphi, Pseudomonas aeruginosa, Staphylo-
coccus aureus, Listeria monocytogenes and Bacillus cereus. The results of MIC revealed that com-
pounds 12a
other hand, compounds 12a
pounds 12b exhibited high activity against adenovirus type 7. In silico target prediction, dock-
ing and validation of the compounds 12a were performed. The dialkylglycine decarboxylase
-
c
showed the most effective antimicrobial activity against tested strains. On the
,
b
exhibited high activity against rotavirus Wa strain while com-
,
c
-c
bacterial enzyme was predicted as a potential bacterial target receptor using pharmacophore-
based correspondence with previous leads; giving the highest normalized scores and a high corre-
lation docking score with mean inhibition concentrations. A novel binding mechanism was pre-
dicted after docking using the MOE software and its validation.
Key words: Benzimidazole derivatives, Arylhydrazone derivatives, Quinoxaline derivatives,
Antiviral activity, Antimicrobial and antifungal activities, Molecular modeling
Correspondence to: Fatma A. Bassyouni, Chemistry of Natural
and Microbial Products Department and Pharmaceutical
Research Department, Center of Excellence for Advanced Sci-
ences, National Research Centre, 12622, Cairo, Egypt
Tel: 20-111-859-6967, Fax: 20-2-333-70913
E-mail: fatma.nrc@hotmail.com
2063

2064
F. A. Bassyouni et al.
Sigma-Aldrich and Merck. Melting points were deter-
mined in open capillary tubes on an Electro thermal
9100 digital melting point apparatus and are uncor-
rected. The infrared spectra were recorded in potassium
bromide disks on a pye Unicam SP 3300 and Shimadzu
Selected by Editors
INTRODUCTION
A wide variety of benzimidazole derivatives have FT-IR 8101 PC infrared spectrophotometers. The NMR
been described for their chemotherapeutic importance spectra were recorded on a Varian Mercury VX-300
(Cook, 1990; Boiani and Gonzalez, 2005). Recently, NMR spectrometer. 1H-NMR (500 MHz) and 13C NMR
nitrogen heterocyclic compounds have been gaining (75.46 MHz) were run in CDCl3 or dimethylsulphoxide
special interest because they constitute an important (DMSO-d6). Mass spectra were recorded on a Shimadzu
class of natural and non natural products, many of GC/MS-QP 1000 EX mass spectrometer at 70 e.V.
which exhibit useful biological activities. Oxadiazole Elemental analyses were carried out at the Micro
derivatives are well known to have a wide range of analytical Center of Cairo University, Giza, Egypt. 2-
biological activities, examples of such activities are (1
H-benzimidazol-2-yl) acetonitrile (1) was prepared
analgesic, anti-inflammatory (Sanjeevkumar et al., according to the reported literatures (Buchi et al.,
2010), antimicrobial (Shivi and Monika, 2011) and anti- 1960).
parasitic effects (Haugwitz et al., 1985) but triazoles
and their derivatives are found to be associated with
various biological activities (Brik et al, 2005; Whiting
et al., 2006). In addition, different types of quinoxaline
Synthesis of
hydrazonoyl cyanide (2)
A cold solution of 4-methyl phenyldiazonium salt (10
p-tolyl-1H-benzimidazole-2-carbo-
including their fused ring derivatives have been re- mmol) was prepared by adding a solution of sodium
ported to display diverse pharmacological activities nitrite (1 g into 10 mL H2O) to a cold solution of
p
-
(Sarges et al., 1990; Bertelli et al., 1998; Carta et al., toulidine hydrochloride (10 mmol) with stirring. The
2001; Jaso et al., 2003). Many papers have been published resulting solution of aryldiazonium (10 mmol) was
dealing with 2-arylhydrazones as precursors to heteroa- then added to a cold solution of 2-(1
H-benzimidazol-2-
romatics (Fan and Katritzky, 1996; Al-Saleh et al., yl) acetonitrile (
1) (10 mmol) in absolute ethanol (50
2004; Ghozlan et al., 2007). Several of benzimidazole mL) containing sodium acetate (1 g into 10 mL H2O).
analogs have been synthesized and screened for their The mixture was stirred at room temperature for 2 h
pharmacological activity such as antibacterial and anti- and the solid product was collected by filtration and
fungal (Podunavac-Kuzmanoviæ et al., 1999; Goker et crystallized from absolute ethanol. Yield 85%. Light
al., 2000; Khalafi-Nezhad et al., 2005; Nguyen et al., yellow crystals; m.p. 242-244oC; Anal. Calcd. for C16H13N5:
2005; Ayhan-Kilcigil and Altanlar, 2006; Podunavac- C, 69.80; H, 4.76; N, 25.44. Found: C, 69.92; H, 4.70;
Kuzmanoviæ et al., 2007) and they are present in N, 25.35. 1H-NMR (500 MHz, DMSO-d6):
numerous anti-parasitic, anti-tumor, anti-diabetic, anti- CH3), 7.13-7.78 (8H, m, Ar-H), 10.73 (1H, s, NH, D2O-Ex-
δ 2.20 (3H, s,
asthmatic and antiviral agents (Garuti et al., 1999; Valdez changeable), 11.45 (1H, s, NH, D2O-Exchangeable); 13C-
et al., 2002; Vijayakumar and Jafar, 2010). Also, some NMR (DMSO-d6):
of them are known to exhibit appreciable anti-proto- 119.3, 122.9, 124.5, 131.2, 132.1, 140.5, 141.5, 151.3; IR
zoal activities (Kazimierczuk et al., 2002) as well as in (KBr)
= 3329, 3349 (2NH), 2221 (C
N) cm−1; MS: m/
= 275 [M+].
