Virtual Screening of Peptidyl Arginine Deiminase Type 4 Inhibiting Potential of Chosen Flavonoids

 

Udhaya Lavinya B., Sangeetha N., Manisha P., Ramkumar K., Kavitha M.,

Evan Prince Sabina*

School of Biosciences and Technology, VIT University, Vellore-632014, Tamilnadu, India.

 

ABSTRACT:

Peptidyl arginine deaminase type 4 (PADI4) has been identified as a potential therapeutic target for rheumatoid arthritis. The aim of current study was to screen 20 chosen flavonoids for PADI4 (PDB Id.: 4X8C) inhibiting potential. The compounds were docked using PatchDock online server for molecular docking. The docked complex was visualized and the interacting patterns were analysed using PyMol software. The results revealed that compounds such as bacopaside II and X, canthaxanthine and broussonol E showed significant interaction with 4X8C with docking scores of 7864, 8432, 7962 and 8544. The study shows binding and interaction patterns of the chosen flavonoids with 4X8C. However, these compounds need to be explored for anti-arthritic activity.

 

 

 

1. INTRODUCTION:

Rheumatoid arthritis (RA) is a chronic inflammatory disease affecting multiple joints in the body (1). The autoimmune disorder is characterized by the elevated expression of numerous inflammatory cytokines and chemokines (2–4). Various therapeutic targets for rheumatoid arthritis have been identified over last two decades, of which peptidyl arginine deiminases (PADIs) gained considerable attention. PADIs are enzymes that are responsible for the conversion of arginine to citrulline and PADI type 4 encoded by the PADI4 gene has increased risk of RA (5).

 

The role of citrullinated proteins in the pathogenesis of RA mainly by the induction of anti-citrullinated peptide antibodies (ACPA) has been studied. The ACPA is employed in the diagnosis of RA (6) due to its high specificity similar to rheumatoid factor (RF). Recently, research has been focused on developing effective inhibitors against PADI4 enzyme as it is overexpressed in RA (7). Studies involving the screening and identification of PADI4 inhibitors have been carried out extensively in recent years (8,9).

 

Flavonoids are naturally occurring beneficial compounds that are being examined for their specific potential as alternative medicines for various conditions. These naturally occurring compounds are known for their anti-microbial, anti-oxidant, anti-inflammatory, anti-cancer, anti-diabetic and anti-hyperlipidemic properties (10,11). Current study is an effort to screen the chosen flavonoids for their PADI4 inhibiting potential by in silico docking experiments.

 

2. METHODOLOGY:

2.1) Selection of flavonoid compounds for docking:

We have chosen 20 flavonoids based on evidence from scientific literature on their antimicrobial and antioxidant properties [1].

 

The canonical SMILES of flavonoids were retrieved from PubChem database (https://pubchem. ncbi. nlm.nih. gov/). Corina molecular networks server (https://www. mnam.com/online_demos/corina_demo) was used to generate the 3D structure of each compound and pdb formats of the same were retrieved to be used as ligands in docking experiments.

 

2.2) Preparation of receptor protein for docking:

Research collaboratory for structural bioinformatics (RCSB) protein data bank (http://www.rcsb.org/pdb/explore/explore.do?structureId=4X8C) used to retrieve the pdb file of PADI4 (PDB Id: 4X8C). The protein pdb file was prepared for docking by removal of ligands and water molecules and addition of hydrogen. Figure 1 shows the structure of PADI4.

 

Figure 1: Structure of PADI4 (PDB Id.: 4X8C)

 

2.3) Active resolution of 4X8C:

3D LigandSite, an online tool used for the prediction of ligand binding sites of 4X8C. The pdb file of 4X8C was submitted on 3DLigandSite (http://www.sbg.bio.ic.ac.uk/3dligandsite/). The results were obtained through the provided link to user’s e-mail.

 

2.4) Docking and visualization of flavonoids with 4X8C:

PatchDock molecular docking server (http://bioinfo3d.cs.tau.ac.il/PatchDock/) was used to perform the docking experiments. The software  gives the docked complex of the each flavonoids with 4X8C protein and the docking algorithm is based on shape complementarity principles and geometry (12). The docking scores, area and atomic contact energy (ACE) were noted. PyMol software was used for the visualization and analysis of each docked complex.

 

RESULTS AND DISCUSSION:

The ligand binding site prediction of 4X8C revealed that the active site residues were ASP 176 and ASP 179 (Figure 2).

