1. Muhammad Athar Abbasi et al., J.Chem.Soc.Pak., Vol. 38, No. 01, 2016 166
Enzyme Inhibitory and Molecular Docking Studies on
Some Organic Molecules of Natural Occurrence
1
Muhammad Athar Abbasi*, 1
Ghulam Hussain, 1
Aziz-ur-Rehman, 1
Durre Shahwar,
2
Khalid Mohammed Khan, 3
Ayesha Mohyuddin, 4
Muhammad Ashraf, 4
Jameel Rahman
5
Muhammad Arif Lodhi, and 5
Farman Ali Khan
1
Department of Chemistry, Government College University, Lahore-54000, Pakistan.
2
HEJ Research Institute of Chemistry, International Center for Chemical and Biological Sciences,
University of Karachi, Karachi-75270, Pakistan.
3
Department of Chemistry, University of Management and Technology, Lahore-54770, Pakistan.
4
Department of Chemistry; The Islamia University of Bahawalpur, Bahawalpur-63100, Pakistan.
5
Department of Biochemistry, Abdul Wali Khan University, Mardan-23200, Pakistan.
atrabbasi@yahoo.com; abbasi@gcu.edu.pk*
(Received on 23rd
June 2015, accepted in revised form 3rd
December 2015)
Abstract: In the present study, in vitro enzyme inhibitory studies on cinchonidine (1), cinchonine
(2), quinine (3), noscapine (narcotine, 4) and santonine (5) were carried out. The various enzymes
included in the study were lipoxygenase, xanthine oxidase, acetyl cholinesterase, butyryl
cholinesterase and protease. The results revealed that 2, 3, and 4 were moderate active against
lipoxygenase and xanthine oxidase enzymes. The molecule 3 possessed weak activity against butyryl
cholinesterase enzyme while remaining molecules were inactive against this enzyme. However, all
these compounds were inactive against acetyl cholinestrase and protease enzymes. The synthesized
compounds were computationally docked into the active site of lipoxygenase enzyme. The
compounds 3 and 4 showed decent interactions, hence strengthening the observed results.
Keywords: Cinchonidine, cinchonine, quinine, noscapine, lipoxygenase, xanthine oxidase.
Introduction
Lipoxygenase enzymes can be found in a
wide variety of plant and animal tissues. In
lipoxygenase type-1 (LOX), the iron is present in the
divalent state. It is oxidized to the catalytically active
Fe3+
by the reaction product 15-hydroperoxy-
eicosatetraenoic acid (15-HPETE) and leukotrienes
from arachidonic acid as a substrate. Its also oxidized
by 13-hydroperoxy-octadecadienoic acid (13-
HPODE) from linoleic acid as a substrate [1, 2].
Leukotrienes are important biologically active
mediators in a variety of inflammatory events. It has
been found that these LOX products play a key role
in variety of disorders such as bronchial asthma,
inflammation [3, 4].
Xanthine oxidase is considered to be an
important biological source of superoxide radicals.
These and other reactive oxygen species (ROS)
participate to the oxidative stress on the organism.
These are also involved in large number of
pathological processes like inflammation,
atherosclerosis, cancer, aging etc [5].
Acetyl cholinesterase (AChE) and butyryl
cholinesterase (BChE) comprise a family of enzymes
which include serine hydrolases. The different
specificities for substrates and inhibitors for these
enzymes are due to the differences in amino acid
residues of the active sites of AChE and BChE. The
enzyme system is responsible for the termination of
acetylcholine at cholinergic synapses. These are key
components of cholinergic brain synapses and
neuromuscular junctions. The major function of
AChE and BChE is to catalyze the hydrolysis of the
neurotransmitter acetylcholine and termination of the
nerve impulse in cholinergic synapses [6]. In the
Alzheimer’s disease patients, a reduction in the
Acetylcholine (ACh), a neurotransmitter, appear to
be acute element in the development of dementia,
hence Alzheimer’s disease and other type of
dementia could be administered by the use of agents
that reinforce the level of acetylcholine. The
inhibition of AChE play a key role not only
stimulating cholinergic transmission in the brain, but
also decreasing the collection of amyloid β peptide
(AB) and the formation of the neurotoxic fibrils in
Alzheimer’s disease [7]. The search for new
cholinesterase inhibitors is considered an important
and ongoing strategy to introduce new drug
candidates for the treatment of Alzheimer’s disease
and other related diseases [8].