δ 20.9 (CH3), 112.3, 113, 114.5, 118.9,
ν
≡
vitro anti-HIV activities (Akbay et al., 2003).
z
Motivated by the afore-mentioned findings and in
the course of our interest in the synthesis of a wide range
of heterocyclic systems for biological screening in our
laboratory (Fatma et al., 2009; Hanaa et al., 2009; Hatem
et al., 2010; Eslam et al., 2010; Tamer et al., 2010), we
Preparation of 2-(1H-Benzimidazol-2-yl)-N-hy-
droxy-2-(4-methylphenyl-hydrazono)-acetami-
dine (3)
Hydroxylamine hydrochloride (0.1 mol) was added
describe here a facile synthesis of different novel hetero- to a solution of
cyclic compounds containing benzimidazole deriva- drazonoyl cyanide (
tives and tested them for their antimicrobial and anti- mL), then anhydrous sodium acetate (0.1 mol) was add-
N'-p-tolyl-1H-benzimidazole-2-carbohy-
2) (0.1 mol) in absolute ethanol (50
viral activities with study their molecular modeling.
MATERIALS AND METHODS
Chemistry
ed and the reaction mixture was heated under reflux
with stirring for 1 h (the reaction mixture was moni-
tored by TLC), the mixture was left to cool to room tem-
perature. The solid precipitated was filtered and
crystallized from absolute ethanol. Yield 80%; m.p.
Reagents used for the synthesis were purchased from 187-189oC; Anal. Calcd. for C16H16N6O: C, 62.32; H, 5.23;

Pharmacological Activity of New Heterocyclic Benzimidazoles
2065
N, 27.26. Found: C, 62.39; H, 5.20; N, 27.22; 1H-NMR collected by filtration and crystallized from petroleum
(500 MHz, DMSO-d6): 2.22 (3H, s, CH3), 5.83 (2H, s, ether (60-80) to give yellow crystals of product (Yield
NH2), 6.19 (2H, s, NH2), 7.25-7.76 (8H, m, Ar-H), 10.73 78%).
δ
5
(1H, s, NH, D2O-Exchangeable), 11.45 (1H, s, NH, D2O-
Exchangeable), 12.46 (1H, s, OH, D2O-Exchangeable);
Method B: (10 mmol) of 1,2,4-oxadiazole derivative
was added to an ethanolic sodium ethoxide solution
4
13C-NMR (DMSO-d6):
δ
20.9 (CH3), 112.3, 113, 114.5, [prepared from sodium metal (0.23 g) in (50 mL) of
118.9, 119.3, 123.9, 124.5, 131.2, 138.2, 143.6, 145.1, absolute ethanol]. The reaction mixture was heated
152.6, 155.9; IR (KBr) = 3411 (OH), 3252 (NH2), under reflux for 4 h. The precipitated formed was filter-
3310, 3359 (2NH) cm−1; MS: m/z = 308 [M+].
ed and crystallized from petroleum ether (60-80) to
ν
give yellow crystals of compound 5. Yield 74%; m.p.
280-282oC; Anal. Calcd. for C18H16N6O: C, 65.05; H,
4.85; N, 25.29. Found: C, 65.13; H, 4.75; N, 25.19; 1H-
NMR (300 MHz, DMSO-d6): δ 2.08 (3H, s, CH3), 2.38
Synthesis of 3-((1
hydrazono)methyl)-5-methyl-1,2,4-oxadiazole (4)
A mixture of equimolecular amounts of compound
H-benzimidazol-2-yl)(2-p-tolyl-
3
(10 mmol) and acetic anhydride (1.02 g, 10 mmol) in (3H, s, CH3), 7.28-7.89 (8H, m, Ar-H), 10.73 (1H, s, NH,
the presence of acetic acid (20 mL) was heated under D2O-Exchangeable), 11.25 (1H, s, NH, D2O- Exchange-
reflux for 2 h. The reaction mixture was monitored by able); 13C-NMR (DMSO-d6):
δ 20.9 (CH3), 24.7, 114.5,
TLC. After cooling, the mixture was poured onto ice- 116.1, 122.6, 122.9, 123.9, 124.5, 131.2, 140.9, 142.6,
water. The solid formed was collected by filtration and 144.6, 147.5, 148.2, 149.2, 152.6, 155.9, 175.3 (C=O);
crystallized from absolute ethanol to give yellow IR (KBr)
ν = 3324, 3374 (2NH), 1620-1640 (C=N), 1685
crystals. Yield 76%; m.p. 247-249oC; Anal. Calcd. for (CO) cm−1.
C18H16N6O: C, 65.05; H, 4.85; N, 25.29. Found: C,
65.17; H, 4.79; N, 25.23; 1H-NMR (500 MHz, DMSO-d6):
Synthesis of 2,6-dihydro-2-(4-methylphenyl)-1,
2,3-triazolo[4'',5''-4',5'-pyrimido[1,6-a]benzimi-
dazole-5(4H)-one (8)
δ
1.90 (3H, s, CH3), 2.22 (3H, s, CH3), 7.22-7.87 (8H,
m, Ar-H), 10.73 (1H, s, NH, D2O-Exchangeable), 11.45
(1H, s, NH, D2O-Exchangeable); 13C-NMR (DMSO-d6):
δ
A suspension of compound 6 (10 mmol) in dry pyri-
20.9 (CH3), 24.7, 113.1, 114.5, 118.9, 119.3, 122.9, 124.5, dine (20 mL) was cooled in an ice-bath to 0oC. Ethyl
130.3, 131.2, 132.1, 140.5, 141.5, 146.6, 151.4, 161.1; IR chloroformate (2.0 mL, 18 mmol) was added dropwisly
(KBr)
ν
= 3304, 3365 (2NH) cm−1; MS: m/z = 332 [M+]. over a period of 30 min. The reaction mixture was then
heated under reflux for 2 h, with dissolution occurring
first, then precipitation formed after 15 min. The reac-
tion mixture was monitored by TLC. Following this,
(10 the mixture was left to cool to room temperature. The
Synthesis of 5-(1
-1,2,3-triazol-4-amine (6)
A mixture of equimolar amounts of compound
mmol) and of N-dimethylformamide (DMF) (10 mmol) precipitate formed was collected by filtration, washed
H-benzimidazol-2-yl)-2-p-tolyl-
2H
3
N,
with a few drops of TEA was heated under reflux for 2 with absolute ethanol (30 mL) and dried, then crystal-
h (The reaction mixture was monitored by TLC). The lized from dimethylformamide/ethanol (3:7) to afford
reaction mixture was left to cool to room temperature. compound
The precipitated solid, so-formed, was washed with C17H12N6O: C, 64.55; H, 3.82; N, 26.57. Found: C, 64.67;
8
. Yield 65%; m.p. >300oC; Anal. Calcd. for
1
water (50 mL), then filtered and crystallized from H, 3.70; N, 26.47; H-NMR (500 MHz, DMSO-d6):
δ
absolute ethanol/DMF (9:1). Yield 84%; m.p. 230-232oC; 2.41 (3H, s, CH3), 7.04-7.78 (8H, m, Ar-H), 11.99 (1H, br
Anal. Calcd. for C16H14N6: C, 66.19; H, 4.86; N, 28.95. s, NH, D2O-Exchangeable); 13C-NMR (75.4 MHz, DMSO-
Found: C, 66.25; H, 4.95; N, 28.86; 1H-NMR (500 MHz, d6):
δ
22.45 (CH3), 110.99, 111.10, 119.25, 121.48, 125.98,
2.26 (3H, s, CH3), 5.89 (2H, s, NH2), 6.84- 128.47, 133.12, 134.79, 135.72, 138.34, 143.11, 165.89
7.87 (8H, m, Ar-H), 10.73 (1H, s, NH, D2O- Exchange- (C=O); IR (KBr) = 3320 (NH), 1680 (C=O), 1630-1645
able); 13C-NMR (DMSO-d6): 20.9 (CH3), 114.5, 119.3, (C=N) cm−1; MS: m/z = 316 [M+].
