Design, synthesis and docking studies of new furobenzopyranones and pyranobenzopyranones as photoreagent towards DNA and as antimicrobial agents

Article abstract of DOI:10.1016/j.ejmech.2009.10.016

A number of new furobenzopyranones and pyranobenzopyranones carrying an electron- withdrawing function at the position 3 are synthesized in order to obtain new photoreagents towards DNA. Our interest in this study is to investigate the effect of introduction of electron withdrawing function on the position 3 of the benzo-a-pyranone ring of linear furobenzo-a-pyranone (5,8-dimethoxypsoralen) or angular pyranobenzo-a-pyranone on the biological activity, by preparing 3-cyano, carboxylic acid, carboxylic acid ester, acid hydrazide, thiosemicarbazide, or mercaptotriazole derivatives. 5-acetyl-6-hydroxybenzofuran, and 8-acetyl-7-hydroxy-4-phenylbenzopyranone are the key starting compounds on which 3-cyano-4-methylfurobenzopyranone and 3-cyano-4-methyl pyranobenzopyranone moieties were built respectively. The photobiological activity of the newly synthesized compounds was evaluated. It looks most promising for enhancement of photoreactivity of compounds towards DNA, and a certain effect was observed in the dark determining the antimicrobial activity. Compounds 5, 6, 7, 13, 14 exhibit potential photoreactivity towards DNA, while 3-mercaptotriazole derivatives 7, 14 possess only photosensitizing activity. To investigate the antimicrobial data on structural basis, molecular modelling and docking studies of the tested compounds into the crystal structure of topoisomerase II DNA Gyrase B complexed with the natural inhibitor bearing the coumarin moiety clorobiocin (1kzn), using Molsoft ICM 3.4-8C program was performed in order to predict the affinity and orientation of the synthesized compounds at the active site. The ICM score values and hydrogen bonds formed with the surrounding amino acids show good agreement with predicted binding affinities obtained by molecular docking studies as verified by antimicrobial screening, where compounds 5, 6, 13 were the most active compounds against Bacillus subtilis, Staphylococcus aureus, and Escherichia coli. Compound 13 has good affinity with the receptor and forms six hydrogen bonds with Asp-73, and two bonds with Thr-165, compound 6 has ICM score value -85.66 and forms one hydrogen bond with Asp-73, and three with Thr-165, and compound 5 has ICM score value -53 but forms one hydrogen bond with Asp-73, and four bonds with Thr-165 which may reveal the potent antimicrobial activity referred to the natural antimicrobial Clorobiocin which forms two hydrogen bonds with Asp-73 and three with Thr-165.

Full text of DOI:10.1016/j.ejmech.2009.10.016

European Journal of Medicinal Chemistry 45 (2010) 317–325
Contents lists available at ScienceDirect
European Journal of Medicinal Chemistry
journal homepage: http://www.elsevier.com/locate/ejmech
Original article
Design, synthesis and docking studies of new furobenzopyranones and
pyranobenzopyranones as photoreagent towards DNA and as antimicrobial agents
,
b
Nahla A.H. Farag a , Wafaa El-Tayeb
*
a Pharmaceutical Chemistry Department, Faculty of Pharmacy, Misr International University, Km 28 Cairo-Ismailia Road, P.O. Box 1, Heliopolis, Cairo, Egypt
b Microbiology Department, Faculty of Pharmacy, Misr International University, Km 28 Cairo-Ismailia Road, Cairo, Egypt
a r t i c l e i n f o
a b s t r a c t
Article history:
A number of new furobenzopyranones and pyranobenzopyranones carrying an electron- withdrawing
function at the position 3 are synthesized in order to obtain new photoreagents towards DNA. Our
interest in this study is to investigate the effect of introduction of electron withdrawing function on the
position 3 of the benzo-a´-pyranone ring of linear furobenzo-a´-pyranone (5,8-dimethoxypsoralen) or
Received 16 February 2009
Received in revised form
7 October 2009
Accepted 9 October 2009
Available online 14 October 2009
´
angular pyranobenzo-a-pyranone on the biological activity, by preparing 3-cyano, carboxylic acid,
carboxylic acid ester, acid hydrazide, thiosemicarbazide, or mercaptotriazole derivatives. 5-acetyl-6-
hydroxybenzofuran, and 8-acetyl-7-hydroxy-4-phenylbenzopyranone are the key starting compounds
on which 3-cyano-4-methylfurobenzopyranone and 3-cyano-4-methyl pyranobenzopyranone moieties
were built respectively. The photobiological activity of the newly synthesized compounds was evaluated.
It looks most promising for enhancement of photoreactivity of compounds towards DNA, and a certain
effect was observed in the dark determining the antimicrobial activity.
Keywords:
Furocoumarins
Furobenzopyranone
Pyranobenzopyranone
Photochemotherapeutic agents
Photosensitizing activity
Antimicrobial activity
Topoisomerase II DNA gyrase B
Enzyme inhibitor
Compounds 5, 6, 7, 13, 14 exhibit potential photoreactivity towards DNA, while 3-mercaptotriazole
derivatives 7, 14 possess only photosensitizing activity.
To investigate the antimicrobial data on structural basis, molecular modelling and docking studies of
the tested compounds into the crystal structure of topoisomerase II DNA Gyrase B complexed with the
natural inhibitor bearing the coumarin moiety clorobiocin (1kzn), using Molsoft ICM 3.4-8C program was
performed in order to predict the affinity and orientation of the synthesized compounds at the active
site. The ICM score values and hydrogen bonds formed with the surrounding amino acids show good
agreement with predicted binding affinities obtained by molecular docking studies as verified by anti-
microbial screening, where compounds 5, 6, 13 were the most active compounds against Bacillus subtilis,
Staphylococcus aureus, and Escherichia coli. Compound 13 has good affinity with the receptor and forms
six hydrogen bonds with Asp-73, and two bonds with Thr-165, compound 6 has ICM score value ꢀ85.66
and forms one hydrogen bond with Asp-73, and three with Thr-165, and compound 5 has ICM score
value ꢀ53 but forms one hydrogen bond with Asp-73, and four bonds with Thr-165 which may reveal
the potent antimicrobial activity referred to the natural antimicrobial Clorobiocin which forms two
hydrogen bonds with Asp-73 and three with Thr-165.
Ó 2009 Elsevier Masson SAS. All rights reserved.
1. Introduction
lymphomas and as selective immunosuppressive agents for the
cure of various autoimmune diseases and to prevent rejection in
´
Linear furocoumarins (furobenzo-a-pyranones, psoralens) are
a well-known family of natural and synthetic photosensitizing
compounds which exhibit very interesting photobiological activity.