Serine protease inhibitor plays a key role in
the natural defense system of plants against insect
*
To whom all correspondence should be addressed.

2. Muhammad Athar Abbasi et al., J.Chem.Soc.Pak., Vol. 38, No. 01, 2016 167
predation by restricting insect proteinases. Trypsin is
a serine protease which has recently attracted much
more importance and plays a role in the devastation
of fibrous proteins [9]. Acute activity of trypsin
causes cancer, hepatitis, muscular dysentery and
arthritis. Nature has bestowed some of drugs for
various illnesses. A number of metabolites obtained
from natural sources, has moderate to efficient
trypsin inhibitory activity [10]. Here, we report the
screening of 1-5 against lipoxygenase, xanthine
oxidase, acetyl cholinesterase, butyrl cholinesterase
and protease enzymes to explore their therapeutic
potentials. Additionally, a computational approach
was adopted to find out the binding modes of these
synthesized inhibitors against LOX enzymes.
Molecular Operating Environment (MOE) was used
for docking studies. The results revealed that the
designed inhibitors have decent affinity with the
binding cavity of target enzymes [11].
Experimental
Sample Materials
The compounds 1-5 are naturally occurring
molecules in various plant sources but in the present
studies these were purchased directly from Sigma-
aldrich/merck Company and their structures were
confirmed by comparison of their spectral data with
reported data for 1 [12], 2, 3 [13], 4 [14] and 5 [15].
Lipoxygenase Assay
Lipoxygenase activity was assayed
according to the method [16] with minor
modifications. 200 µL lipoxygenase assay mixture
containing 150 µL sodium phosphate buffer (100
mM, pH 8.0), 10 µL test compound and 15 µL
purified lipoxygenase enzyme was prepared. The
contents were mixed, pre-read at 234 nm and pre-
incubated for 10 minutes at 25 °C. The reaction was
initiated by addition of 25 µL substrate solution. The
change in absorbance noticed after 6 min at 234 nm
was used as index for the inhibition. All reactions
were performed in triplicates. The positive and
negative controls were incorporated in the assay.
Baicalein (0.5 mM well-1
) was used as a positive
control. The percentage inhibition (%) was calculated
as,
where Control =Total enzyme activity without
inhibitor
Test = Activity in the presence of test compound
IC50 values (concentration at which there is
50% enzyme inhibition) of compounds was
calculated using EZ–Fit Enzyme kinetics software
(Perella Scientific Inc. Amherst, USA). IC50 values
were determined by serial dilution of the compounds
from 0.5 mM to 0.25, 0.125, 0.0625, 0.03125,
0.015625 mM and from the graph. Values are mean
of 3 independent experiments.
Xanthine Oxidase Assay
The XO activities with xanthine as the
substrate were measured spectrophotometrically with
the following modifications. The xanthine solution
(0.15mM) was prepared by initially dissolving
xanthine (Sigma) in a minimal volume of NaOH, and
adjusting pH to 7.5. The XO solution was pre pared
by diluting XO from cow’s milk (Sigma) to a final
concentration of 0.2 U:ml in cold 50 mM potassium
phosphate buffer (pH 7.5). The assay mixture
consisted of 0.250 ml plant extract solution (0.4
mg:ml 50 mM potassium phosphate buffer, pH 7.5),
0.385 ml 50 mM potassium phosphate buffer (pH
7.5) and 0.330 ml xanthine solution, giving a final
concentration of 100 mg plant extract per ml assay
mixture. The reaction was initiated by adding 0.035
ml XO solution, and the change in absorbance
recorded at 295 nm for 3 min at room temperature.
Allopurinol (Sigma) was used as a standard inhibitor
at a final concentration of 100 mg:ml in the assay
mixture. Xanthine oxidase activity was expressed as
percent inhibition of xanthine oxidase, calculated as
(1 - B/A) x100, where A is the change in absorbance
of the assay without the plant extract (Dabs. with
enzyme_Dabs. without enzyme), and B is the change
in absorbance of the assay with the plant extract
(Dabs. with enzyme_Dabs.without enzyme) [17].
