In-silico Molecular Docking Study of Coumarin Derivatives in order to Investigate the Inhibitory Effects of Human Monoamine Oxidase Enzyme and DFT Studies

Journal of Environmental Treatment Techniques

2019, Volume 7, Issue 3, Pages: 349-356

J. Environ. Treat. Tech.

ISSN: 2309-1185

Journal weblink: http://www.jett.dormaj.com

In-silico Molecular Docking Study of Coumarin

Derivatives in order to Investigate the

Inhibitory Effects of Human Monoamine

Oxidase Enzyme and DFT Studies

Marzieh Asadi , Moslem Sedaghat , Zahra Sasani Pour , Ali Mohammad Amani ,

Ahmad Movahedpour , Sina Vakili , Marzieh Shefaghat , Mahsa Maleknia , Saam

Noroozi *

¹Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University

of Medical Sciences, Shiraz, Iran

Department of Medical Nanotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of

Medical Sciences, Shiraz, Iran

Student research committee, Shiraz University of Medical Sciences, Shiraz, Iran.

Department of Biochemistry, Shiraz University of Medical Sciences, School of Medicine, Shiraz, Iran

Student of Fasa University of Medical Sciences, Fasa, Iran

Department of Biochemistry, Fasa University of Medical Sciences, Fasa, Iran

Received: 11/05/2019

Accepted: 02/08/2019

Published: 01/12/2019

Abstract

In the present study, DFT calculations of four coumarin derivatives and also their molecular docking with “human

monoamine oxidase enzyme” (HMAO) were performed in order to study the inhibitory effect of these compounds. The

optimized molecular geometries and vibrational frequencies were calculated at the B3LYP/6-31+G(d) level of theory

without any imaginary frequency. The total energy, dipole moment and energies of the frontier molecular orbitals were

calculated for all the compounds. All quantum calculations were performed using the Gaussian 03 software. The molecular

docking of coumarin derivatives and phenelzine with HMAO enzyme were calculated and inhibitory effect of coumarins

were compared with phenelzine. Also the binding free energy, amino acid residue and hydrogen bond interactions between

all the compounds and HMAO enzyme were calculated. The binding energies for coumarins and Phenelzine are in the range

of 7.04 – -6.15 Kcal/mol. The binding energy potency follows the order of: 4>2>3>1> Phenelzine. The binding energy of all

the compounds with HMAO enzyme was stronger than Phenelzine.

Keywords: Coumarin, antidepressant, Monoamine oxidase, DFT study, molecular docking

various coumarin derivatives are able to block

Introduction

inflammation by inhibiting different targets but none of

them has found a way to the clinics so far.(7)

Fylaktakidou et al (2004) reviewed the capability of

different natural and synthetic coumarins as anti-

inflammatory and antioxidant molecules (8). Curini et

al (2006) reported an array for the biological

Coumarins (also known as 1, 2-benzopyrone or

hydroxycinnamic acid-8-lactone) are categorized as an

important class of natural compounds, mainly found in

Rutaceae and Umbelliferae families. These compounds

are divided into several classes such as simple

coumarins,

furanocoumarins,

pyranocoumarins,

applications

prenyloxycoumarins

and

biscoumarins, triscoumarins, and coumarinolignans.

Coumarins have too many biological applications

including antidepressant (1), antimicrobial (2), antiviral

prenyloxyfuranocoumarins (9). In addition to anti-

inflammatory properties, coumarins ha ve also been

considered as potential anticancers (10, 11) and also

amonoamine oxidase inhibitors (12).