122.9, 124.5, 131.2, 132.1, 135.5, 140.5, 141.5, 146.6,
154.4; IR (KBr)
= 3386 (NH), 3244 (NH2) cm−1.
DMSO-d6):
δ
ν
δ
ν
Synthesis of 1,2-bis(2-cyanomethyl-1
H-benzim-
idazol-1-yl)ethane-1,2-dione (10)
2-cyanomethyl benzimidazole
solved in MeOH (100 mL) and diethyl oxalate (2.26 g,
was heated 0.016 mol) was added in a (2:1) molar ratio. The solu-
1 (0.033 mol) was dis-
Synthesis of
-1,2,3-triazol-4yl)acetamide (5)
Method A: (10 mmol) of compound
N-(5-(1H-benzimidazol-2-yl)-2-p-tolyl-
2H
6
under reflux in the presence of acetic anhydride (10 tion was heated under reflux with stirring for 4 h, and
mmol) for 3 h. After cooling, the reaction mixture was then conc. HCl (6 mL) was added dropwisely with con-
poured onto crushed ice. The precipitated formed was stant stirring. The resulting crystalline product was

2066
F. A. Bassyouni et al.
filtered, washed thoroughly with n-hexane, dried under
vacuum and then crystallized from methanol. Yield
79%; m.p. 103-105oC; Anal. Calcd. for C20H12N6O2: C,
65.21; H, 3.28; N, 22.82. Found: C, 65.30; H, 3.15; N,
22.76; 1H-NMR (500 MHz, CDCl3):
δ
3.13 (4H, s, CH2),
7.73-7.85 (8H, m, Ar-H); IR (KBr) = 2219-2230
(C
N), 1684, 1695 (C=O) cm−1; MS: m/z = 368 [M+].
ν
≡
Reaction of compound 10 with diamino com-
pounds (11a-c): General procedure for the syn-
thesis of compounds (12a-c)
A mixture of compound 10 (10 mmol) and the appro-
priate diamino derivatives namely,
amine, 3,4-diaminobenzoic acid or pyridine-2,3-diamine,
compounds 11a (10 mmol) was added in absolute
o-phenylenedi-
-c
ethanol (25 mL) in the presence of few drops of TEA
was heated under reflux with stirring for 6-8 h. The
reaction mixture was monitored by TLC. The solid
precipitate was then filtered and crystallized from
Scheme 1. Synthesis of 1
H
-benzimidazole-2-carbohydra-
zonoly cyanide derivative (
2
) and (1
H-benzimidazole-2-yl)-
chloroform to give the corresponding compounds 12a
-
N-hydroxy-acetamidine derivative (
3
).
c
in 70-75% yield.
2'-(1,1'-(quinoxaline-2,3-diyl)bis(1H-benzimidazole-
2,1-diyl))diacetonitrile (12a)
(obtained via coupling reaction of 2-(1H-benzimidazol-
2-yl) acetonitrile
1 with 4-methyl phenyldiazonium salt)
Yield 70%; m.p. 144-146oC; Anal. Calcd. for C26H16N8: which was reacted with hydroxylamine hydrochloride
C, 70.90; H, 3.66; N, 25.44. Found: C, 70.80; H, 3.60; in the presence of ethanol/sodium acetate to afford
1
1
N, 25.35; H-NMR (500 MHz, CDCl3):
δ
ν
3.59 (4H, s, amidooxime
3 (Scheme 1). H-NMR of compound 3
CH2), 7.11-7.95 (12H, m, Ar-H); IR (KBr)
= 2215 (C N), revealed expected signal for an oxime OH at 12.46
≡
1620-1640 (C=N) cm−1; MS: m/z = 440 [M+].
ppm. The other two signals for hydrazone NH at 11.46
and amino protons also appear at 10.73 ppm. This
2,3-bis(2-(cyanomethyl)-1H-benzimidazol-1-yl)qui- may be interpreted by assuming that amidooximes
3
noxaline-6-carboxylic acid (12b)
exists in structures
The IR spectra of product
3
(I) or
3
(II) Fig. 1.