Cholinesterase Assays
The AChE and BChE inhibition study were
done according to the method [18] with slight
modifications. 100 µL reaction mixture contained 60
µL Na2HPO4 buffer having conc. of 50 mM with pH
7.7 was prepared. Test compound of volume ten µL
& conc. of 0.5 mM well-1
was poured, accompanied
by the accession of ten µL enzyme of conc. 0.005
unit well-1
. All contents were immixed and pre-read
at a wavelength of 405 nm. After that pre-incubation
of the contents for 10 min at 37 ºC was performed
and the initiation of the reaction was done through 10
µL of conc. 0.5 mM well-1
substrate i.e
acetylthiocholine iodide (for AChE) or
butyrylthiocholine chloride (for BChE). Then the ten
µL of DTNB with conc. 0.5 mM well-1
were added.
After incubation of 15 min at 37 ºC, absorbance at
405 nm was measured by 96-well plate reader
Synergy HT, Biotek, USA. All the observations were

3. Muhammad Athar Abbasi et al., J.Chem.Soc.Pak., Vol. 38, No. 01, 2016 168
carried out in triplicate with their respective controls.
Eserine of conc. 0.5 mM well-1
was applied as a
positive control. The results were calculated as per
formula mentioned for the lipoxygenase assay.
Protease Inhibition Assay
The protease inhibitory potential of isolated
and its synthesized derivatives were evaluated using
the colorimetric method with some modification. Tris
buffer (100 mM) of pH 7.5 (1.0 mL),trypsin (0.3
mL), and the tested compound (0.1 mL) were
incubated at room temperature for 10 min. BApNA
(50 μL) was added to the reaction and the absorbance
read at 410 nm after an incubation period of 30 min
at 37 ◦ C. Phenylmethylsulfonylfluoride (PMSF) was
used as standard inhibitor. The % inhibition was
calculated by using the following formula:
q %= A-B x 100
A
where A is the absorbance of blank and B is the
absorbance of the tested compound.Protease [10].
Molecular Docking Study
Protein Preparation
The protein molecules included in our study,
α-glucosidase and BChE were retrieved from Protein
Data Bank. Water molecules were removed and the
3D protonation of the protein molecule was
performed using MOE applications. The energy of
the protein molecules were minimized via energy
minimization algorithm of MOE tool. The following
parameters were used for energy minimization;
gradient: 0.05, Force Field: MMFF94X+Solvation,
Chiral Constraint: Current Geometry. Energy
minimization was terminated when the root mean
square gradient falls below the 0.05. The minimized
structure was used as the template for Docking.
Molecular Docking
The binding mode of the ligands into the
binding pocket of protein molecule was predicted by
MOE-Dock implemented in MOE. After the
completion of docking, the best poses for Hydrogen
Bonding/π-π interactions were analyzed by using
MOE applications [11]. All the compounds were
docked into the active site of lipoxygenase enzyme.
The interaction analysis revealed that 3 and 4 have
shown acceptable binding modes.
Results and Discussion
Cinchonidine (1), cinchonine (2), quinine
(3), and noscapine (narcotine, 4) are the alkaloids
which are used for the treatment of biological
diseases like malaria, analgesic pain, anti-
inflammatory, cancer, and stroke treatment [5]. The
santonin (5) is a sesqui-terpene molecule (Fig. 1).
The IC50 values of all these compounds have been
illustrated in Table-1 against a series of enzymes
(Table-1).
Enzyme Inhibition Activity
To find effective inhibitors of enzymes from
natural sources, we tested 1-5 against aforementioned
enzymes. Against lipoxygenase 2, 3 and 4 possessed
moderate inhibitory potential with IC50 values
99.12±0.03, 189.12±0.11, 177.13±0.13 µmoles/L
relative to baicalein, a reference standard having IC50
value of 22.4±1.3 µmoles/L (Table 1). The
compounds 1 and 5 displayed very weak activities
against this enzyme perhaps owing to changed
stereochemistry of hydroxyl group in 1 as compared
to 2 and a unique skeleton in 5. A moderate
inhibitory potential was also ascribed by molecules 2-
5 against xanthine oxidase with more than 50%
inhibition except 1 which showed very less activity
(Table 1). The altered stereochemistry of hydroxyl
group in 1 as compared to 2 might be attributed here
again for the loss of activity against this enzyme.
When the inhibitory potential of 1-5 against acetyl
cholinesterase and protease were determined, it was
revealed that none of these compounds has activity
against these enzymes (Table 1). Quinine (3) was the
only alkaloid which possessed weak inhibitory
potential against butyryl cholinesterase enzyme with
IC50 value of 61.25 ± 0.01 µmoles/L relative to
Eserine, the reference standard having IC50 value of
0.85±0.001 µmoles/L.