Some of these are used in PUVA photochemotherapy (Psoralen plus
UVA) to treat a variety of skin diseases. They are also employed in
extracorporeal photochemotherapy to treat cutaneous T-cell
organ transplants [1,2]. Furthermore, psoralen derivatives are now
recognized as effective antiviral agents, especially against envel-
oped viruses such as the herpes simplex virus or HIV-1 [3,4].
The preferred compound is 8-methoxypsoralen (8-MOP) but 5-
methoxypsoralen (5-MOP) and 4,50,8-trimethoxypsoralen (TMP)
are also used. They show good antiproliferative effect due to their
capability to photo damage DNA, leading to monofunctional and
two different kinds of bifunctional adducts; inter-strand cross-links
(ISC) [5] and DNA–protein cross-links (DPC), tying together a DNA
base and a protein amino acid [6–8].
* Corresponding author. Tel.: þ20 224534418, þ2 0123378871; fax: þ20
4771560.
2
E-mail address: nahlahassan91@yahoo.com (N.A.H. Farag).
0223-5234/$ – see front matter Ó 2009 Elsevier Masson SAS. All rights reserved.
doi:10.1016/j.ejmech.2009.10.016

318
N.A.H. Farag, W. El-Tayeb / European Journal of Medicinal Chemistry 45 (2010) 317–325
O
OMe
CH3
O
OMe
O
O
CH3
O
OMe
N
CH3
O
O
O
OMe
OMe
CH3
OH
a
b
OH
c
OMe
O
O
O
O
OMe
O
OMe
OMe
1
2
3
4
d
O
O
CH3
O
OMe
OMe
N
CH3
OMe
O
O
N
O
H
N
H
N
CH3
O
OMe
f
SH
NH2
N
H
e
N
N
H
S
O
O
O
O
OMe
OMe
7
5
6
Scheme 1. Reagents, (a) ethyl cyanoacetate, sodium ethoxide, (b) Sodium hydroxide 15%, (c) thionyl chloride, methanol, (d) Hydrazine hydrate, ethanol, (e) Benzyl isothiocyanate,
ethanol, (f) 2 N sodium hydroxide.
The bifunctional damage, in particular the induction of ISC, was
regarded as the main cause responsible for the furocoumarin
toxicity, i.e., skin erythemas, genotoxicity with induction of point
mutations in bacteria [1,9–12].
a heterotetramer A2B2 [31]. Mechanistic studies have revealed the
steps involved in the gyrase supercoiling reaction [32]. This process
involves the wrapping of DNA around the A2B2 complex, cleavage of
this DNA on both strands, and the passage of a segment of DNA
through the double strand break. Relegation of the break results in
the introduction of two negative supercoils. These processes
require the binding and hydrolysis of ATP [33]. Inhibition of DNA
gyrase blocks relaxation of supercoiled DNA, relaxation being
a requirement for transcription and replication. DNA gyrase is
a selective target for antibacterial agents, such as the most studied
quinolone and coumarin antibiotics. Quinolone drugs (e.g. cipro-
Extensive photochemical and photobiological studies have been
performed mainly on two series of furobenzopyranones, that is
psoralens (linear furobenzopyrones) [13,14] and, angelicins
(angular furobenzopyranones) [15–19]. In addition, new DNA
monofunctional furobenzopyranones as 6-carbethoxy analogues
[20], furobenzopyranones with modified annulations geometry
[21] as well as pyridopsoralens [22–24], azapsoralens [25], furo-
quinolinones [26], thienoquinolinones [27] have been prepared.
They prevent inter-strand cross-link formation, consequently lack
skin phototoxicity [22–26], and at the same time maintain the
photosensitizing activity. Also, synthesis of different series of tet-
rahydrobenzo- and benzofurobenzopyranone derivatives as new
monofunctional DNA photobinding agents were reported [27–29].
On the other hand, in DNA replication, one group of enzymes
has proved to be effective target for therapeutic agents, which is
topoisomerase enzyme. DNA gyrase is a type II topoisomerase
found in all bacteria and controls the topological state of DNA [30].
DNA gyrase consists of two subunits GyrA (875 amino acids) and
GyrB (804 amino acids) with the active species being
´
floxacin) affect the protein subunit GyrA and coumarins (benzo-a-
pyranones) (e.g. novobiocin, clorobiocin) act on GyrB [34].
Owing to our interest for drug molecules able to photoreact with
DNA, and their biological activity, we planned to prepare a new
´
series of linear furobenzo-a-pyranone derived from the conden-
sation of 3-cyano-4-methyl-2H-pyran-2-one at 5, 6 of benzofuran
nucleus to give a linear geometry, and another new series of
´
angular pyranobenzo-a-pyranone derived from the condensation
of 3-cyano-4-methyl-2H-pyran-2-one at 7, 8 of benzopyranone
nucleus to have an angular structure, and compare the effect of
different electron withdrawing substituents on the photobiological
activity towards DNA, and also observe their effects in the dark.
O
O
O
O
O
a
CH3
b
O
CH3
O
O
CH3
O
N
CH3
O
O
O
O
c
C6H5
O
C6H5
C6H5
OH
OMe
C6H5
OH
O
O
O
8
9
10
11
d
O
O
O
N
N
O
O
O
CH3
O
CH3
O
H
N
CH3
O
O
O
O
S
e
SH
f
C6H5
N
H
N
NH2
C6H5
N
H
C6H5
HN
O
O
14
13
12
Scheme 2. Reagents, (a) ethyl cyanoacetate, sodium ethoxide, (b) Sodium hydroxide 15%, (c) thionyl chloride, methanol, (d) Hydrazine hydrate, ethanol, (e) Benzyl isothiocyanate,
ethanol, (f) 2 N sodium hydroxide.

N.A.H. Farag, W. El-Tayeb / European Journal of Medicinal Chemistry 45 (2010) 317–325
319
Table 1
Photosensitizing and antimicrobial activities of furobenzopyranone analogues 2–7 and pyranobenzopyranone analogues 9–14 are expressed in terms of zone of growth
inhibition (measured in mm).
Cpd. No.
Bacillus subtilis gþve
Staphylococcus aureus gþve
Escherichia coli gꢀve
Pseudoomonas aeruginosa gꢀve
Candida albicans
Before UV
After UV
xanthotoxin (8-MOP)
tetracyclin
amphotericin B
2
3
4
5
6
–
30
–
–
–
12
–
36
–
–
–
–
–
–
–
–
–
–
–
30
–
–
34
–
–
–
–
18
–
–
–
–
–
–
20
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
30
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
14
12
11
–
–
–
–
12
10
–
–
–
–
–
18
–
7
9
10
11
12
13
14
–
22
12
amino acids. Molsoft as flexible docking program enable us to
predict favorable protein–ligand complex structures with reason-
able accuracy and speed [37].