Yield 75%; m.p. 135-137oC; Anal. Calcd. for C27H16N8O2:
3 indicated the absence of
C, 66.94; H, 3.33; N, 23.13. Found: C, 66.82; H, 3.24; the cyano group absorption band and the presence of
1
N, 22.96; H-NMR (500 MHz, CDCl3):
δ 3.48 (4H, s, absorption band due to the presence of the NH2 group
CH2), 7.06-7.90 (11H, m, Ar-H); IR (KBr)
ν
= 3412 at 3252 cm−1, one band due to the OH group at 3411
(OH), 2221 (C
≡
N), 1625-1654 (C=N) cm−1; MS: m/z
=
cm−1, in addition to two bands at 3310, 3359 cm−1 due
to the presence of two NH groups. The mass spectra of
485 [M++1].
product
3 showed a peak corresponding to the mole-
2,2'-(1,1'-(pyrido[3,2-b]pyrazine-2,3-diyl)bis(1H- cular ion at m/z 308.
benzimidazole-2,1-diyl))diacetonitrile (12c)
Attempted cyclization of compound 3 via refluxing
Yield 72%; m.p. 150-152oC; Anal. Calcd. for C25H15N9:
C, 68.02; H, 3.42; N, 28.56. Found: C, 68.16; H, 3.34;
1
N, 28.48; H-NMR (500 MHz, CDCl3):
δ 3.55 (4H, s,
CH2), 7.10-7.90 (11H, m, Ar-H + Pyridine H); IR (KBr)
ν
= 2218 (C
≡
N), 1630-1645 (C=N) cm−1.
RESULTS AND DISCUSSION
Chemistry
The synthetic pathways adopted for the preparation
of the desired new compounds are illustrated in
Fig. 1. Stereoisomeric conformers of compound 3.
Schemes 1-3. The synthesis of arylhydrazononitrile
2

Pharmacological Activity of New Heterocyclic Benzimidazoles
2067
in acetic anhydride afforded the corresponding product (subsequent Boulton-Katritzky Rearrangement, 1996).
that can be assigned as arylhydrazono-1,2,4-oxadiazole Moreover, the cyclization of compound under reflux-
derivative (Scheme 2). The structure of product was ing condition in the presence of dimethylformamide
assigned on the basis of its elemental analyses and (DMF) and triethylamine afforded 1,2,3 triazole amine
spectrum data. The 1H-NMR spectrum of compound
via water elimination. Alzaydi (2009) established
revealed two singlet signals at 1.90 and 2.22 ppm that amidooxims cyclized into 1,2,3 triazoles under
due to two methyl group protons in addition to an aro- similar conditions. The IR spectrum of the compound
matic multiple at 7.22-7.87 ppm. Arylhydrazono-1,2,
showed an absorption band at 3244 cm−1 attributed to
4-oxadiazole derivative underwent thermal rearran- the NH2 group and another absorption band at 3386
gement into acetamido 1,2,3-triazole derivative
upon cm−1 due to NH group. However, it has been found that
refluxing in the presence of ethanolic sodium ethoxide the reaction of product with ethyl chloroformate in
3
4
4
4
6
δ
δ
6
4
5
6
Scheme 2. Synthesis of 1H-benzimidazole-5-methyl-1,2,4-oxadiazole derivative (4) and 1H-benzimidazole-1,2,3-triazole
derivatives ( and ).
5,
6,
8
9

2068
F. A. Bassyouni et al.
the presence of pyridine and heating under reflux TEA under refluxing condition afforded one product
afforded one product identified as 2,6-dihydro-2-(4- each time and they were identified as 2,2'-(1,1'-(qui-
methylphenyl)-1,2,3-triazolo[4'',5''-4',5']pyrimido[1,6-a]
benzimidazole-5(4H)-one ( ).
This conclusion was further confirmed chemically zol-1-yl)quinoxaline-6-carboxylic acid (12b) and 2,2'-
via the acylation reaction of compound with acetic (1,1'-(pyrido[3,2-b]pyrazine-2,3-diyl)bis(1H-benzimida-
anhydride afforded an identical product in all respects zole-2,1-diyl))diacetonitrile (12c), respectively (Scheme
(m.p., mixed m.p. and IR) with those corresponding to 3). The structures of compounds 12a were establi-
noxaline-2,3-diyl)bis(1H-benzimidazole-2,1-diyl))diace-
8
tonitrile (12a), 2,3-bis(2-(cyanomethyl)-1H-benzimida-
6
-c
product
Compound
its tautomeric enol-form
of the isolated product revealed the oxo-form
the existence of strong absorption peaks in the region of the same compound exhibits singlet signals at
of
= 1680 cm−1 corresponding to the keto group and ppm due to the presence of two methylene protons in
NH absorption band at 7.11-
= 3320 cm−1. The isolated addition to aromatic protons as a multiple at
products and were performed by their elemental 7.95.
analyses and spectral data. The mass spectra of the
isolated products such as compound showed a peak
corresponding to the molecular ion at m/z 360, and
compound showed a molecular ion peak at m/z 316.
Furthermore, treatment of 2-(1
acetonitrile ( ) with dietyloxalate in the presence of and adenovirus type 7 in vitro using the end point
methanol/conc. HCl and refluxed in a 2:1 molar ratio titration technique.
afforded only one product identified as 1,2-bis(2-cya- Cytotoxicity assay: All samples (100 mg) were
nomethyl-1 -benzimidazol-1-yl)ethane-1,2-dione (10 dissolved in 500 L of ethanol or acetic acid. Cell mono-
5
(Scheme 2).
