Investigation on the Binding Interaction Between Clomipramine and Doxepin with LeuT by Molecular Docking Analysis

 

M. Govindammal, M. Prasath*, B. Sathya, M. Selvapandiyan

Department of Physics, PG Extension Centre Periyar University, Tamilnadu, India

*Corresponding Author E-mail: sanprasath2006@gmail.com

Molecular docking is a computational method, has becoming an increasingly important tool for drug discovery.  The drugs Clomipramine and Doxepin are selected and docked with the protein LeuT for docking analysis. Both the selected drugs are tricyclic antidepressant drugs. By using the protein Leucine Transporter the binding interactions are found for the molecule.  The drug Clomipramine and Doxepin is used as a potent inhibitor of leucine transport (LeuT). LeuT is a stable, sodium-coupled Leucine transporter from the eubacteriumAquifexaeolicus. It is the only member of the neurotransmitter sodium symporter (NSS) and belongs to the family of secondary transporters. The lowest binding energy and the shortest distance between the different amino acids are resulted and tabulated. The computational method of molecular docking analysis is very interested for discovering new medicine for human health for the disease depression.  

 

 

 

INTRODUCTION:

Clomipramine

Clomipramine(3-(3-chloro-10,11-dihydro-5H-dibenzo[b,f]azepin-5-yl)-N,N-dimethylpropan-1-amine) is used as an antidepressant drug. Clomipramine is also known (trademarked) as Anafranil. It is the 3-chlorinated derivative of the imipramine and also a dibenzazepine-derivative of tricyclic antidepressant (TCA) drug. It was developed in the early 1960s by the Swiss drug manufacturer. Clomipramine has a number of uses in medicine including in the treatment of Obsessive compulsive disorder¹, Major depressive disorder², Panic disorder^3,4,Body Dysmorphic Disorder⁵.

 

TCAs are structurally similar to phenothiazines. They contain a tricyclic ring system with an alkyl amine substituent on the central ring. In non-depressed individuals, clomipramine does not affect mood or arousal, but may cause sedation. In depressed individuals, clomipramine exerts a positive effect on mood. TCAs are potent inhibitors of serotonin and norepinephrine reuptake. Tertiary amines TCAs, such as clomipramine

 

Doxepin

Doxepin(E/Z)-3-(dibenzo[b,e]oxepin-11(6H)-ylidene)-N,Ndimethylpropan-1 amine is a tricyclic antidepressant (TCA) drug⁶.  The brand names of oral formulations include Deptran and Sinequan. Doxepin is used as a drug to treat depression, anxiety disorders, pruritus, insomnia⁷, and also as a second-line treatment of chronic idiopathic urticaria⁸. Its oral formulations are approved by FDA for the treatment of depression, anxiety, and insomnia.

 

Clomipramine

 

Doxepin

 

Fig 1: Molecular structure of Clomipramine and Doxepin

 

 

Computational details

Docking calculations were performed with version 1.5.2 of the program AutoDock⁹. It combines a rapid energy evaluation through pre-calculated grids of affinity potentials with a variety of search algorithms to find suitable binding positions for a ligand on a given macromolecule. Cygwin software is used to produce the protein-ligand complex. The PyMOL¹⁰ software was used to view the protein-ligand complex. 

 

The X-ray crystal structure of the LeuT was obtained from Brookhaven Protein Data Bank (PDB code: 2Q6H)¹¹ from that, the protein was separated for the docking study. The ligand structure was prepared using the Chemdraw software and converted into pdb format. These files are used as the input files for docking analysis.

 

Leucine Transport (LeuT)

The drug Clomipramine and Doxepin is used as an inhibitor of leucine transport (LeuT). LeuT is a stable, sodium-coupled leucine transporter from the EubacteriumAquifex aeolicus¹². It is the only member of the Neurotransmitter Sodium Symporter (NSS) belongs to the family of secondary transporters¹³. The crystal structure of LeuT provided the first molecular indication into an NSS member, but it did not give any detail information about the atomic basis of inhibition. The bacterial NSS proteins have 30% sequence identity with human SERT and NET, also worm and fly DATs. It is reported that the bacterial NSS proteins also have high binding affinity to TCAs¹⁴. So the Leucine transporter (LeuT) is taken as the receptor for docking analysis to investigate the binding energy and intermolecular interactions between the Clomipramine, Doxepin and LeuT.