2. Chemistry
The route used for the synthesis of the new furobenzopyranone
derivatives assessed in this study is shown in Scheme 1. 4,9-
Dimethoxy-7-oxo-5-methyl-7H-furo
carbonitrile 2 was synthesized directly, in good yield, by refluxing
1-(6-hydroxy-4,7-dimethoxybenzofuran-5-yl) ethanone with
[3,2-g]benzopyrane-6-
1
ethyl cyanoacetate in sodium ethoxide [38,39]. Compound 2 was
routinely hydrolyzed to the corresponding 4,9-Dimethoxy-7-oxo-
Fig. 1. Binding mode of the original ligand 1cbn (Clorobiocin) into its binding site of
topoisomerase DNA gyrase B, it has ICM score ꢀ123.03, and form 10 hydrogen bonds
shown as white dotted lines (Table 2), showing two hydrogen bonds between O3 (OH-
4) and NH of D73 distance 2.53 A, and between NH (NHCO)and O of D73 amino acid
distance 2.32 A, and another three hydrogen bonds between O-10 and HG1 of T165
distance 1.95 A, and between H-4 and O of T165 distance 1.29 A, and between H-3 and
O of T165 distance 2.28 A. (For interpretation of the references to color in the text, the
reader is referred to the web version of this article).
5-methyl-7H-furo[3,2-g]benzopyrane-6-carboxylic acid
3
by
refluxing with 15% sodium hydroxide for three hours then acidified
[40]. Esterification of 3 in methanol using thionyl chloride afforded
methyl 4,9-dimethoxy-7-oxo-5-methyl-7H-furo[3,2-g]benzopyr-
ane-6-carboxylate 4 [40]. Reaction of 4 with hydrazine hydrate
yielded the hydrazone 5 in good yield [19,41]. Refluxing 4,9-
Dimethoxy-7-oxo-5-methyl-7H-furo[3,2-g]benzopyrane-6-carbo-
hydrazide 5 with benzyl isothiocyanate in ethanol gave the corr
esponding thiosemicarbazide 6 [42]. Finally, cyclization of 4-benzyl-
1-(4,9-Dimethoxy-7-oxo-5-methyl-7H-furo[3,2-g]benzopyrane-6-
Computer docking technique plays an important role in the drug
design and discovery, as well as in the mechanistic study by placing
a molecule into the binding site of the target macromolecule in
a non-covalent fashion [35,36], and to predict the correct binding
geometry for each ligand at the active site, which reveals the ICM
score values and hydrogen bonds formed with the surrounding
Fig. 2. Binding mode of compound 5 in the binding site of topoisomerase DNA gyrase
B, it has ICM score ꢀ53.48, and form 8 hydrogen bonds shown as white dotted lines
(Table 2) showing one hydrogen bond between H-12 (NH of NHNH2) and OD1 of D73
amino acid distance 2.29 A, and another four hydrogen bonds between O-5 (2-oxo)and
OG1 of T165 distance 2.42 A, and between O-2 (1-O-) and HG1 of T165 distance 1.71 A,
and O5 (2-oxo) and NH of T165 of distance 2.57 A, and between H-14 (NH of
NHNH2)and O of T165 distance 2.67 A. (For interpretation of the references to color in
the text, the reader is referred to the web version of this article).
Fig. 3. Binding mode of compound 6 in the binding site of topoisomerase DNA gyrase
B, it has ICM score ꢀ85.66, and form 9 hydrogen bonds shown as white dotted lines
(Table 2), it shows one hydrogen bond between H13 of (CONHNHCS) and O of D73
distance 2.17 A, and and another three hydrogen bonds between O-5 (2-oxo-)and HG1
of T165 distance 2.40 A, and between H-12 (NH of CONH) and OG1 of T165 amino acid
distance 1.74 A, and another bond between H-14 (NH of NHCSNHNH) and O of T165
amino acid distance 1.60 A (For interpretation of the references to color in the text, the
reader is referred to the web version of this article).

320
N.A.H. Farag, W. El-Tayeb / European Journal of Medicinal Chemistry 45 (2010) 317–325
(2(1H)oxo-4-phenyl-pyrano)[2,3-f]benzopyran-3-carbonitrile
9
was synthesized through refluxing 8-Acetyl-7-hydroxy-4-phenyl-
2H-1-benzopyran-2-one 8 with ethyl cyanoacetate in sodium
ethoxide [38,39], followed by its hydrolysis to give 2(1H)-oxo-4-
methyl-(2(1H)oxo-4-phenyl-pyrano)[2,3-f] benzopyran -3-car
boxylic acid 10 [40]. It was then estrified to afford Methyl-2(1H)-
oxo-4-methyl-(2(1H)oxo-4-phenyl-pyrano)[2,3-f]
[1]benzopy
ran-3-carboxylate 11 [40]. Its hydrazone derivative (1H)-oxo-4-
methyl-(2(1H)oxo-4-phenyl-pyrano)[2,3-f]benzopyran-3-carbohy-
drazide 12 was formed by its reaction with hydrazine hydrate in
ethanol [19,41]. Refuxing 12 with benzyl isothiocyanate in ethanol
gave the corresponding thiosemicarbazone 13 [42]. Finally, cycli-
zation of 4-benzyl-1-(2(1H)-oxo-4-methyl-(2(1H)oxo-4-phenyl-
pyrano)[2,3-f]benzopyran-3-carbonyl) thiosemicarbazide 13 with
2 N sodium hydroxide afforded 3-(4-benzyl-5-mercapto-4H-1,2,4-
triazol-3-yl)-4-methyl-2H-(2(1H)oxo-4-phenyl-pyrano)[2,3-f]ben-
zopyran-2-one 14 [42,43–45].
Fig. 4. Binding mode of compound 13 in the binding site of topoisomerase DNA gyrase
B, it has ICM score ꢀ96.07, and form 10 hydrogen bonds shown as white dotted lines
(Table 2), it shows six hydrogen bonds between O-3 (2-oxo) and NH of D73 distance
2.65 A, and H-12 (CONHNHCSNH) and OD2 of D73 distance 1.40 A, and H-13
(CONHNHCSNH) and OD2 of D73 distance 2.56 A, and H-13 (NH of NHNHCS) and O of
D73 amino acid distance 0.89 A and H-12 (CONHNHCSNH) and O of D73 distance 2.39
A, and H-14(CONHNHCSNH) and O of D73 distance 2.17 A, and another two hydrogen
bonds between O-2 (5-O-)and HG1 of T165 distance 2.56 A, and between H-12
(CONHNHCSNH) and O of T165 amino acid distance 1.55 A. (For interpretation of the
references to color in the text, the reader is referred to the web version of this article).
3. Results and discussion
carbonyl) thiosemicarbazide 6 with 2 N sodium hydroxide afforded
mercaptotriazole derivative 7 [42,43–45].
