Investigation of selected 13 FDA approved drugs for TRPV1 Antagonism using molecular docking: An insight application for the treatment of Neuronal pain

Pankaj Prashar, Pardeep Kumar, Ankita Sood, Anamika Gautam, Harmeet Kaur,

Arvinder Kaur, Ruksaar Ebrahim, Shubham Sharma, Indu Melkani, Narendra Kumar Pandey, Bimlesh Kumar*

School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, India.

*Corresponding Author E-mail: bimlesh1Pharm@gmail.com; bimlesh.12474@lpu.co.in

ABSTRACT:

Transient receptor potential vanilloid type 1 (TRPV1) is one of the important target sites on which different drugs can act to prevent the pathogenesis of neuropathic pain. Neuropathic pain is a torture and unbearable pain occurs due to damage of somatosensory nervous system. Here in present investigation FDA approved drugs were evaluated to find out its propensity towards action on TRPV1 receptor. 13 FDA approved drugs were selected which were untouched act through TRPV1 receptor. Hence before going to start preclinical work molecular docking was performed to find out its action and binding towards isoform of TRPV1 i.e 2N27, 3J5R. the result of the study indicates that rutin and glimepiride showed better affinity among all selected drugs and rutin was better with respect to glimepiride. The binding site and interactions were also studied supported this study. Hence its can be concluded that Rutin and glimepiride exhibited best possible interaction by antagonizing the effect of TRPV1 receptor so can be consider for the treatment of neuropathic pain.

KEYWORDS: Neuropathic pain, TRPV1, 2N27, 3J5R, rutin, glimepiride.

INTRODUCTION:

Pain representing damage of somatosensory nervous system is known as neuropathic pain (NP). It is one of the kinds of maladaptive response^[1,2]. Expression of such torture and unbearable pain occurs in various diseases (diabetes, cancer, HIV) state and due to induction of chemicals (alcohol, pyridoxine, chemotherapeutic drugs)^[3-5]. Recent report producing an evidence that about 8-10% of world population suffering from NP^[1,6]. Various signs and symptoms of NP includes hyperalgesia, allodynia, spontaneous pain and persistent burning pain^[7,8]. Molecular level study suggested the significant contribution of transient receptor potential vanilloid type 1 (TRPV1) receptor in central and peripheral type of NP^[9,10]. TRPV1 expresses in dorsal root ganglia (DRG) hence can convey information of sensory neve to central nervous system (CNS).

Hence, now a days it becomes important target for the treatment of diabetes, obesity, inflammatory bowel disorder (IBD), chronic pain and neuronal complications^[11-13]. TRPV1 reported to control the level of heat, cold, acid, pollutants (negative charges) as well as pro-inflammatory mediators^[14]. It is a six transmembrane structure having N- and C-terminal located intracellularly. It is non-selective cation channel, so at elevated temperature, acidic pH and under its activation take place which produces phosphorylation of serine/threonine kinases. Among these kinases, protein kinase A (PKA) and protein kinase C (PKC) reported to develop pain sensation^[15,16]. Development and propagation of peripheral NP takes place due to nerve growth factor (NGF) as it has been observed to upregulate TRPV1 receptor. In damaged and undamaged neurons, TRPV1 undergoes downregulation and upregulation respectively^[17]. It is well known that C fibers and myelinated A fibers are also involved in NP and TRPV1 related to both kind of fibers. The up-regulation of the TRPV1 receptor at peripheral and central NP conditions supports the sensitivity of the vanilloid system^[18-21]. Immunohistochemical reports that the activation/inhibition of TRPV1 receptor expressed on glutamatergic neurons and generates a symptom of NP ^[15]. Activation of TRPV1 receptor mediates the death of microglial cell and apoptosis of astrocytes through Ca²⁺ regulated mitochondrial rupture and Ca²⁺ regulated activation of p38 respectively. Consequently inhibition of these receptors using various antagonists may provide a new avenue to ameliorate diabetes, obesity, migraine, epilepsy and neuropathic pain etc.^[22-24]. Molecular docking is less time consuming and has low cost implications. Such experimentation provides better understanding of receptor structure, affinity of attachment of receptor with the drug substances. Apart from this by adopting such experimentation unnecessary torture on animal can be minimize. Hence it can be a valuable tool to find out the specific antagonists of TRPV1 receptor which must be available in crystalline structure forms^[25]. Various isoforms of TRPV1 receptor are available among them 2N27 and 3J5R were selected for the present investigation. We have selected thirteen FDA approved drugs which were evaluated for NP but as per best of our knowledge none of the drugs investigated as TRPV1 blocker. Hence selected thirteen FDA approved drugs were undergone screening against TRPV1 receptor so that they can be biologically evaluated further for painful neuropathic condition.