Monoamine oxidase (MAO) is a ﬂavoenzyme with

iron that exists within cells, being connected to the

surface membrane of mitochondria and involved in the

degradation of biogenic amines. Two MAO isoenzymes

i.e. MAO-A and MAO-B, are closely linked in opposite

orientations to the X chromosome and expressed in the

external part of mitochondrial membrane. MAO-A and

MAO-B are able to oxidize neuro-transmitters and

(

3), anticancer (4), anti-inflammatory, antioxidant, and

anticoagulant (5, 6). Coumarins like esculetin, fraxetin,

daphnetin and other related coumarin derivatives are

known as inhibitors, not only LOX and COX

enzymes, but also the neutrophil-dependent superoxide

anion generation. Many investigators reported that

Corresponding author: Saam Noroozi, Department of

Biochemistry, Fasa University of Medical Sciences,

Fasa, Iran. E-mail: saam.noroozi@gmail.com.

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Journal of Environmental Treatment Techniques

2019, Volume 7, Issue 3, Pages: 349-356

xenobiotic amines using the oxidative deamination

process (13). MAO is abundantly found in noradrenergic

nerve terminals but it is also present in many other

places, like liver or intestinal epithelium. MAO-A, the

primary type in ﬁbroblasts, preferentially degrades

serotonin, norepinephrine and dopamine. Meanwhile,

MAO-B, found in platelets, human brain and other

primates, preferentially degrades the phenyl ethylamine

and benzylamine (12).

The activity of MAO helps maintaining the neuron

ﬁring rates throughout the body within homeostatic

limits. Part of the biochemical activity of MAO produces

hydroxyl radicals, very toxic members of the oxygen free

to the protein and the structure was optimized and

applied for molecular docking.

II. Molecular docking

The optimized geometries for all the ligands

calculated by DFT calculations were applied as input

files for the conformational search by systematic search

method. The conformer with lowest energy was

employed for the docking calculations. AutoDock 4.2

software, using the Lamarckian genetic algorithm

together with the AutoDock tools, was used to set up and

perform docking calculations of all compounds binding

to the receptors.(21) In order to perform docking, the

protein structure having pdb format is prepared as shown

in part I and applied in the present study. Polar

hydrogens are added for saturation while the non-polar

hydrogens are merged and Gasteiger charges are

computed. A grid box with grid spacing of 0.375 Å and

dimension of 60 × 95 × 80 grid points along x, y and z

axes are made around the active sites. In this regard, the

grid center was set at 2, 16, and 38 Å. The grid box

contains the complete active site of the protein receptor

and offers enough space for the ligand translational and

rotational walk.

AutoGrid was employed to make the grid map for

different atoms in the ligands and receptor. After the

completion of the grid map, Autodock was used for 50

runs with the following: maximum of the numbers for

the energy evaluations are set to 2500000 and a

maximum number of 27000 GA operations are produced

by an initial population for 150 individuals. For each of

the docking cases, the lowest energy value for the docked

conformations was chosen as the binding mode on the

basis of the AutoDock scoring function. Visualization of

the docked pose has been performed by Discovery Studio

and Chimera molecular graphics software.

radical group that

might be involved in

neurodegenerative disorders such as Parkinson’s disease.

As mentioned above, MAO plays a determining role in

the metabolism of many neurotransmitters and can be

utile in the treatment with several psychiatric and

neurological diseases. These characteristics determine

the pharmacological interests for the MAO inhibitors. In

fact, human MAO-B inhibitors e.g. selegiline (R-()-

deprenyl) and rasagiline are advantageous compounds

for the treatment with Parkinson (14) and Alzheimer’s

diseases (15, 16). Besides, the selective MAO-A

inhibitors, like clorgyline (irreversible) and moclobemide

(

reversible), are useful for the treatment with

neurological disorders like depression and anxiety (17,

8). In this project, we have investigated the DFT

calculations of some coumarin derivatives and their

molecular docking with human monoamine oxidase

enzyme in order to investigate the inhibitory effect of

these compounds.

Materials and Methods

.1 DFT study

One of the most important tasks for the

computational works is to determine the optimized

geometries of the compounds. In this study, the

molecular structures of the all the compounds were

optimized and the electronic properties were calculated.