3.1. Photosensitizing and antimicrobial screening
The same pathway was performed for the synthesis of pyr-
anobenzopyranone derivatives, Scheme 2. 2(1H)-oxo-4-methyl-
In this study the compounds (2–7, 9–14) were screened for anti-
microbial and photosensitizing activity by the disc diffusion method
Table 2
ICM Scores of Clorobiocin, the compounds, and hydrogen bonds formed with amino acid residues and their lengths.
Compounds
Clorobiocin
ICM scores
No. of hydrogen bonds
10
Involved group of amino acid
Atom of ligand involved
Length of hydrogen bond (Å)
ꢀ123.03
N46..HD21
N46..HD21
D73....NH
D73.....O
I60.....NH
E58....Oe1
Q72...NH
T165...HG1
T165....O
T165....O
N46...HD21
G77...NH
T165...HG1
T165...HG1
N46..HD21
G77...NH
T165...HG1
T165...HG1
E50...Oe2
N46...HD21
G77....NH
T165...HG1
T165...HG1
N46...HD21
T165..HG1
T165...O
T165...NH
V71.....O
V71.....O
D73..OD1
O-7
O-8
O-3 (OH-4)
H-3
O-5
O-10
O-5
O-10
H-4
2.14
1.65
2.53
2.32
1.82
2.75
2.39
1.95
1.29
2.28
2.15
1.97
2.48
2.14
2.10
2.15
2.16
2.19
2.47
2.04
2.21
2.21
2.13
1.88
2.42
2.67
2.57
2.61
1.88
2.29
1.71
1.76
2.29
1.65
2.28
1.74
2.40
2.66
2.17
1.60
1.92
2.49
2.66
2.33
H-3(OH-4)
O-3(2-oxo)
O-5(2-oxo)
O-5(2-oxo)
O-2(1-O-)
O-3(4-OCH3)
O-5(2-oxo)
O-5(2-oxo)
O-2(1-O-)
H-12(CONH)
O-3(4-OCH3)
O-5(2-oxo)
O-5(2-oxo)
O-2(1-O-)
O-3(4-OCH3)
O-5 (2-oxo)
H-14((CONHNH2)
O-5(2-oxo)
H-13 (CONHNH2)
H-14 (CONHNH2)
H-12(CONHNH2)
O-2 (1-O-)
O-5 (2-oxo)
O-2 (1-O-)
O-4 (OCH3)
O-4 (OCH3)
H-12 (CONHNHCSNH)
O-5 (2-oxo-)
H-14 (CONHNHCSNH)
H-13 (CONHNHCSNH)
H-14 (CONHNHCSNH)
O-3(4-OCH3)
O-5(2-oxo)
O-5(2-oxo)
O-2(1-O-)
2
3
ꢀ55.36
ꢀ59.21
4
5
4
5
ꢀ63.09
ꢀ53.48
4
8
T165.HG1
6
ꢀ85.66
9
G77....NH
G77....NH
R136.HH11
R136.HH12
R165..OG1
T165...HG1
V71....O
D73....O
T165...O
N46..HD21
G77....NH
T165...HG1
T165...HG1
7
ꢀ80.48
4

N.A.H. Farag, W. El-Tayeb / European Journal of Medicinal Chemistry 45 (2010) 317–325
321
Table 2 (continued )
Compounds
ICM scores
No. of hydrogen bonds
4
Involved group of amino acid
Atom of ligand involved
Length of hydrogen bond (Å)
9
ꢀ74.32
N46..HD21
R76..He
G77..NH
O-4(6-oxo)
O-3(2-oxo)
O-2(1-O-)
O-3(2-oxo)
O-4(6-oxo)
O-2(1-O-)
O-3(2-oxo)
O-5(O of OH)
O-3(2-oxo)
O-5(O of OH)
O-4(6-oxo)
O-3(2-oxo)
O-2(1-O-)
O-3(2-oxo)
O-5(OCH3)
O-4(O of CO)
O-3(2-oxo)
O-5(6-oxo)
O-1 (1-O-)
1.61
2.47
1.98
2.41
1.71
1.60
1.76
2.53
2.73
2.03
1.64
2.21
1.76
2.61
2.49
1.76
2.56
2.76
1.44
2.36
2.67
1.65
2.65
2.51
2.66
2.56
1.55
1.40
2.56
0.89
2.39
2.17
2.09
R136.HH11
10
ꢀ77.46
6
N46..HD21
G77....NH
R136.HH11
R136.HH11
R136..HH12
R136.HH12
N46...HD21
R76...He
G77....NH
R136.HH11
R136.HH12
N46...HD21
R76...He
R76...HH11
G77..NH
R136.HH11
R136.HH11
G77....O
D73....NH
D74....NH
G75...NH
T165 ..HG1
T165...O
D73...OD2
D73...OD2
D73.....O
D73.....O
D73.....O
N46...HD21
11
12
ꢀ79.51
ꢀ70.22
5
7
O-3(2-oxo)
N-2(NH2)
H-14 (CONHNHCSNH)
O-3 (2-oxo)
O-5 (6-oxo)
13
ꢀ96.07
10
O-5 (6-oxo)
O-2 (5-O-)
H-12 (CONHNHCSNH)
H-12 (CONHNHCSNH)
H-13 (CONHNHCSNH)
H-13 (CONHNHCSNH)
H-12 (CONHNHCSNH)
H-14 (CONHNHCSNH)
O-4(OCH3)
14
ꢀ93.65
1
[47] compared with reference compound xanthotoxin, which can be
clinically investigated. The test organism used was Bacillus subtilis.
Also, compounds were tested for their antimicrobial activity
[48] against Staphylococcus aureus representatives of gram positive
bacteria, Escherichia coli and Pseudomonas aeruginosa as represen-
tatives of gram negative bacteria and the fungus Candida albicans,
the results are presented in Table 1.
hydrogen bond with Asp-73, and another four bonds with Thr-165
(Table 2, Fig. 2). Compound 6 possess ICM scores of ꢀ85.66 form
one hydrogen bond with Asp-73, and another three bonds with
Thr-165 (Table 2, Fig. 3). Compound 13 which is the most active
compound as antibacterial agent possess ICM scores of ꢀ96.07 form
six hydrogen bonds with Asp-73, and another two bonds with Thr-
165 (Table 2, Fig. 4).
4. Conclusion
3.2. Molecular modelling studies
The data reported herein indicates that pyranobenzopyrones
represents a new interesting class of potentially useful compounds
as photosensitizer.
To predict the antimicrobial data on a structural basis, Auto-
mated docking studies were carried out using Molsoft ICM 3.4-8C
program [36], the scoring functions and hydrogen bonds formed
with the surrounding amino acids are used to predict their binding
modes, their binding affinities and orientation of these compounds
at the active site of the topoisomerase II DNA gyrase B enzyme. The
protein–ligand complex was constructed based on the Xray struc-
ture topoisomerase II gyrase B with its bound inhibitor Clorobiocin
available through the RCSB Protein Data Bank (PDB entry 1KZN)
[49]. The scoring functions of the compounds were calculated from
minimized ligand protein complexes.