shed on the basis of their elemental analysis and spec-
8
may be formulated as the oxo-form
8
or tral data. For example, the structure of compound 12a
9
(Scheme 2). The IR spectra is supported by its mass spectrum which shows a
due to molecular ion peak at m/z 440. The 1H-NMR spectrum
3.59
8
δ
ν
ν
δ
5,
6
8
5
Biological activities
In vitro antiviral activity
The synthesized compounds 2, 3, 4, 5, 10 and 12a-c
8
H-benzimidazol-2-yl) were evaluated for their effects on rotavirus Wa strain
1
H
)
µ
(Scheme 3). The structure of the latter product was layers Hep2 and MA104 (obtained from The Holding
established on the basis of its elemental analysis and Company for Biological Products & Vaccines VACSERA)
spectrum data. The IR spectrum of product 10 revealed were trypsinized, and after addition of culture medium,
cyano absorption bands near 2219-2230 cm−1 and car- they were plated in a 96-well flat bottomed plate
bonyl absorption bands near 1684 and1695 cm−1. In (Greiner-Bio one) with 5 103 cells per well for both
×
addition to its mass spectrum revealed a peak corres- cell lines. After 24 h incubation, each diluted tested
ponding to the molecular ion at m/z 368. materials (10 fold dilutions of decontaminated samples
Treatment of 1,2-bis(2-cyanomethyl-1 -benzimida- using 12 L of 100X of antibiotic, antimycotic mixture
zol-1-yl)ethane-1,2-dione (10) with -phenylenediamine added to 500 L of each sample) was added to the appro-
11a), 3,4-diaminobenzoic acid (11b) or pyridine-2,3- priate wells and the plates were further incubated for
diamine (11c) in the presence of absolute ethanol and 48 h at 37oC in a humidified incubator with 5% CO2.
H
µ
o
µ
(
Scheme 3. Synthesis of 1,2-bis(1 -benzimidazole-1-yl)ethan-1,2-dione derivative (10), quinoxaline-bis(1
H
H-benzimidazole)
derivatives (12a ) and pyrido-bis(1H-benzimidazole-2,1-diyl)diacetonitrile derivative (12c).
,b

Pharmacological Activity of New Heterocyclic Benzimidazoles
2069
The supernatants were removed from the wells and and untreated uninfected cells, respectively.
cell viability was evaluated using microscopical examin-
Data analysis: The CC50 and IC50 for each compound
ation, trypan blue and the MTT techniques (Mosmann, were obtained from dose-effect-curves. The CC50 and
1983; Walum et al., 1990; Simões et al., 1999). The IC50 are the averages of four assays with five concen-
results are obtained from triplicate assays with at trations within the inhibitory range of the compounds.
least 5 extract concentrations.
The therapeutic index (i.e. selective index) is defined
Antiviral testing: The in vitro antiviral method was as the toxic dose of a drug for 50% of the population
used to estimate the inhibition of the cytopathogenic (TD50) divided by the minimum effective dose for 50%
effect (CPE) of the pure compounds on MA104 and of the population (ED50).
HEP-2 cell monolayers infected with rotavirus
−Wa
Compounds 2, 3, 4, 5 and 12a-c were evaluated
strain (ATCC VR-2018, obtained by prof. Dr. Albert against Hep2 and MA104 based assay by determining
Bosch, University of Barcelona, Spain) and adenovirus CC50 and IC50 as described previously in Tables III
type 7 (obtained by prof. Dr. Ali Fahmy, Vacsera, Egypt) and IV.
using the end-point titration technique (EPTT) (Vlietinck
In the series of the tested compounds 2, 3, 4, 5, 10
et al., 1995). Confluent monolayer of MA104 and HEP- and 12c showing no significant selective activity
2 cells was grown in 96-well microtiter plates, which against rotavirus Wa strain could be identified while
were infected with serial ten-fold dilutions of rotavirus the tested compounds 2, 3, 4, 5, 10 and 12a showing
Wa strain and adenovirus type 7 respectively. The no significant selective activity against adenovirus
viruses were allowed to be adsorbed for 60 min at type 7 could be identified as demonstrated in Tables I
37oC, maintenance medium, supplemented with 2% and II. Among them, compounds 12a and 12b exhibit-
serum and antibiotics were added. The plates were ed potent antiviral activities against rotavirus Wa
incubated at 37oC, and the viral cytopathogenic effect strain and compounds 12b and 12c exhibited potent
was recorded by light microscopy after 2 to 8 days.
antiviral activities against adenovirus type 7 as shown
in Tables I and II.
MTT assay
However, the antiviral activity is accompanied by
Antiviral colorimetric assay: Both MA104 and CC50 for the Hep2 and MA104 cell lines, the cytotoxicity
Hep2 cell monolayers were grown in 96-well microtiter of the tested compounds on both cell lines was within
plates. Dilutions of the extracts, prepared as described the same range (Tables III and IV). Screening of IC50
above for the EPTT assay, were added 1 h before viral values revealed that compounds 12a and 12b showed
infection. Ten infectious doses of virus were added to significant potent activities, whereas, compounds
2, 3,
each well and incubated at 37oC in a humidified 5%
4, 5,
10 and 12c were inactive against rotavirus Wa
CO2 atmosphere for 48 h. Controls consisted of untre- strain but compounds 12b and 12c showed significant
ated infected, treated uninfected and untreated uninfect- potent activities against adenovirus type 7, whereas
ed cells. Cell viability was evaluated by the MTT colori- compounds 2, 3, 4, 5, 10 and 12a were inactive against
metric technique according to the Mosmann method adenovirus type 7. The therapeutic indexes for com-
(Mosmann et al., 1983). Briefly, the supernatants were pound 12b were 5.85 and 6.00 for rotavirus Wa strain
removed from the wells and 28 µL of an MTT (Sigma) and adenovirus type 7 respectively. The therapeutic
solution (2 mg/mL in PBS) was added to each well. index of compound 12a was 6.6 for rotavirus Wa strain
The plates were incubated for 1.5 h at 37oC, and 130
Table I. Minimal non-toxic dose and anti-rotavirus Wa
µL of DMSO-d6 was added to the wells to dissolve the
strain activity of tested compounds
2, 3, 4, 5, 10 and 12a-
MTT crystals. The plates were placed on a shaker for
15 min and the optical density was determined at 492
nm (OD492) on a multiwall spectrophotometer.