Besides, the optimized geometries of the molecules were

visualized with ChemCraft program. All the calculations

were performed applying the Becke’s three parameters

hybrid exchange functional with the Lee-Yang-Parr

gradient corrected correlation functional (B3LYP hybrid

functional). All the atoms were described with a split

valence Pople basis set plus polarization and diffuse

functions, 6-31+G(d) (19). Frequency calculations were

performed for all the optimized geometries to ensure that

the obtained structures represent local minima. All the

calculations were established employing the Gaussian 03

program suite.

3 Results and discussion

3.1 Computational study

The geometries of all the structures were completely

optimized using the B3LYP/6-31+G(d) level of theory.

The optimized structures are depicted in figure1. For all

the structures, total energy, dipole moment, energy levels

of HOMO (highest occupied molecular orbital) and

LUMO (lowest unoccupied molecular orbital) and

HOMO-LUMO energy gap (∆E) were calculated and are

summarized in Table 1.

As a matter of fact, frontier molecular orbitals

(FMOs) are the most important orbitals in a molecule.

FMOs play determining roles in the interaction between

the molecules and also in the electronic spectrum of a

molecule. For all the compounds, the calculations

indicated that the charge density distribution for the

HOMO level is predominantly localized on the π-

conjugated system of aromatic carbons together with the

lone pairs on oxygen atoms of hydroxyl and methoxy

groups. Meanwhile, the charge density of the LUMO is

localized on the anti-bonding aromatic system. FMOs in

all the optimized structures were visualized using the

gauss view 5. The density plots of HOMO and LUMO

orbitals are revealed in Figure 2. Vibrational frequency

calculations were performed for all the compounds using

the similar levels for which the imaginary frequencies

were not observed. The detailed vibrational assignments

for the main frequencies in all the compounds are listed

in Table 2.

2.2 Molecular docking study

I. Protein preparation

PDB database was applied to retrieve the raw X-ray

crystal structures of HMAO (PDB: 1GOS)(20), but this

structure cannot be used directly for the molecular

docking investigations. Since this structure involving the

heavy atoms, cofactors, waters, metal ions and ligand

and it fails to provide information on topologies, bond

orders and formal atomic charges. Therefore, this PDB

structure has been changed employing the protein

preparation wizard available in chimera software. At the

initial step, all the components, excluding the chain A of

protein, were removed. All hydrogen atoms were added

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2019, Volume 7, Issue 3, Pages: 349-356

Table 1: The computed electronic properties for all compounds at B3LYP/6-31+G(d) level of theory.

Properties

Compound

HOMO-LUMO

gap (eV)

4.450

B3LYP (a.u.)

µ (Debye)

HOMO (a.u.)

LUMO (a.u.)

-572.2417

-647.4505

-686.7536

-726.0606

3.926

4.017

6.504

6.814

-0.2260

-0.2134

-0.2186

-0.2160

-0.0624

-0.0620

-0.0652

-0.0630

4.119

4.174

4.163

Figure 1: The optimized structure of the all compounds.

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2019, Volume 7, Issue 3, Pages: 349-356

Figure 2: Density plot of HOMO and LUMO orbitals for all compounds

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2019, Volume 7, Issue 3, Pages: 349-356

.2 Molecular docking study

The molecular docking operations for the coumarin

with the examination of the known structure of HMAO

in a non-covalent complex with four diﬀerent ligands.

Only complexes containing non-covalent ligands were

selected which is due to that the bond length of a

covalent bond is less than that of non-covalent bond.

Thus, during the docking process for a covalent inhibitor,

a ligand docked in a correct location will poorly be

scored even its position may be correct, experimentally.

At first, the crystal structure of HMAO (PDB: 1GOS)

was optimized (See Figure 3 for the 3D structure). The

derivatives and phenelzine with HMAO enzyme were

performed. Phenelzine, having the molecular formula of

β-phenylethylhydrazine, is

inhibiting antidepressant which is effective in the

treatment with panic disorder and social anxiety disorder.