In order to compare the binding affinity of the newly synthesized
benzopyranone analogues, we docked compounds 2–7, 9–14 into the
empty binding site of topoisomerase II DNA gyrase B (1kzn), with its
bound inhibitor clorobiocin, Figs.1–4 show the docking solutions with
the highest predicted binding affinity for topoisomerase II DNA gyrase
B. Fig.1b show binding mode of the original ligand into its binding site,
while Figs. 2–4 show binding modes of compounds 5, 6,13 respectively.
As shown from the Table 2, and Figs. 1–4 the following results
can be drawn:
Substituted
furobenzopyranones,
pyranobenzopyranones
represent analogues of tricyclic systems with additional substitu-
ents in position 3 that increase the conjugation of the system.
Derivatives with cyano, carboxylic acid, and/or ester moieties are
devoid of any activities, but substitution with acid hydrazide,
thiosemicarbazide decrease ICM scores and increase affinity with
the enzyme and it was found that hydrogen bonds formation with
Asp-73 and Thr-165 amino acid residues may be responsible for the
antibacterial activity as referred to Clorobiocin.
According to these results, we can conclude that compound 13
appears to be the most interesting compound among the newly
synthesized and seem potentially attractive as photo-
chemotherapeutic drug, and as antibacterial against gram positive
and gram negative bacteria.
5. Experimental protocols
Clorobiocin (the original ligand) reveals ICM score of ꢀ123.03
and form two hydrogen bonds with Asp-73 and another three
bonds with Thr-165 (Table 2, Fig. 1). Compound 5 exhibits relatively
weak binding affinity with ICM score of ꢀ53.48 but form one
5.1. Chemistry
Melting points were determined on Gallenkamp and Kofler
melting point apparatus and are uncorrected. Elemental analyses

322
N.A.H. Farag, W. El-Tayeb / European Journal of Medicinal Chemistry 45 (2010) 317–325
(C, H, N) were performed by Micro Analytical Center, Faculty of
Science, Cairo University, the values were found to be within ꢁ0.4%
of the theoretical ones unless otherwise indicated. Infrared spectra
were recorded on Shimadzu IR 435 Spectrophotometer or on
a Genesis II FTIR TM, Mattson, 5225, Verona Road, Madison wi.
53711 USA, using KBr discs. 1H NMR spectra were scanned on
Varian 360 MHz and 90 MHz spectrometers (chemical shifts are
given in part per million (ppm) downfield from TMS). Mass spectra
were made on a Finnigan Mat 212-spectrometer (EI. 120 eV, R
1000). Analytical thin-layer chromatography (TLC) was performed
on precoated silica gel plates 60-F-254 (Merck; 0.25 mm), devel-
oping with chloroform.
(2.3 g g, 75%), m.p 144 ꢂC. IR (KBr,cmꢀ1): 3224, 3150 (NH),
1731,1683 (C]O), 1610 (NH), 1590 (C]C), 1H NMR (CDCl3-d6): a¨
2.51 (s, 3H, CH3), 4.05, 4.14 (s, 2 ꢃ 3H, 2 ꢃ OCH3), 6.95–6.96 (d, 1H,
H-6 of benzofuran, J6,7 ¼ 2.2), 7.64–7.68 (d, 1H, H-7 of benzofuran,
J7,6 ¼ 1.8), 11.20 (3 ꢃ s,3 ꢃ 1H, NH(s) exch.), MS: (m/z, %) ¼ (318,
24.9). Anal. Calc. for C15H14N2O6: C, 56.60; H, 4.40; N, 8.80.Found: C,
56.4; H, 4.6; N, 8.90.
5.1.5. 4-Benzyl-1(5,9-Dimethoxy-2-oxo-4-methyl-2H-furo[3,2-
g]benzopyrane-3-carbonyl) thiosemicarbazide (6)
A
mixture of 5,9-Dimethoxy-2-oxo-4-methyl-2H-furo[3,2-
g]benzopyrane-3-carbohydrazide (5, 3.18 g, 0.01 mol), and benzyl
isothiocyanate (1.42 ml, 0.01 mol) in ethanol 20 ml, was refluxed
for 2 h. After cooling, the solid was filtered, and crystallized from
ethanol. (3.7 g, 80%), m.p 210 ꢂC. IR (KBr,cmꢀ1): 3300,3150
(3 ꢃ NH), 1715ꢀ1700 (2 ꢃ C]O), 1380 (C]S), 1H NMR (CDCl3-d6): a¨
2.35 (s, 3H, CH3), 4.18 (s, 2H, CH2 of benzyl), 4.05, 4.18 (s, 2 ꢃ 3H,
2 ꢃ OCH3), 6.95–6.96 (d, 1H, H-6 of benzofuran, J6,7 ¼ 2.2), 7.64-7.68
(d, 1H, H-7 of benzofuran, J7,6 ¼ 1.8), 7.45–6.65 (m, 5H, phenyl
proton), 9.60, 10.30, 11.20 (3 ꢃ s, 3 ꢃ 1H, 3 ꢃ NH exch.). Anal. Calc.
for C23H21N3O6S: C, 59.10; H, 4.49; N, 8.99.Found: C, 58.7; H, 4.5; N,
8.96.
5.1.1. 5,9-Dimethoxy-2-oxo-4-methyl-2H-furo[3,2-g]benzopyrane-
3-carbonitrile (2)
A
solution of 1-(6-hydroxy-4,7-dimethoxybenzofuran-5-yl)
ethanone (1, 2.4 g, 0.01 mol) in sodium ethoxide 30 ml, was
reacted with ethyl cyanoacetate (1.13 ml, 0.01 mol) by refluxing
the mixture for 20 h and allowed to cool, The precipitate
obtained was collected, dried and crystallized from ethanol/
dioxane giving 2 as yellow powder (1.8 g, 66%), mp 254 ꢂC. IR
(KBr,cmꢀ1): 2240 (CN), 1720 (C]O), 1710 (C]O), 1500 (C]C), 1H
NMR (DMSO-d6): a¨ 2.51 (s, 3H, CH3), 4.05, 4.14 (s, 2 ꢃ 3H,
2 ꢃ OCH3), 6.95–6.96 (d, 1H, H-6 of benzofuran, J6,7 ¼ 2.2), 7.64–
7.68 (d, 1H, H-7 of benzofuran, J7,6 ¼ 1.8), MS: (m/z, %) ¼ (285,
100). Anal. Calc. for C15H11O5N: C, 63.16; H, 3.86: N, 4.91.Found: C,
63.50; H, 4.40; N, 4.80
5.1.6. 3-(4-Benzyl-5-mercapto-4H-1,2,4-triazol-3-yl)-5,9-
Dimethoxy-4-methyl-2H-furo[3,2-g]benzopyrane-2-one (7)
A solution of 4-benzyl-1-(5, 9-Dimethoxy-2-oxo-4-methyl-2H-
furo[3,2-g]benzopyrane-3-carbonyl) thiosemicarbazide (6, 4.7 g,
0.01 mol) in 2 N sodium hydroxide (12 ml) was refluxed for 2 h. The
reaction mixture was cooled, and acidified with dilute hydrochloric
acid to pH 5–6. The produced precipitate was filtered and crystal-
lized from isopropanol.