Molecular Docking Analysis
In case of compound 3, a total of 3
interactions were observed. The active site residues
His518 and Gln716 interacts with the hydroxyl group
of vinylquinuclidin methanol moiety whereas, His13
interacts with methoxyquinoline moiety respectively
(Fig. 2). The analysis of the interaction of compound
4 showed that two of the active side residues interact
with the docked molecule. His13 interacts with
methoxy group of dimethoxybenzene moiety. The
active site residue His518 interacts with double
bonded oxygen of furan moiety as shown in Fig. 3.

4. Muhammad Athar Abbasi et al., J.Chem.Soc.Pak., Vol. 38, No. 01, 2016 169
Table-1: The enzyme inhibition studies on compounds 1-5.
Compound
No.
LOX
(%) at
0.5mM
LOX
(IC50)
µmoles/L
XO
(%)at
0.5mM
XO
(IC50)
µmoles/L
AChE
(%) at
0.5mM
AChE
(IC50)
µmoles/L
BChE
(%) at
0.5mM
BChE
(IC50)
µmoles/L
Protease
(%) at
0.5mM
Protease
(IC50)
µmoles/L
1 17.06 Nil 16 Nil 22.86 Nil 27.41 Nil 30.15 Nil
2 94.27±0.53 99.12±0.03 71.9±0.01 95±0.03 15.68 Nil -0.37 Nil 39 Nil
3 80.85±0.28 189.12±0.11 91.19±0.05 170±0.11 25.49 Nil 86.29±1.53 61.25±0.01 32 Nil
4 91.36±0.31 177.13±0.13 85.47±0.05 85±0.51 -1.02 Nil 20.58±0.25 Nil 0.34 Nil
5 17.45 Nil 90.89±0.01 180±0.51 5.83 Nil 1.34 Nil 24 Nil
Control Baicalein 22.4±1.3 Allopurinol 6.6 ±0.13 Eserine 0.04±0.001 Eserine 0.85±0.001 PMSF 0.11±0.02
Note: LOX = Lipoxygenase, XO = Xanthine Oxidase, AChE = Acetyl Cholinesterase, BChE = Butyryl Cholinesterase, PMSF =
Phenylmethanesulfonylfluoride.
N
HO N
H
Cinchonidine (1)
N
HO N
H
Cinchonine (2)
N
HO N
H
H3CO
Quinine (3)
N
O
O
OCH3
CH3
OCH3
O
O
H
H
H3CO
Noscapine
(4)
O
O
CH3
H
CH3
O
CH3
1
2
3 4
5
6
7
8
9
10
11
12
H
H
Santonin (5)
Fig. 1: Structures of Compounds 1-5.
Fig. 2: The 2D interaction analysis of Quinine (3)
against LOX.
Fig. 3: The 2D interaction analysis of Noscapine (4)
against LOX.

5. Muhammad Athar Abbasi et al., J.Chem.Soc.Pak., Vol. 38, No. 01, 2016 170
Conclusion
It was concluded from the present
investigation that among the studied molecules, the
compounds 2-4 are overall moderate inhibitors of
lipoxygenase whereas, maximum inhibitory potential
was shown by 2 with IC50 values 99.12±0.03 it is
might be due to the presence of hydroxyl group.
Minimum inhibitory potential was shown by 3 with
IC50 values 189.12±0.11 µmoles/L which might be
due to the presence of hydroxyl and methoxy group
relative to baicalein, a reference standard having IC50
value of 22.4±1.3 µmoles/L. The compounds 2-5 are
overall moderate inhibitors of xanthine oxidase
whereas, maximum inhibitory potential was shown
by 4 with IC50 values 85±0.051 it is might be due to
the presence of three olkoxy, three ether and one
ketonic group. Minimum inhibitory potential was
shown by 5 with IC50 values 180±0.51 µmoles/L
which might be due to the presence of two ketonic
and one ether group relative to allopurinol, a
reference standard having IC50 value of 6.6±.13
µmoles/L. Lipoxygenase and xanthine oxidase
enzymes can find their utility in a large number of
pathological processes like inflammation,
atherosclerosis, cancer and aging etc. These
molecules can further be evaluated for in vivo studies
by the pharmaceutical industries in drug discovery
program.