c
on MA104 cells determined by the end-point titration
technique
Maximum non
toxic dose
Viral reduction
factor
Tested compounds
The 50% cytotoxic concentration (CC50) of the test
extract was defined as the concentration that reduce
the OD492 of treated uninfected cells to 50% of that of
untreated uninfected cells. The 50% antiviral effective
concentration, i.e. 50% inhibitory concentration of the
viral effect (IC50) was expressed as the concentration
that achieves 50% protection of treated infected cells
from viruses induced destruction. The percent protection
2
50
µg/mL
1
3
4
5
10
12a
12b
12c
50
50
50
50
25
25
25
µg/mL
µg/mL
µg/mL
µg/mL
µg/mL
µg/mL
µg/mL
1
1
1
1
102
102
1
was calculated as [(A-B)/C-B)]
C were the OD492 of treated infected, untreated infected,
× 100, where A, B and

2070
F. A. Bassyouni et al.
Table II. Minimal non-toxic dose and anti-adenovirus
method technique (Sgouras et al., 2004; Wiart, 2007)
using two different concentrations of the compounds
(100 and 200 µg/mL) dissolved in 1 mL dimethyl sul-
type 7 activities of tested compounds
2, 3, 4, 5, 10 and
12a on Hep2 cells determined by the end-point titration
-
c
technique
phoxide (DMSO-d6) as a qualitative method for studying
the antimicrobial activity of the tested compounds
against the following tested stains; bacterial strains:
Escherichia coli O157, Salmonella typhimurium, E.
coli O119, S. paratyphi, Pseudomonas aeruginosa, Sta-
phylococcus aureus, Listeria monocytogenes, Bacillus
cereus. Fungal strains are Candida albicans and Asper-
Maximum non
toxic dose
Viral reduction
factor
Tested compounds
2
3
4
50
50
50
50
50
25
25
25
µg/mL
µg/mL
µg/mL
µg/mL
µg/mL
µg/mL
µg/mL
µg/mL
1
1
1
1
1
5
10
12a
12b
12c
gillus niger. As control, positive Ciprofloxacin (100
mL) was used as standard antibacterial, and flucona-
zole (100 g/mL) was used as standard antifungal while
µg/
1
101
101
µ
dimethyl sulphoxide (DMSO-d6) was used as control
negative.
Table III. Anti-rotavirus Wa strain activity of the tested
compounds 10 and 12a on MA104 Cells deter-
mined by the MTT method
The results of the antibacterial and antifungal activ-
ities are shown in Table V, respectively. The results
revealed that most of the synthesized compounds
exhibited variable degrees of inhibition against the
tested microorganisms. Susceptibility of the bacterial
and fungal isolates to our synthesized compounds was
investigated by measuring their inhibitory effect on
the growth of microorganisms compared to the solvent
used.
2,
3,
4,
5
,
-c
Tested
compounds
CC50
g/mL)
IC50
Therapeutic
index
(
µ
(
µg/mL)
2
3
4
142.7
156.5
153.4
137.5
164.2
104.4
101.8
108.6
ND
ND
ND
ND
ND
15.8
17.4
ND
ND
ND
ND
ND
ND
6.6
5
10
12a
12b
12c
Antibacterial activity
5.85
ND
The antibacterial activity of the tested compounds
2
,
3
,
4
,
6
and 12a
against E. coli O157 showed that compound 12c gave
the best results in both conc. (200 and 100 g/mL) with
-c using the agar well diffusion test
ND: not detected
µ
Table IV. Anti-adenovirus type 7 activities of the tested
compounds 10 and 12a on Hep2 Cells deter-
mined by the MTT method
mean zone of inhibition equal to 23 mm and 17 mm,
2,
3,
4,
5
,
-c
respectively, followed by compound 12b and compound
3
with the mean zone of inhibition equal to 16 mm.
Against S. typhimurium, compound 12c gave the best
results in conc. (200 g/mL) and compound 12b (200
g/mL) then compound 12c in conc. (100 g/mL) with
Tested
compounds
CC50
g/mL)
IC50
Therapeutic
index
(
µ
(
µg/mL)
µ
2
3
4
165.4
171.5
157.4
149.8
173.2
121.6
112.9
114.7
ND
ND
ND
ND
ND
ND
18.8
17.6
ND
ND
ND
ND
ND
ND
6
µ
µ
the mean zone of inhibition equal to 32 mm, 20 mm
and 19 mm, respectively, followed by compound 12a
5
(100
of inhibition equal to 18 mm and 16 mm. Against E.
coli O119, compound 12a (200 g/mL) showed the best
results with the mean zone of inhibition equal to 15
mm followed by compound 12c (200 g/mL) with the
mean zone of inhibition equal to 13 mm. Against S.
paratyphi, compound 12a (200 g/mL) gave the best
and the therapeutic index of compound 12c was 6.51 results with the mean zone of inhibition equal to 17
µg/mL) and 12b (100 µg/mL) with the mean zone
10
12a
12b
12c
µ
6.51
µ
ND: not detected
µ
for adenovirus type 7 as shown in Tables III and IV.
mm followed by compound 12c with the mean zone of
inhibition equal to 16 mm. Against P. aeruginosa, com-
pound 12a (200 µg/mL) exhibited the best results with
Antibacterial and antifungal activities
Some of the newly synthesized compounds were the mean zone of inhibition equal to 16 mm followed
preliminarily evaluated for their antibacterial and by compound 12c with the mean zone of inhibition
antifungal activities. Compounds
were evaluated in vitro by the agar well diffusion test the best results in both conc. (200 and 100
2
,
3
,
4
,
6
and 12a
-
c
equal to 15 mm. Against S. aureus, compound 12c gave
g/mL)
µ

Pharmacological Activity of New Heterocyclic Benzimidazoles
2071
with the mean zone of inhibition equal to 16 mm and in conc. (200-100
µg/mL) with the mean zone of inhibi-
14 mm, respectively, followed by compound 12b in tion equal to 17 mm and 15 mm, respectively as shown
both conc. (200 and 100 g/mL) with the mean zone of in Table V.