5.1.2. 5,9-Dimethoxy-2-oxo-4-methyl-2H-furo[3,2-g]benzopyrane-
3-carboxylic acid (3)
A
solution of 5,9-Dimethoxy-2-oxo-4-methyl-2H-furo[3,2-
g]benzopyrane-3-carbonitrile (2, 2.80 g, 0.01 mol) and sodium
hydroxide (150 ml, 15%) was refluxed for 3 h, after chilling, the
mixture was acidified with dilute HCl, water (200 ml) was added,
leave overnight. The solid was filtered and washed several times
with water and dried. The crude products were crystallized from
methanol. (2.3 g, 75%), m.p 137 ꢂC. IR (KBr,cmꢀ1): 3300–2200 (OH
of COOH), 1718, 1640 (2 ꢃ C]O), 1600 (NH), 1500 (C]C), 1H NMR
(DMSO-d6): a¨ 2.51 (s, 3H, CH3), 4.05, 4.14 (s, 2 ꢃ 3H, 2 ꢃ OCH3),
6.95–6.96 (d,1H, H-6 of benzofuran, J6,7 ¼ 2.2), 7.64–7.68 (d,1H, H-7
of benzofuran, J7,6 ¼ 1.8), 11.50 (OH of COOH). Anal. Calc. for
C15H12O7: C, 59.21; H, 3.95.Found: C, 59.3; H, 4.00.
(3.2 g, 70%), m.p 287 ꢂC. IR (KBr,cmꢀ1): 2450 (SH), 1715–1700
(2 ꢃ C]O), 1511 (C]C), 1H NMR (CDCl3-d6): a¨ 2.35 (s, 3H, CH3), 5.20
(s, 2H, CH2 of benzyl), 4.05, 4.18 (s, 2 ꢃ 3H, 2 ꢃ OCH3), 6.95–6.96 (d,
1H, H-6 of benzofuran, J6,7 ¼ 2.2), 7.64–7.68 (d, 1H, H-7 of benzo-
furan, J7,6 ¼ 1.8), 7.45–6.65 (m, 5H, phenyl proton), MS: (m/z,
%) ¼ (449, 59.5). Anal. Calc. for C23H19 N3O5S: C, 61.47; H, 4.23; N,
9.35.Found: C, 61.2; H, 4.0; N, 9.7.
5.1.7. 8-Acetyl-7-hydroxy-4-phenyl-2H-1-benzopyran-2-one (8)
Was previously reported [46].
5.1.8. 2(1H)-oxo-4-Methyl-8-phenyl-6(5H)-oxo-pyrano[2,3-
f]benzopyran-3-carbonitrile (9)
5.1.3. Methyl 5, 9-Dimethoxy-2-oxo-4-methyl-2H-furo[3,2-
g]benzopyrane-3-carboxylate (4)
A solution of 8-Acetyl-7-hydroxy-4-phenyl-2H-1-benzopyran-
2-one (8, 2.8 g, 0.01 mol) in sodium ethoxide 30 ml, was reacted
with ethyl cyanoacetate (1.13 ml, 0.01 mol) by refluxing the mixture
for 20 h and allowed to cool, The precipitate obtained was collected,
dried and crystallized from ethanol/dioxane giving 9 as yellow
powder (2.2 g, 66%), m.p 254 ꢂC.
To
a cold solution of 5,9-Dimethoxy-2-oxo-4-methyl-2H-
furo[3,2-g]benzopyrane-3-carboxylic acid (3, 3.1 g, 0.01 mol) in
methanol, add thionyl chloride (1.12 ml, 1.2 mol) dropwise, stirr for
20 min, then reflux for 4 h, distill under reduced pressure. The
separated product were collected, washed, dried and crystallized
from ethanol. (2.7 g, 85%), m.p 167 ꢂC. IR (KBr,cmꢀ1): 1720, 1690
(2 ꢃ C]O), 1620 (NH), 1550 (C]C), 1H NMR (DMSO-d6): a¨ 2.50 (s,
3H, CH3), 4.05, 4.10, 4.14 (3 ꢃ s, 3 ꢃ 3H, 3 ꢃ OCH3), 6.95–6.96 (d, 1H,
H-6 of benzofuran, J6,7 ¼ 2.2), 7.64–7.68 (d, 1H, H-7 of benzofuran,
J7,6 ¼ 1.8). Anal. Calc. for C16H14O7: C, 60.38; H, 4.40.Found: C, 60.5;
H, 4.6.
IR (KBr,cmꢀ1): 2240 (CN), 1690, 1720 (2 ꢃ C]O), 1560 (C]C), 1H
NMR (DMSO-d6): a¨ 2.51 (s, 3H, CH3), 6.39 (s, 1H, H-7), 7.04–7.08 (d,
1H, H-9, J9,10 ¼ 9.3), 7.22–7.25 (d, 1H, H-10, J10,9 ¼ 9.9), 7.27–7.44 (m,
5H, C6H5-8). Anal. Calc. for C20H11NO4: C, 72.95; H, 3.34: N,
4.26.Found: C, 63.5; H, 4.40; N, 4.6
5.1.9. 2(1H)-oxo-4-Methyl-8-phenyl-6(5H)-oxo-pyrano[2,3-
f]benzopyran-3-carboxylic acid (10)
5.1.4. 5,9-Dimethoxy-2-oxo-4-methyl-2H-furo[3,2-g]benzopyrane-
3-carbohydrazide (5)
A solution of (9, 3.3 g, 0.01 mol) and sodium hydroxide (150 ml,
15%) was refluxed for 3 h, after chilling, the mixture was acidified
with dilute HCl, water (200 ml) was added, leave overnight. The
solid was filtered and washed several times with water and dried.