References
1. H. C. Clapp, A. Banerjee and S. A. Rotenberg,
Inhibition of soybean lipoxygenase by n-
alkylhydroxylamines. J. Biochem., 24, 1826
(1985).
2. C. Kemal, P. Louis-Flemberg, R. Krupinski-
Olsen and A. L. Shorter, Reproductive
inactivation of soybean lipoxygenase activity. J.
Biochem., 26, 7064 (1987).
3. D. Steinhilber, 5-Lipoxygenase: A Target for
Antiinflammatory Drugs Revisited, Curr. Med.
Chem., 6, 71 (1999).
4. G. A. Alitonou, F. Avlessi, D. K. Sohounhloue,
H. Agnaniet, J. M. Bessiere and C. Menut,
Investigations on the essential oil of
Cymbopogon giganteus from Benin for its
potential use as an anti-inflammatory agent, Int.
J. Aroma., 16, 37 (2006).
5. B. Halliwell, J. M. C. Gutteridge and C. E. J.
Cross, “Free radicals, antioxidants, and human
disease: where are we now?” Lab. Clin. Med.,
119, 598 (1992).
6. M. Cygler, J. D. Schrag, J. Sussman, L. M.
Harel and I. Silman, Relationship between
Sequence Conservation and Three-Dimensional
Structure in a Large Family of Esterases,
Lipases, and Related Proteins. Protein Sci., 2,
366 (1993).
7. M. R. Loizzo, R. Tundis, F. Menichini and F.
Menichini, Natural products and their
derivatives as cholinesterase inhibitors in the
treatment of neurodegenerative disorders: an
update, Curr. Med. Chem., 12, 1209 (2008).
8. G. Bertaccini and P. Substance, Handbook of
Experimental Pharmacology, Springer, Berlin,
59/II, p. 85 (1982).
9. S. Liliane and S. Michel, Trypsin and
Chymotrypsin Inhibitors in Insects and Gut
Leeches, Curr. Pharm. Des., 8, 125 (2002).
10. A. Jedinák, T. Maliar, D. Grancai and M. Nagy,
Inhibition activities of natural products on
serine proteases, Phytother. Res., 20, 214
(2006).
11. A. Wadood, M. Riaz, S. B. Jamal and M. Shah,
Interactions of ketoamide inhibitors on HCV
NS3/4A protease target: molecular docking
studies, Mol. Biol. Rep., 1, 337 (2014).
12. T. Bürgi, A.Baiker, Conformational behavior of
cinchonidine in different solvents: A combined
NMR and ab initio investigation, J. Am. Chem.
Soc., 120, 12920 (1998).
13. H. Shibuya, C. Kitamura, S. Maehara, M.
Nagahata, H. Winarno, P. Simanjuntak, H-S.
Kim, Y. Wataya, and K. Ohashi,
Transformation of Cinchona Alkaloids into 1-N-
Oxide Derivatives by Endophytic Xylaria sp.
Isolated from Cinchona pubescens, Chem.
Pharm. Bull., 51, 71 (2003).
14. M. A. Abbasi, Aziz-ur-Rehman, M. Z. Qureshi,
M. S. Shahid, S. Rasool, M. Ashraf, Nitrated
and Brominated Narcotine and its Cleaved
Adduct as Butyrylcholinesterase Inhibitors, Pak.
J. Chem., 3, 1 (2013).
15. S. K. Paknikar, B. L. Malik, R. B. Bates, S. Caldera
and T. V. Wijayaratne, Stereochemistry of 45-
dihydroxy-α-santonin and structure of a new
santonin oxidation product, Tetrahedron Lett., 35,
8117 (1994).
16. A. L. Tappel, The mechanism of the oxidation of
unsaturated fatty acid catalyzed by hematin
compounds, Arch. Biochem. Biophy. 44, 378
(1953).
17. L. Marcocci, L. Packer, M. T. Droy-Lefaix, A.
Sekaki and M. Garde`s-Albert, The nitric
oxide-scavenging properties of Ginkgo biloba
extract EGb 761, Methods Enzymol., 234, 462
(1994).
18. G. L. Ellman, K. D. Courtney, V. Andres and R.
M. Featherstone, A new and rapid colorimetric
determination of acetylcholinesterase activity,
Biochem. Pharmacol., 7, 88 (1961).