Due to the mentioned reason, Phenelzine, as

monoamine oxidase

commercial drug, was chosen to be compared with

present the compounds in this study. Our studies started

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2019, Volume 7, Issue 3, Pages: 349-356

docking calculations were performed and the best

conformation based on the binding energy value for each

ligand was chosen for the analysis. The best

conformation docked to the HMAO is shown in Figure 4

for all the compounds.

In all the cases, binding energy values, amino acid

residue and amino acids involved in hydrogen

bonding interactions for the best conformation are listed

in table 3 and visualized in figure 5. The calculated

binding free energies for the Phenelzine and compounds

Compound 3 and 4 also exhibit two and three classical

hydrogen bondings, respectively. Compound 4, despite

of the lower number of hydrogen bondings rather than

compound 2 and also the absence of π–π interactions,

possesses the highest amount of energy, which is due to

the orientation of the molecule. In this regard, Phenelzine

also forms six hydrogen bondings with val10, leu33 and

arg233 amino acids. Based on the docking results, the

interactions in the compounds 1-4 with HMAO enzyme

are stronger than Phenelzine.

–4 are in the range between -7.04 and -6.15 Kcal/mol.

The binding energy strength for the compounds obeys

the order

Conclusion

According the molecular docking studies, all the

of: 4>2>3>1> Phenelzine. Compound 1 forms classical

and non-classical hydrogen bondings with respectively

ARG233 and VAL235 via oxygen head of its hydroxyl

group. In this context, π–π interaction is established

between THR 393 and aromatic system.

compounds have higher binding affinities compared to

that of phenelzine. Consequently, they can be applied as

appropriate choices as an antidepressant drug. Also, this

study showed that the orientation of the molecule has an

important role in receptor-ligand interactions.

Compound 2 has four classical hydrogen bondings with

HMAO (VAL10, LEU33, ALA35 and ARG233) and

also one non-classical bond with VAL235 which are due

to the presence of two hydroxyl groups located in

different orientations. Moreover, π–π interactions are

formed between THR 393 and aromatic system.

Acknowledgments

The authors appreciate Fasa University of Medical

Sciences for financial supports of this work.

Figure 3: The optimize structure of HMAO, visualize with chimera

Figure 4: Docked of all the compounds in active site of HMAO

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2019, Volume 7, Issue 3, Pages: 349-356

Figure 5: Hydrogen bond interaction and amino acid residue (3D and 2D)

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2019, Volume 7, Issue 3, Pages: 349-356

Table 3: The results of molecular docking for all the compounds and HMAO enzyme

Binding Energy

Compounds

Amino acid residue

Hydrogen bond

(Kcal/mol)

VAL10, LEU33, GLU34, ALA35

ARG233, PRO234, VAL235, ILE264

LEU268, LYS271, TYR393

VAL10, LEU33, ALA35, ARG233

VAL235, ILE264, LEU268, LYS271

TYR393

VAL10, LEU33, ALA35, ARG233

PRO234, VAL235, ALA263, ILE264

PRO265, LEU268, TYR393

val10,gly11, gly13, leu33, glu34, ala35

arg233, pro234, val235, ile264, lys271

tyr393

Compound 1

-6.66

ARG233, VAL235

VAL10, LEU33

ALA35, ARG233

VAL235

Compound 2

Compound 3

Compound 4

phenelzine

-6.91

-6.67

-7.04

-6.15

VAL235

gly13

val10, leu33, glu34, ala35, arg233

pro234, val235, ile264, tyr393, pro265

leu268

val10, leu33

arg233

2. Patil PO, Bari SB, Firke SD, Deshmukh PK, Donda

ST, Patil DA. A comprehensive review on synthesis

and designing aspects of coumarin derivatives as

monoamine oxidase inhibitors for depression and

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