MATERIALS AND METHODS:

For the processing of antagonism of TRPV1 receptors Protein Data Bank (PDB), Autodock Vina 4.5 software, ChemDraw professional 17.1 software and graph Pad prism software was used. Further their binding affinities and analysis of interaction between protein and ligands were interpreted.

Retrieval of protein structures:

Two protein structures (PDB ID: 2N27, 3J5R) were retrieved from protein data bank and used molecular docking using Autodock Vina 4.5 software. Protein structure 2N27 comprises only chain A in which total number of atoms and total residues were observed as 1192 and 148 respectively. However, protein structure 3J5R embrace total 4 chains i.e. A, B, C, D in which total number of atoms and total residues were recorded as 17564 and 2392 respectively.

Retrieval of ligand structures:

Thirteen drugs were selected as mentioned in table 1. Their structures were drawn by using ChemDraw professional 17.1 software and then converted to. mol2 format in Chem3d software. Further, selected drugs were screened against both TRPV1 proteins receptors.

Preparation of TRPV1 protein:

Two isoforms of TRPV1 protein 2N27 and 3J5R were prepared using Autodock Vina 4.5 software. Before initiating the process of protein preparation, all heteroatoms and co-factors were observed and removed from protein crystal structures even water molecules were also not present in both the crystal structures. The protein preparation includes repairing missing atoms, adding polar hydrogen’s to atoms, no bond order with renumbering, addition of Kollaman charges.

Ligand preparation:

All thirteen ligands (Malonaldehyde, Fisetin, Curcumin, Duloxetine, Flunarazine, Fluoxetine, Glibenclamide, Glimepiride, Glipizide, Imipramine, Rutin, Sildenafil, And Vanillin) were prepared for molecular docking using Autodock Vina 4.5 software. The retrieved ligand structures were converted to PDBQT format in Autodock. Preparation of these ligands includes addition of polar hydrogen’s, Kollaman charges, choosing torsion and detection of root.

Molecular docking:

Autodock, molecular docking was done as described by Forli et al., 2006 ^[26] which involve preparation of ligands and receptor’s coordination files in PDBQT format, generation of grid box and configuration files. Each ligand was subjected to both isoforms of the TRPV1 receptor as single docking run. Furthermore, interactions among ligands and both proteins were observed and compared with each other.

Table 1. Selected compounds for the study along with their Smiles notation

Ligand	Canonical smile notation
Malonaldehyde	C(C=O)C=O
Fisetin	C(CC(=O)NC(CS)C(=O)NCC(=O)O)C(C(=O)O)N
Curcumin	COC1=C(C=CC(=C1)C=CC(=O)CC(=O)C=CC2=CC(=C(C=C2)O)OC)O
Duloxetine	CNCCC(C1=CC=CS1)OC2=CC=CC3=CC=CC=C32
Flunarazine	1CN(CCN1CC=CC2=CC=CC=C2)C(C3=CC=C(C=C3)F)C4=CC=C(C=C4)F
Fluoxetine	CNCCC(C1=CC=CC=C1)OC2=CC=C(C=C2)C(F)(F)F
Glibenclamide	COC1=C(C=C(C=C1)Cl)C(=O)NCCC2=CC=C(C=C2)S(=O)(=O)NC(=O)NC3CCCCC3
Glimepiride	CCC1=C(CN(C1=O)C(=O)NCCC2=CC=C(C=C2)S(=O)(=O)NC(=O)NC3CCC(C 3)C)C
Glipizide	CC1=CN=C(C=N1)C(=O)NCCC2=CC=C(C=C2)S(=O)(=O)NC(=O)NC3CCCCC3
Imipramine	CN(C)CCCN1C2=CC=CC=C2CCC3=CC=CC=C3
Rutin	CC1C(C(C(C(O1)OCC2C(C(C(C(O2)OC3=C(OC4=CC(=CC(=C4C3=O)O)O)C5=CC(=C(C=C5)O)O)O)O)O)O)O)O
Sildenafil	CCCC1=NN(C2=C1N=C(NC2=O)C3=C(C=CC(=C3)S(=O)(=O)N4CCN(CC4)C)OCC)C
Vanillin	COC1=C(C=CC(=C1)C=O)O