The crude products were crystallized from methanol. (2.6 g, 75%),
m.p 137 ꢂC. IR (KBr,cmꢀ1): 3300ꢀ2200 (OH of COOH), 1718,
1690,1640 (3 ꢃ C]O), 1595 (C]C), 1H NMR (DMSO-d6): a¨ 2.35 (s,
A
solution of Methyl 5, 9-Dimethoxy-2-oxo-4-methyl-2H-
furo[3,2-g]benzopyrane-3-carboxylate (4, 3.2 g, 0.01 mol), and
hydrazine hydrate 99% (1.0 ml, 0.02 mol) in ethanol 30 ml, heat
under reflux for 6 h The reaction mixture was chilled and filtered.
The obtained precipitate was collected, dried and recrystallized
from methanol.

N.A.H. Farag, W. El-Tayeb / European Journal of Medicinal Chemistry 45 (2010) 317–325
323
3H, CH3), 6.15 (s,1H, H-7), 7.27 (s, 5H, C6H5-8), 7.04–7.08 (d, 1H, H-9,
5.2.1. Pre-experimental procedure
J9,10 ¼ 9.3), 7.22–7.25 (d, 1H, H-11, J11,10 ¼ 9.9), 7.44–7.57 (m, 5H,
aromatic protons), 11.80 (OH of COOH). Anal. Calc. for C20H12O6: C,
68.97; H, 3.49.Found: C, 69.2; H, 3.3.
a) Nutrient agar medium: 0.3% of beef extract, 0.5% of pepone,
0.1% of dipotassium hydrogen phosphate, and 1.5% agar.
b) Broth culture of the organism B. subtilis, was incubated
overnight and then broth culture of the organism was prepared
(each plate contains 15 ml of the agar medium previously
seeded with 0.2 ml of 18 h growth culture in liquid media for the
organism).
c) Paper discs: Whatman No.1 filter paper disc (6 mm) were
sterilized and impregnated with the tested compounds
10 mg/ml dimethylformamide (DMF), and allowed to dry
overnight.
5.1.10. Methyl-2(1H)-oxo-4-methyl-8-phenyl-6(5H)-oxo-
pyrano[2,3-f]benzopyran-3-carboxylate (11)
To a cold solution of (10, 3.48 g, 0.01 mol) in methanol, add
thionyl chloride (1.4 ml, 1.2 mol) dropwise stirr for 20 min, then
reflux for 4 h, distill under reduced pressure. The separated product
were collected, washed, dried and crystallized from ethanol. (3.0 g,
85%), m.p 167 ꢂC. IR (KBr,cmꢀ1): 1720, 1690 (3 ꢃ C]O), 1H NMR
(DMSO-d6): a¨ 2.51 (s, 3H, CH3), 4.05 (s, 3H, OCH3), 6.15 (s, 1H, H-7),
7.27 (s, 5H, C6H5-8), 7.04–7.08 (d, 1H, H-9, J9,10 ¼ 9.3), 7.22–7.25 (d,
1H, H-10 J10,9 ¼ 9.9), 7.44–7.57 (m, 5H, aromatic protons). Anal. Calc.
for C21H14O6: C, 69.61; H, 3.87.Found: C, 69.7; H, 3.6.
5.2.2. Experimental
0.02 ml of the prepared broth culture was added carefully in the
sterile Petri dishes then; 10 ml of the liquefied nutrient agar
medium was added, allowed to be mixed uniformly and solidified
agar layer. Each dish contains a disc impregnated with DMF
(neglect effect of the solvent), and another disc impregnated with
xanthtoxin 10 mg/ml DMF as reference compound.
Two groups of plates were used, one as test plate was incubated
in the dark at 37 ꢂC for 3 h before irradiation to allow for diffusion
of the tested compounds through the agar layer, and the duplicate
plate was left in the incubator overnight as control to determine the
antimicrobial activity.
Covers were removed from the tested Petri dishes and exposed
to UV lamp (365 nm) for 20 min. After irradiation, the plates were
reincubated in the dark at 37 ꢂC overnight and examined for anti-
microbial and photosensitizing activities by measuring the
produced inhibition zones.
5.1.11. 2(1H)-oxo-4-Methyl-8-phenyl-6(5H)-oxo-pyrano[2,3-
f]benzopyran-3-carbohydrazide (12)
A solution of Methyl-2(1H)-oxo-4-methyl-8-phenyl-6(5H)-oxo-
pyrano[2,3-f]benzopyran -3-carboxylate (11, 3.6 g, 0.0 1 mol), and
hydrazine hydrate 99% (1.0 ml, 2 mol) in ethanol 30 ml, heat under
reflux for 6 h The reaction mixture was chilled and filtered. The
obtained precipitate was collected, dried and recrystallized from
methanol.
(2.7 g, 75%), m.p 144 ꢂC. 3224, 3150 (NH), 1731,1683, 1670
(3 ꢃ C]O),1600 (C]C), 1H NMR (CDCl3-d6): a¨ 2.51 (s, 3H, CH3), 6.39
(s, 1H, H-7), 7.27 (s, 5H, C6H5-8), 7.04–7.08 (d, 1H, H-9, J9,10 ¼ 9.3),
7.22–7.25 (d, 1H, H-10 J10,9 ¼ 9.9), 7.44–7.57 (m, 5H, aromatic
protons),11.20 (s,1H, NH exch.). Anal. Calc. for C20H14N2O5: C, 66.30;
H, 3.87; N, 7.73.Found: C, 66.5; H, 3.9; N, 7.7.
5.1.12. 4-Benzyl-1-(2(1H)-oxo-4-methyl-8-phenyl-6(5H)-oxo-
pyrano[2,3-f]benzopyran-3-carbonyl) thiosemicarbazide (13)
A mixture of (12, 3.6 g, 0.01 mol), and benzyl isothiocyanate
(1.42 ml, 0.01 mol) in ethanol 20 ml, was refluxed for 2 h. After
cooling, the solid was filtered, and crystallized from ethanol. (3.1 g,
60%), m.p 210 ꢂC. IR (KBr,cmꢀ1): 3300,3150 (3 ꢃ NH), 1715–1700
(3 ꢃ C]O), 1510 (C]C), 1380 (C]S), 1H NMR (CDCl3-d6): a¨ 2.35 (s,
3H, CH3), 4.05 (s, 2H, CH2 of benzyl), 6.39 (s, 1H, H-7), 7.04–7.08 (d,
1H, H-9, J9,10 ¼ 9.3), 7.22–7.25 (d, H-10, J10,9 ¼ 9.9), 7.45–6.65 (m,
10H, phenyl protons), 9.40, 10.30, 11.65 (3 ꢃ s, 3 ꢃ1H, 3 ꢃ NH exch.).
Anal. Calc. for C28H21N3O5S: C, 65.75; H, 4.11; N, 8.22.Found: C, 65.9;
H, 3.9; N, 8.5.
5.3. Antimicrobial activity
5.3.1. Test organisms
The antimicrobial activity of compounds was evaluated in
vitro against B. subtilis, and S. aureus (as representative examples
of gram positive bacteria). E. coli and P. aeruginosa (as represen-
tative examples of gram negative bacteria) and the fungus C.
albicans.
