Research Article - Journal of Drug and Alcohol Research ( 2022) Volume 11, Issue 12

Computational Study of Phytoconstituents in Myxopyrum Smilacifolium Blume against Inflammatory Mediator TNF-α

Raveesha Peeriga1*, Lakshmana Rao Atmakuri2, Sindhu Sri Reddy1, Sireesha Kancherla1, Pravallika Gunturu1, Alekhya Kodali1, Sri Akhil Yenduri1, Jhansi Chintalapudi1, Mohansai Maragani1, Praneeth Varma1, Anusha Kandula1, Adithya Veeroji1, Parimala Kolli1, Aminabee Shaik1 and Bharghava Bhushan Rao Pathangi3
 
1Department of Pharmacognosy, V. V. Institute of Pharmaceutical Sciences, India
2Department of Pharmacutics, A. M. Reddy Memorial College of Pharmacy, India
3Department of MBA, Koneru Lakshmaiah Educational Foundation, India
 
*Corresponding Author:
Raveesha Peeriga, Department of Pharmacognosy, V. V. Institute of Pharmaceutical Sciences, India, Email: peerigaraveesha@gmx.us

Received: 30-Nov-2022, Manuscript No. JDAR-23-88492; Editor assigned: 02-Dec-2022, Pre QC No. JDAR-23-88492 (PQ); Reviewed: 16-Dec-2022, QC No. JDAR-23-88492; Revised: 21-Dec-2022, Manuscript No. JDAR-23-88492 (R); Published: 28-Dec-2022, DOI: 10.4303/JDAR/236215

Abstract

Secondary metabolites in plants have been used in health care for the treatment of various ailments since ancient times. The current study was carried out to investigate on phytoconstituents in Myxopyrum smilacifolium against an inflammatory mediator TNF-α. Ligand and protein pdbqt files were prepared and docking was done by using Autodock 4.0 and Biovia Studio Visualizer. The docking finding revealed that Myxopyroside shown -5.1 kcal/mol which is high and mere significant docking score of natural immunosuppressive capsaicin and standard drug Methylprednisolone of -4.8 kcal/mol and -5.4 kcal/mol respectively. The obtained results were proven to posses the inhibition activity against TNF-α. The evaluated pharmacokinetic parameters of the only 3 phytoconstituents obeyed Lipinski’s rule of 5. Exploration of simulation studies on Myxopyroside are in need to ensure inhibition of inflammatory mediator TNF-α.

Keywords

Autodock 4.0; Smilacifolium; Myxopyroside; TNF-α; Lipinski’s

Introduction

Harmful stimuli like pathogens, damaged cells, toxic substances etc., activate the immune system’s response leads to Inflammation. Thereby the immune system removes injurious stimuli and initiates the process of healing [1,2]. In other words Inflammation is said as a defence mechanism [3]. Inflammatory pathways shows its impact on pathogenesis of chronic diseases, involves the inflammatory mediators and signalling pathways. An inflammatory stimulus activates intracellular signalling pathways leads to the active production of inflammatory mediators. The primary inflammatory stimuli includes cytokines such as interleukin-1β, interleukin-6, and tumour necrosis factor-α (TNF-α), IL-1 and IL-6 receptor and the TNF receptor (TNFR) [3-5].

Since ancient times, herbs played an important role in human health care as they produce several substances which exert biological activities. These substances are resultant of biogenetic pathway of secondary metabolism. These secondary metabolites exert numerous therapeutic actions [6,7]. Due to importance of the secondary metabolites, plants became the prime source for the development of new drugs [8-11]. Myxopyrum smilacifolium Blume4 is a shrub commonly has been used in Traditional system of Medicine, even though the findings on the phyto-constituents are limited [12,13]. Hence, the present study is carried for computational study on the phyto-constituents present in Myxopyrum smilacifolium Blume’s against inflammatory mediator.

Materials and Methods

In silico study

Receptor and ligand preparation: The PDF files of phyto- constituents of Myxopyrum smilacifolium’s were gathered from PubChem and the protein TNF-α was obtained from Protein Data Bank (PDB ID: 2az5) at www.rcsb.org/ pdb shown in Figure 1. The attributes of ligand i.e., x,y,z coordinates towards selected protein were noted by using Biovia Discovery Visualizer after removing the water molecule. Further with the help of Autodock 4.0 the PDB files of ligand and protein were converted into pdbqt files. By using commands in command prompt the docking is per formed. The interactions between each ligand and protein are analysed by using Biovia Discovery Visualizer. SwissADME programming is used to predict the physiochemical characteristics and pharmacokinetics of the chosen substances.

drug-tnf

Figure 1: TNF-α (Protein ID: 2az5).