Table 2. Binding affinities of all selected compounds for both isoforms of TRPV1

Ligands		Receptors
Ligands	Binding affinities	2N27	Binding affinities	3J5R
1,1,3,3 Tetra methoxy propane	-3.6	GLN135, GLN143, GLU140	-3.4	MET568, LYS571, MET572
FSN	-7.1	ALA128, ASP129, ILE125, GLU140, GLN135	-6.3	PHE580, LEU678, MET677, LEU674, VAL583, LEU673
DULOXETINE	-6.3	VAL136, G; LU140, ILE125, GLN143, PHE12	-5.7	TRP372, SER379
CURCUMIN	-7.4	ALA15, PHE16, PHE19, VAL35, ILE27, LEU32, THR28, PHE68,	-7.0	MET568, LYS571, ILE689, THR685, ILE696, ASN695, ASP411
FLUNARIZINE	-8.6	LEU39, VAL35, LEU32, ALA15, PHE12, THR146	-8.1	ARG575, MET572, LYS571, MET568, ILE689, ILE696, SER693
FLUOXETINE	-6.2	ALA128, ASP129, VAL136, ILE125	-5.7	ARG575, LYS571, MET568
GLIBENCLAMIDE	-8.0	GLN135, LEU39, MET124, GLU140, MET144, PHE12	-6.9	LYS571, ILE689, GLU692, PRO407, HIS410, SER693, ILE696
GLIMEPIRIDE	-8.7	GLU11, ALA15, LEU18, VAL15, PHE19	-8.0	VAL686, ASN687, THR685, ALA690, LYS688, ILE689, GLN691, MET568, ILE569, MET572
GLIPIZIDE	-8.3	GLU11, ALA128, VAL35, SER38	-7.6	ILE689, LYS571, ILE696, GLU570, TYR511, SER404
IMIPRAMINE	-6.7	PHE12, LEU39, PHE16, ALA15, PHE19, LEU32	-7.0	SER404, LEU699, LYS571, LEU574
RUTIN	-9.3	PHE12, ALA15, GLU140, GLN135, ASP129, SER38, LEU39, ASN42	-7.2	HIS410, THR685, LEU574, LYS571, ILE696, SER693
SILDENAFIL	-7.7	PHE12, ALA147, MET72, ALA15, PHE19, LEU32, SER36	-7.5	ILE689, ARG575, LYS571, SER693
VANILLIN	-4.9	GLN135, ICE125, ASP129	-5.0	ILE703, SER510, SER512, GLN700

Among them rutin exhibited more value of binding affinity with respect to others. In this docking method binding affinity of predocked ligands i.e. 4D205 for 2N27 and UNK762 for 3J5R was also observed and it was recoded as -5.6 and -8.9 respectively. It indicates that rutin and glimepiride both have more binding at 2N27 with respect to 3J5R. After molecular docking, rutin and glimepiride were found to have interactions with various amino acids with their binding site (Figure 1.)

Amino acids GLU11, ALA15, LEU18, VAL15, PHE19, PHE12, ALA15, GLU140, GLN135, ASP129, SER38, LEU39, ASN42 of 2N27 protein and VAL686, ASN687, THR685, ALA690, LYS688, ILE689, GLN691, MET568, ILE569, MET572 HIS410, THR685, LEU574, LYS571, ILE696, SER693 of 3J5R protein represented in table 2. Rutin showed binding with PHE12, ALA15, GLU140, GLN135, ASP129, SER38, LEU39, ASN42 amino acids of 2N27 while HIS410, THR685, LEU574, LYS571, ILE696, SER693 amino acids of 3J5R. On the other hand, Glimepiride bound with GLU11, ALA15, LEU18, VAL15, PHE19 amino acids at 2N27 while VAL686, ASN687, THR685, ALA690, LYS688, ILE689, GLN691, MET568, ILE569, MET572 amino acids at 3J5R.

CONCLUSION:

TRPV1 represents its excessive expression in case of peripheral as well as central NP. Hence it becomes interesting target for finding of novel compound act on this. Present study reported Rutin and glimepiride exhibited best possible therapeutic drug for the treatment of NP by antagonizing the effect of TRPV1 receptor.

ACKNOWLEDGEMENTS:

Authors are thankful to second International Conference of Pharmacy, held by School of Pharmaceutical Sciences, Lovely Professional University on September 13-14, 2019 to fund the publication of this manuscript.

CONFLICTS OF INTEREST:

Declared none.

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Received on 19.11.2019 Modified on 10.02.2020

Research J. Pharm. and Tech. 2020; 13(11):5328-5332.

DOI: 10.5958/0974-360X.2020.00931.2