inhibition equal to 14 mm. Against L. Monocytogenes,
compound 12c gave the best results in conc. (200 g/
µ
µ
Minimum inhibitory concentration (MIC)
Using the Microtiter dilution plate method, the min-
g/ imum inhibitory concentration (MIC) (Andrews et al.,
mL) with the mean zone of inhibition equal to 15 mm
followed by compound 12b and 12a in conc. (200
µ
mL) with the mean zone of inhibition equal to 14 mm. 2001; Rybak et al., 2001)which is considered as another
Against B. cereus, compound 12a exhibited the best quantitative approach used for the evaluation of the
results in both conc. (200 and 100
mean zone of inhibition equal to 18 mm and 16 mm, 12a
µ
g/mL) with the antibacterial activity of the synthesized compounds
-c
against highly inhibited organisms is shown in
respectively, followed by compound 12c and 12b with Table VI. Minimum inhibitory concentration (MIC)
the mean zone of inhibition equal to 15 and 14 mm as gives more details about the quantitative hindrance
shown in Table V.
ability of the tested compounds against the tested
bacterial strains: E. coli O157, S. typhimurium, E. coli
O119, S. paratyphi, P. aeruginosa, S. aureus, L. mono-
Antifungal activity
The results obtained from the present study record- cytogenes, B. cereus. This procedure was carried out
ed a remarkable difference in the antifungal effect of for the tested compounds 12a with the initial con-
the tested compounds and 12a . The anti- centration of (100 g/mL). Two fold serial dilutions of
-c
2,
3,
4,
6
-c
µ
fungal activity of the tested compounds using the agar the tested compounds and reference antibiotic (cipro-
well diffusion test against C. albicans showed that floxacin) and fluconazole were prepared using Muller
compound 12c exhibited the best results in conc. (200 Hinton broth at solution concentrations of 100 and
µ
g/mL) with the mean zone of inhibition equal to 16 0.097. Tubes were then inoculated with the tested
mm followed by compound 12b in conc. (200
g/mL) organisms, grown in their suitable broth at 37oC for
and compound 12a in conc. (200 g/mL) followed by 24 h for bacteria and 48 h for fungi (about 1
105
L of the above inoc-
µ
µ
×
compound 12b in conc. (100
µg/mL) with the mean cells/mL). Each well received 100 µ
zone of inhibition equal to 15 mm and 14 mm, respec- ulums and was incubated at 37-28oC for 24-48 h for
tively. Against A. niger, compound 12c gave the best bacterial and mycotic growth, respectively. The lowest
results in conc. (200
inhibition equal to 18mm followed by compound 12b MIC.
µg/mL) with the mean zone of concentration that showed no growth was taken as
Table V. Antibacterial and antifungal activities of compounds 2, 3, 4, 6 and 12a-c
Mean
zone of
inhibition
Mean
zone of
inhibition
Tested
compounds
E. coli S. typhi- E. coli
O157 murium O119 paratyphi aeruginosa aureus cytogenes cereus
S.
P.
S.
L. mono-
B.
C.
albican
A.
niger
s
2 (100
2 (200
3 (100
3 (200
4 (100
4 (200
6 (100
6 (200
12a (100
12a (200
12b (100
12b (200
12c (100
12c (200
µ
µ
µ
µ
µ
µ
µ
µ
g/mL)
g/mL)
g/mL)
g/mL)
g/mL)
g/mL)
g/mL)
g/mL)
g/mL)
8
8
13
16
7
8
-
-
8
-
8
12
12
7
-
8
9
11
-
7
-
-
11
15
10
12
12
13
26
-
7
11
12
-
7
-
-
12
17
13
14
14
16
24
8
8
11
11
8
8
8
8
10
-
8
8
8
9
11
-
7
10
11
12
12
8
5.25
8.25
10.63
11.88
3.75
7.63
3.75
6.63
12.88
15.00
13.50
14.63
14.13
18.13
24.25
-
7
11
-
8
13
-
7.5
12
-
7
-
-
7
-
-
7
-
8
8
8
8
10
10
18
13
16
20
19
32
22
-
9
-
12
10
16
18
13
14
12
15
22
12
15
16
14
14
12
15
23
12
11
14
12
14
13
15
24
µ
12
14
14
14
14
16
28
12
14
14
15
12
16
12
12
15
17
14
18
12
13
14.5
16
13
17
µ
µ
µ
g/mL) 13
g/mL) 16
g/mL) 16
µg/mL)
17
23
25
µg/mL)
Ciprofloxacin
(100 g/mL)
Fluconazole
(100 g/mL)
µ
-
-
-
-
-
-
-
-
-
19
21
20
µ

2072
F. A. Bassyouni et al.
Table VI. Minimum inhibitory concentration of the tested compounds 12a-c against tested bacterial strains
Fungal
isolates
Bacterial isolates
Tested compounds
E. coli
S.
E. coli
S.
P.
S.
L.
B.
C.
A.
O157 typhimurium O119 paratyphi aeruginosa aureus monocytogenes cereus albicans niger
12a (100
12b (100
12c (100
Ciprofloxacin (100
Fluconazole (100
µ
µ
µ
g/mL)
g/mL)
g/mL)
6.25
3.125
1.56
12.5
6.25
0.19
0.19
-
25
6.25
1.56
25
12.5
12.5
1.56
1.56
-
12.5
6.25
3.125
12.5
-
25
12.5
6.125
25
3.125
3.125
1.56
1.56
-
3.125
6.25
6.25
12.5
-
12.5
6.25
1.56
-
12.5
6.25
6.25
-
µ
g/mL) 25
µg/mL)
-
-
-
1.56
1.56
The results of MIC for compounds 12a, 12b and 12c evidence reported. These models are necessary to obtain
with the initial concentration (100 g/mL) revealed a consistent and more precise picture of biological active
µ
that against E. coli O119, the MIC of the tested com- molecules at the atomic level and thus, provide new
pounds was best with compound 12c followed by com- insights that can be used to design novel therapeutic
pounds 12b and 12a with MIC equal to 1.56, 3.125 agents. The molecular docking was performed and
and 6.25, respectively. Against S. typhimurium, the analyzed with the Sybyl-X V1.1 interface software.