 

Optimization structure

 

Clomipramine

 

Doxepin

 

Fig 2: Optimization structure of Clomipramine and Doxepin

 

RESULTS AND DISCUSSION:

Molecular docking analysis

The docking analysis predicted the lowest docked energy for Clomipromine and Doxepin the binding energy value is -7.10 and -7.34 Kcal/mol.

 

The calculated ten conformational energy values of Clomipromine and Doxepin in the active site of LeuT are listed in table 1. The shortest interactions between the ligand and receptor are given in table 2.

 

Table 1: Lowest binding energy values of Clomipromine and Doxepin.

 

 

Table 2: Nearest neighbours and short contact distances (Å) of Clomipromine and Doxepin with amino acid residues of LeuT active site

Clomipramine···LeuT amino acidresidue and identifier	Distance	Doxepin···LeuT amino acid  residue and identifier	Distance
C(1) ···Val33/CB	3.19	C(5)... Gln34/2HE2	2.58
C(5)···Gln34/2HE2	2.88	Gln34/NE2	2.99
C(8)…Arg30/N	3.12	Gln34/2HE2	2.65
N(1)…Arg30/2HH1	3.45	C(9)…Arg30/2HH1	2.70
C(12)…Leu25/CB	3.28	C(10)…Arg30/2HH1	2.96
Cl(1)…Ile111/CD1	3.03	C(14)…Arg 30/2HH1	2.74
C(16)…Arg30/1HH1	2.94	Leu400/CD2	2.85
Asp404/OD2	3.11	C(18)…Arg 30/2HH1	3.43
Asp404/CG	3.25	O(1)…Arg30/CA	3.39
C(17)…Asp404/OD2	2.88	Arg30/N	3.13

 

Clomipromine-LeuT	Doxepin-LeuT

Fig 3: Intermolecular interactions of Clomipramine and Doxepin with LeuT receptor.

 

 

Clomipramine

The clomipramine also bound at the inner end of the extracellular cavity in LeuT. Figure 3(a) shows the binding cavity of the Clomipramine in the LeuT. The ligand hasformed some hydrogen bonding and hydrophobic interactions with the nearest amino acids in active site; particularly, the halogen (Cl) atom forms a strong interaction with the Ile111 at a distance 3.03Å. The C(1) atom of clomipramine make an electrostatic interaction with Val33 at 3.19Å. The C(5), C(6) and C(16) atoms form some strong hydrogen bonding interactions with the amino acid residues Gln34 and Arg30 at 2.88, 2.47 and 2.94Å respectively. Similarly the C(16), C(17) and C(18) atoms of the ligand form some strong hydrophobic interactions with the Asp404 and Asp401 at a distance of 3.11, 2.88 and 2.97 correspondingly Table 2. 

 

Doxepin

Figure 3(b) shows the binding cavity of the doxepin in the LeuT. Doxepin hasformed some hydrogen bonding, hydrophobic and electrostatic interactions with the nearest amino acids in the active site of protein; The C(5) and C(6) atoms of the ligand make some strong hydrogen bonding interactions with Gln34/2HE2 at a distance of  2.58 and 2.65 Å respectively. Similarly, C(9) and C(10) atoms of the doxepin make some strong hydrogen bonding interactions with Arg30/2HH1 at a distance of  2.70 and 2.96 Å correspondingly. The C(14) atom also forms a strong hydrogen bonding interaction with Arg30/2HH1 at 2.74 Å (figure 2.2) correspondingly. In addition to this the C(17) atom form strong electrostatic interactions with Leu400/CD2 at distance of  2.85 Å (table 2.2). Also the O(1) atom form a electrostatic interaction with the amino acid residue Arg30 at a distance of 3.13

 

Fig 4: Binding cavity of Clomipramine and Doxepin with LeuT receptor.