 

Figure 2: Predicted binding site (blue) of 4X8C

 

The following table (Table 1) shows the docking scores, area and atomic contact energy (ACE) for the 20 chosen ligands upon docking with the target receptor 4X8C. Canthaxanthin was found to have a docking score of 8544 forming two hydrogen bonds. The interacting residues in the aforementioned complex include ARG-651 andTYR-636 (bond length 2.6 Å and 3.0 Å respectively). The compound with second highest score was found to be bacopaside X forming 5 hydrogen bonds of varying bond lengths ranging from 0.8 to 3.5 Å and the interacting residues of this complex include THR-299, ILE-354, VAL-649 and ARG-651. Broussonol E formed 6 hydrogen bonds with 4X8C of bond lengths ranging between 2.5 to 3.3 Å and the interacting residues include GLU-353, HIS-471, ASP-473 and ASN-648. Bacopaside II was found to form 10 hydrogen bonds of bond lengths ranging from 1.3 to 3.5 Å. The interacting residues include ASP-350, GLU-353, LEU-410, VAL-591, ALA-645, ASN-648, VAL-649 and ARG-651.

 

Table 1: Docking scores, area and ACE of the docked complexes

S.No	FLAVONOIDS NAME	SCORE	AREA	ACE
1	Allicin	7104	929.7	-223.99
2	Bacopaside 1	7642	1060.4	-310.94
3	Bacopaside 2	7864	1160.6	-272.23
4	Bacopaside X	8432	1167.2	-371.49
5	Broussonol E	7962	920.7	-187.09
6	Canthaxanthin	8544	1057.8	-151.07
7	Diosmin	6590	912.8	-307.6
8	Dorsilurin K	7416	865.3	-176.26
9	Dorsilurin H	7022	798.9	-141.1
10	Icarin	7280	936.8	-226.83
11	Laxifloranone	6920	810.3	-133.84
12	Liquiritin	7150	835.8	-180.63
13	Lutein	6736	798.9	-193.75
14	Proanthocyanidin	6058	720.9	-225.03
15	Prunin	5986	656.4	-116.8
16	Robinin	5722	634.7	-187.44
17	Silibinin	3196	375.7	-207.93
18	Sophoroflavonoloside	6500	779.5	-213.89
19	Theaflavin-3-o-gallate	6846	901.4	-195.36
20	Troxerutin	6174	712.5	-173.19

 

 

 

Figure 3: Docked poses of the 20 ligands (1-allicin; 2-bacopaside 1; 3-bacopaside 2; 4-bacopaside X; 5-broussonol; 6-canthaxanthin; 7-diosmin; 8-dorsilurin K; 9-dorsilurin H; 10-icariine; 11-laxifloranone; 12-liquiritin; 13-lutein; 14-proanthocyanidin; 15-prunin; 16-robinin; 17-silibinin; 18-sophoraflavonone; 19-theaflavin-3-O-gallate; 20-troxerutin) with 4X8C.

 

Figure 4(a-b): Interaction patterns of the docked complexes with top 3 scores

 

4(a) - 4X8C in complex with Canthaxanthin forming 2 hydrogen bonds of length 2.6 Å and 3.0 Å

 

4(b) - 4X8C in complex with Bacopaside X forming 5 hydrogen bonds of length varying from 0.8-3.5 Å

 

4(c) - 4X8C in complex with Broussonol E forming 6 hydrogen bonds of length 1.2, 2.2 and 3.2 Å

 

4(d) - 4X8C in complex with bacopaside II forming 10 hydrogen bonds of length ranging between 1.3-3.5 Å

 

Bacopasides are compounds isolated from Bacopa monnieri. These saponins are known to possess various beneficial effects such as antioxidant, analgesic and antidepressant effects (13,14). Broussoflavonols are known for their anti-cancer activity (15). Canthaxanthin possesses significant antioxidant and anti-hyperlipidemic properties and studies have been carried out to compare its effects with that of β-carotene (16,17).

 

CONCLUSION:

Current study shows the binding and interaction patterns of the chosen flavonoids with 4X8C. Compounds such as canthaxanthin, bacopasides II and X and broussonol were found to interact significantly with the target receptor. It is evident from literature that these flavonoids possess significant beneficial effects such as antioxidant and anti-inflammatory properties. Hence, they may be beneficial to patients with rheumatoid arthritis where PADI4 expression is increased. However, specific in vitro and in vivo studies would reveal the mechanism of PADI4 inhibition by these compounds.   

 

ACKNOWLEDGEMENT:

The authors are thankful to VIT University for providing the necessary facilities to carryout this research project.

Conflict of interest:

The authors declare that do not have any conflict of interest.

 

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Accepted on 24.12.2017        © RJPT All right reserved

Research J. Pharm. and Tech 2018; 11(2):753-757.