MIC of the tested compounds was the best with com-
The predicted target of our investigation was the
pound 12c followed by compounds 12b and 12a with carboxy-lyases family enzyme that cleaves carbon-car-
MIC equal to 0.19, 6.25 and 12.5, respectively. Against bon bonds. Its systematic class is 2,2-dialkylglycine
E. coli O119, the MIC of the tested compounds was carboxy-lyase (amino-transferring L-alanine-forming).
best with compound 12c followed by compounds 12b It catalyzes the chemical reaction as follow:
and 12a with MIC equal to 1.56, 6.25 and 25, respec-
2,2-dialkylglycine + pyruvate
+ CO2 + L-alanine
dialkyl ketone
tively. Against S. paratyphi, the MIC of the tested
compounds was best with compound 12c followed by
compounds 12b and 12a with MIC equal to 1.56 and
Its annotated molecular functions as described in
12.5, respectively. Against P. aeruginosa, the MIC of the universal protein knowledgebase (Uniport KB) (http:
the tested compounds was best with compound 12c //www.uniprot.org) include pyridoxal phosphate binding
followed by compounds 12b and 12a with MIC equal and transaminase activity.
to 3.125, 6.25 and 12.5, respectively. Against S. aureus,
the MIC of the tested compounds was best with com-
pound 12c followed by compounds 12b and 12a with
MIC equal to 6.125, 12.5 and 25, respectively. Against
Molecular modeling in silico target prediction
and docking methodology
The tested compounds 2, 4, 12a, 12b and 12c were
L. monocytogenes, the MIC of the tested compounds drawn, 3D conformations generated and energy mini-
was best with compound 12c followed by compounds mized using the ChemBioOffice V12 and using the
12a and 12b with MIC equal to 1.56 and 3.125, respec- mmff 94 Merck Molecular Force Field function, with
tively. Against B. cereus, the MIC of the tested com- maximum number of iterations of 500, and a minimum
pounds was best with compound 12a followed by com- RMS gradient of 0.1 (Kerwin, 2010). Charges were as-
pounds 12b and 12c with MIC equal to 3.125 and 6.25, signed using the same function. The PharmMapper
respectively.
server was used to predict targets for compounds based
Against C. albicans, the MIC of the tested compounds on a pharmacophore database pharmtarget db contain-
was best with compound 12c followed by compounds ing 7000 pharmacophors based on a set of 1500 drug
12b and 12a with MIC equal to 1.56, 6.25 and 12.5, targets (Liu et al., 2010). The target scores were ana-
respectively. Against A. niger, the MIC of the tested lyzed and the highest bacterial target structures were
compounds was best with compounds 12c and 12b downloaded for docking. Docking was performed using
followed by compound 12a with MIC equal to 6.25 and Sybyl-X V1.1 (Tripos International). Docking studies
12.5, respectively Table VI.
were performed using the SurFlex-dock application
Sybyl-X version1.1 package. Docking procedure was
followed using the standard protocol implemented in
Molecular modeling study
Modeling studies are required in order to understand SurFlex-dock and the geometry of resulting complexes
the mechanisms of actions of drugs, modes of interac- was studied using the SurFlex-dock Pose Viewer
tions with targets, and to incorporate all experimental utility. Validation was done on each of the targets by

Pharmacological Activity of New Heterocyclic Benzimidazoles
2073
Fig 2. The docking pose of compound 12a into the active site of the dialkylglycine decarboxylase receptor binding site
showing the hydrogen bonds as dotted yellow lines.
Table VII. The Docking scores and interactions of struc-
tures 12a and to the proposed target receptor dialkyl-
glycine decarboxylase
Table VIII. The scores of docking of the structure to the
highest bacterial targets and their correlation to bacterial
activity represented by the mean inhibitory zone
,
b
c
Struc- Docking
No of
H. bonds
Mean
inhibitory zone
Residues involved
Structure
1L5L
1VCF
1D7U
ture
score
6.99
110, GLY111, ALA112,
GLN246, SER215, TRP138
2
4
12a
12b
12c
6.34
6.2
2.18
2.76
4.38
7.83
7.55
2.04
5.66
4.3
5.08
5.2
6.99
5.96
6.16
5.25
3.75
12.88
13.5
14.13
1.0
12a
6
6
4
ARG406, GLN52, LYS272,
TRP138, MET141, ALA112
12b
12c
5.96
6.16
ARG406, GLN246, LYS272,
GLY111
correlation -0.85867 -0.79978 0.818736
computing the correlation of the docking scores with enzyme. However, the structure of compound 12c
the mean zone of inhibition.
achieved a score of 6.16 and formed four hydrogen
bonds with residues ARG406, GLN246, LYS272 AND
GLY111 (Table VII).
Molecular modeling analysis
The pharmmapper server produces the top 300 tar-
The two nitrogens of the Acetonitrile and benzimida-
gets ranked based on the fit score, working on highest zole groups form two H-bonds with THR110 and GLY111.
bacterial targets which are dialkylglycine decarboxyl- In addition, twonitrogens from the other Acetonitrile
ase (1D7U), IPP isomerase (1VCF) and L-threonine- and benzimidazole groups form two H-bonds with
O-3-phosphate decarboxylase (1L5L). By docking com- GLN24 and SER215. Quinoxaline nitrogen forms an
pounds 2, 4, 12a, 12b and 12c to these targets and H-bond with TRP138.
correlating with the bacterial activity represented by
the mean zone of inhibition were calculated to produce
the best correlation and reached 0.82 for 2,2-dialkylgly-
cidecarboxylase (PDB ID: 1D7U) (Tables VII and VIII).
ACKNOWLEDGEMENTS
We are very grateful and thank National Research
For the structure of compound 12a achieved a score Center for financial support of this work through the
of 6.99 and formed six hydrogen bonds with residues fund of the project (No: 8040204).
THR 110, GLY111, ALA112, GLN246, SER215 AND
TRP138 of the enzyme binding site (Fig. 2). While the
structure of compound 12b achieved a score of 5.96
and formed six hydrogen bonds with residues ARG406,
GLN52, LYS272, TRP138, MET141 and ALA112 of the
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