 

 

 

Table 3: The optimized geometrical parameters of Clomipromine molecules  [torsion angle (°)] and compared with docking values using B3LYP/6-31G (d,p) method.    Torsion angles (°)

Bonds	Optimized	Docked
N(1)–C(3)–C(2)–C(7)	1.22	1.25
C(4)–C(3)–N(1)–C(15)	61.45	61.45
N(1)–C(15)–C(16)–C(17)	-180.00	122.39
C(15)–C(16)–C(17)–N(2)	179.98	105.12
C(16)–C(17)–N(2)–C(19)	-175.91	152.20
C(16)–C(17)–N(2)–C(18)	-59.97	-91.88

 

Structural aspects

The geometrical parameters like bond lengths, bond angles and torsion angles of the clomipramine were calculated for drug before (Optimized) and after entering in to the active site (Docked). The comparison tables of the geometrical parameters of clomipramine were listed in Table 3. By viewing the structure of the ligand, we know it has 3 rings; from this it may assumed that the ligand is very rigid. It is reflected in comparison of the bond lengths, bond angles and torsion angles. In the rings there are no much variations found. But some variations is found in the tail part of the ligand. At initial, the trans angles of the N(1)–C(15)–C(16)–C(17), C(15)–C(16)–C(17)–N(2) and C(16)–C(17)–N(2)–C(19) bonds are -180.00°, 179.98° and -175.91°; when the ligand enter into the active site the angles were reduced to 122.39°,  105.12° and 152.20° respectively. But in the C(16)–C(17)–N(2)–C(18) bond the gauche angle is increased from -59.97° to -91.88°. These variations explain the structural change of the ligand in the active site of protein.

 

Table 4: The optimized geometrical parameters of Doxepin molecules  [torsion angle (°)] and compared with docking values using B3LYP/6-31G (d,p) method.

Bonds	Optimized	Docked
C(2)–C(7)–O(1)–C(8)	96.6	96.6
C(7)–O(1)–C(8)–C(9)	-46.5	-46.5
C(10)–C(15)–C(16)–C(17)	120.0	67.6
C(15)–C(16)–C(17)–N(1)	180.0	20.0
C(16)–C(17)–N(1)–C(18)	64.1	102.7
C(16)–C(17)–N(1)–C(19)	64.1	141.5

 

Structural aspects

The geometrical parameters like bond lengths, bond angles and torsion angles of the Doxepin were calculated for drug before (Optimized) and after entering into the active site (Docked). The comparison tables of the geometrical parameters of both forms of doxepin were listed in Table 4. Figure 2 (b), shows the ball and stick model of Doxepin with the atom numbering scheme and their conformational difference. By viewing the structure of the ligand, we know it has 3 rings; from this it may assumed that the ligand is very rigid. It is reflected in comparison table of the bond lengths, bond angles and torsion angle. In the rings there are no much variations found. But some variations are found in the tail part of the ligand. In form (I), the torsion angle of C(10)–C(15)–C(16)–C(17) bond is -120.0°  but the angle is decreased to 67.6° When it enters into the active site. In contrast to this the torsion angles of C(16)–C(17)–N(1)–C(18) and C(16)–C(17)–N(1)–C(19) bonds are increased from 64.1° to 102.7° and 141.5° respectively.  The trans orientation (180°) of C(15)–C(16)–C(17)–N(1) bond changed to cis orientation (20.0°). These variations explain the structural change of the ligand in the active site of protein.   

 

CONCLUSION:

The docking analysis predicted the lowest docked energy for doxepin and the binding energy value is -7.34Kcal/mol. The C(5) and C(6) atoms form some strong hydrogen bonding interactions with the amino acid residues Gln34/2HE2 at a distance of  2.58 and 2.65 Å respectively. The docking analysis predicted the highest docked energy for clomipramine and the binding energy value is -7.10Kcal/mol. The C(5), C(6) and C(16) atoms form some strong hydrogen bonding interactions with the amino acid residues Gln34 and Arg30 at a distance 2.88, 2.47 and 2.94Å  respectively. Clomipramine and doxepin both molecules were docked with LeuT effectively.  Comparing the binding energy values, doxepin has low binding energy value in the docking structure which reveals doxepin interacts strongly with the ligand. This is also supported by number of hydrogen bonds interactions and the changes in the docked molecular structural parameters. Whereas, the clomipramine has more rigid in the docked structure and binded with high binding energy compare to doxepin which reveals the clomipramine drug will go to active site very easily. Hence clomipramine drug will be more useful for fast remedy in reducing depression and doxepin will be strong and effective in curing depression.

 

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Received on 16.04.2017         Modified on 10.06.2017

Accepted on 20.07.2017         © AJRC All right reserved