5.3.2. Method
Agar plate disc diffusion technique [48].
5.1.13. 3-(4-Benzyl-5-mercapto-4H-1,2,4-triazol-3-yl)-4-methyl-8-
phenyl-2H-(6(5H)-oxo-pyrano)[2,3-f]benzopyran-2-one (14)
A solution of (13, 5.1 g, 0.01 mol) in 2 N sodium hydroxide
(12 ml) was refluxed for 2 h. The reaction mixture was cooled, and
acidified with dilute hydrochloric acid to pH 5–6. The produced
precipitate was filtered and crystallized from isopropanol.
(2.5 g, 50%), m.p 287 ꢂC. IR (KBr,cmꢀ1): 2450 (SH), 1715–1700
(2 ꢃ C]O),1590 (C]C), 1H NMR (CDCl3-d6): a¨ 2.35 (s, 3H, CH3), 4.80
(t, 2H, CH2 of benzyl), 6.31 (s, 1H, H-8), 7.04–7.08 (d, 1H, H-9,
J9,10 ¼ 9.3), 7.22–7.25 (d, H-10, J10,9 ¼ 9.9), 7.45–6.65 (m, 10H, phenyl
protons). Anal. Calc. for C28H19N3O4S: C, 68.15; H, 3.85; N,
8.52.Found: C, 68.3; H, 4.0; N, 8.8.
5.3.3. Procedures
Standards of 6 mm in diameter sterilized Whatman filter paper
discs were impregnated with 50 mg/mL solution of the test
compound and standard (tetracycline and amphotercin B) dis-
solved in DMF and allowed to air dry. The discs were applied to the
surface of nutrient agar plates seeded with the test organism (each
plate contains 15 ml of the agar medium previously seeded with
0.2 mL of 18 h growth culture in liquid media for each organism).
The incubated plates were incubated at 37 ꢂC for 48 h and the
inhibition zone was measured in mm around each disc. Discs
impregnated with DMF were used as a control. The antibacterial
reference tetracycline and the antifungal reference amphotericin B
were assayed concurrently.
5.2. Photosensitizing activity
5.4. Molecular modelling studies
In this study the compounds were screened for antimicrobial
and photosensitizing activity by the disc diffusion method [47]
compared with reference compound as xanthotoxin, which can be
clinically investigated. The test organism used was B. subtilis.
5.4.1. Generation of ligand and enzyme structures
The crystal structure of target protein topoisomerase (1kzn) was
retrieved from the Protein Data Bank (http://www.rcsb.org/pdb/
welcome.do). All bound waters ligands and cofactors were

324
N.A.H. Farag, W. El-Tayeb / European Journal of Medicinal Chemistry 45 (2010) 317–325
removed from the protein. The amino acids of the binding site
where defined using data in pdbsum (http://www.ebi.ac.uk/
thoronton-srv/databases/pdbsum/).
5.4.3.3. Display
Conformations.
the
result. Click
Docking/Browse/Stack
ICM stochastic global optimization algorithm attempts to find
the global minimum of the energy function that include five grid
potentials describing interaction of the flexible ligand with the
receptor and internal conformational energy of the ligand, during
this process a stack of alternative low energy conformations is
saved.
The mode of interaction of the 1cbn (Clorobiocin) within 1kzn
was used as a standard docked model as well as for RMSD calcu-
lation. All inhibitors were compared according to the best binding
free energy (minimum) obtained among all the run.
5.4.2. Preparation of small molecule
A set of 3-substituted furobenzopyrone, and pyranobenzopyr-
one analogues synthesized to inhibit topoisomeras II DNA gyrase B
was compiled by us earlier; ChemDraw 3D structures were con-
structed using ChemDraw 3D ultra 8.0 software [Molecular
Modelling and Analysis; Cambridge Soft Corporation, USA (2003)],
and then they were energetically minimized by using MOPAC
(semi-empirical quantum mechanics) with MM2, Jop Type with
100 iterations and minimum RMS gradient of 0.01, and saved as
MDL MolFile (*.mol).
References
[1] L. Pochet, J. Med. Chem. 39 (1994) 1195.
5.4.3. Docking using Molsoft ICM 3.4-8C program
[2] F.P. Gasparro, Extracorporeal Photochemotherapy Clinical Aspects and the
Molecular Basis for Efficacy. Landes, Georgetown, TX, 1994.
[3] G.D. Cimino, H.D. Gamper, S.T. jIsaacs, J.E. Hearst, Annu. Rev. Biochem. 17
(1985) 1151.
[4] J. North, H. Neyndorff, J.P. Levy, Photochem. Photobiol. 17 (1993) 99.
[5] E. Ben-Hur, P.S. Song, Adv. Radiat. Biol. 11 (1984) 131.
[6] F. Bordin, F. Carlassare, L. Busulini, F. Baccichetti, Photochem. Photobiol. 58
(1993) 133.
5.4.3.1. Convert our PDB file 1kzn into an ICM object. This
conversion involves addition of hydrogen bonds, assignment of
atoms types, and charges from the residue templates. Click on
MolMechanics/Convert/Protein, and then delete water
molecules.
[7] O. Gia, S. Mobilio, M. Palumbo, M.A. Pathak, Photochem. Photobiolol. 57 (3)
(1993) 497.
[8] C. Marzano, F. Baccichetti, F. Carlassare, A. Chilin, S. Lora, F. Bordin, Photochem.
Photobiol. 71 (2000) 263.
[9] D.J. Kirkland, K.L. Creed, P. Mannisto, Mutat. Res. 116 (1983) 73.
[10] S. Venturini, M. Tamaro, C. Monti-Bragadin, F. Carlassare, Mutat. Res. 88 (1981)
17.
[11] G.J. Hook, J.A. Heddle, R.R. Marshall, Cytogenet. Cell Genet. 35 (1983) 100.
[12] S.R. Stern, R. Lange, J. Invest. Dermatol. 91 (1988) 120.
[13] Z. Zarebska, E. Waszkowska, S. Caffieri, F. Dall’Acqua, Farmaco 55 (8) (2000)
515.
5.4.3.2. To perform ICM small molecule docking.
a) Setup docking project
i) Set Project Name: Click on Docking/Set project name, press
OK.
ii) Setup the receptor
Click on Docking/Receptor Setup, enter the receptor molecule in
the receptor molecule data entry box (a_*) will do, then click on
identify the binding sites button to identify the potential ligand
binding pockets, press OK.
After the receptor setup is complete, the program normally
displays the receptor with selected binding site residues high-
lighted in yellow xstick presentation.
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ICM makes a box around the ligand binding site based on the
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The step now is to construct energy maps of the environment
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Use interactive docking to dock one ligand at a time. Click on
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