Results

Computation study of phytocompounds in myxopyrum smilacifolium

To investigate about phytocompounds being reasonable for anti-inflammatory property, docking score was analysed via binding affinity of different ligands behaviour towards the selected protein. Absorption, Distribution, Metabolism, Exertion and Toxicity of phyto constituents were predicted by using SwissADME online tool mentioned in Table 1. 2 out of 5 phytocompounds obeyed Lipinski’s Rule of 5. The phyto compounds are along with their PubChem ID and the canonical smiles were represented in Table 2. Docking studies revealed that phytoconstituents Arenarioside, Verbascoside, Myxopyroside had docking score of -16.4 kcal/ mol, -10.6 kcal/mol and -6.5 kcal/mol which showed hydrogen bonding interactions. No phyto compounds formed hydrophobic interactions. The docking score outcomes were predicted and the interactions between protein and ligand mentioned in Figure 2 and Table 3.

Ligand Pubchem ID Canonical Smiles
Verbascoside 5281800 CC1C(C(C(C(O1)OC2C(C(OC(C2OC(=O)C=CC3=CC(=C(C=C3)O)O)CO)OCCC4=CC(=C(C=C4)O)O)O)O)O)O
Arenarioside 6442994 CC1C(C(C(C(O1)OC2C(C(OC(C2OC(=O)C=CC3=CC(=C(C=C3)O)O)COC4C(C(C(CO4)O)O)O)OCCC5=CC(=C(C=C5)O)O)O)O)O)O
Myxopyroside - COC(=O)C1C(O)C(O)C2C1C(OC1OC(CO)C(O)C(O)C1O)OC=C2C(=O)OC
3-Formylindole 10256 C1=CC=C2C(=C1)C(=CN2)C=O
5-Hydroxy methyl furfural 237332 C1=C(OC(=C1)C=O)CO
Capsiacin 1548943 CC(C)C=CCCCCC(=O)NCC1=CC(=C(C=C1)O)OC
Methylpredisolone 6741 CC1CC2C3CCC(C3(CC(C2C4(C1=CC(=O)C=C4)C)O)C)(C(=O)CO)O

Table 1: M. Smilacifolium phyto-constituents representing Canonical Smiles.

Ligands Drug Likeness Molar Refractivity Consensus Log Po/W H bond Acceptor H Bond donors GI Absorption Molecular Formula Molecular Weight
Verbascoside 3 148.42 -0.43 15 9 Low C29H36O15 624.6
Arenarioside 3 174.84 -1.95 19 11 Low C34H44O19 756.7
Myxopyroside 2 94.62 -2.53 13 6 Low C18H26O13 450.391
3-Formylindole 0 43.69 1.72 1 1 High C9H7NO 145.16
5-Hydroxy methyl furfural 0 30.22 0.19 3 1 High C6H6O3 126.11
Capsiacin 0 90.52 3.43 3 2 High C18H27NO3 305.41
Methylpredisolone 0 101.87 1.94 5 3 High C22H30O5 374.47

Table 2: Pharmacokinetic Analysis Myxopyrum Smilacifolium B. Phyto-compounds.

Phyto-compounds Highest conformation Binding Energy (kcal/mole) Hydrogen bonds
Verbascoside -5 GLY A:121, ILE A: 97, ALA A: 96, TYR A:119
Arenarioside -4.9 ALA A:96, LYS A:98, TYR A:119, ILE A: 118, SER A:95
Myxopyroside -5.1 ILE A: 97, GLY A:121, SER A: 95, TYR A: 119
3-Formylindole -3.5 TYR A: 119, ILE A: 118, ALA A:96
5-Hydroxy methyl furfural -3.4 TYR A:119, GLY A:121, ILE A: 118
Capsiacin -4.8 ILE A:118, PRO A:117, ALA A:96, LEU A:120, GLY A:121
Methylpredisolone -5.4 ILE A: 97, GLY A:121, SER A:95, TYR A:119

Table 3: Docking Simulation between TNF-α and Phytocompounds in Myxopyrum Smilacifolium.

drug-receptor

Figure 2: 3D Interactions of Ligands with receptor TNF-α A) Verbascoside B) Arenarioside C) Myxopyroside D) 3-Formylindole E) 5-Hydroxy methyl furfural F) Capsiacin G) Methylpredisolone.

Discussion

Findings of myxopyroside, a substance meant to genus Nyctanthes from single leaf of Myxopyrum. It was evidenced by 13C NMR spectrum for the presence of dihydroxy substituted for sythide dimethyl ester and ester derivatives [13]. Herbs have been tremendous usage from ancient times and still the natural phytochemicals exhibiting their significance in health care for the treatment of various ailments [14]. The overuse of NSAIDs brings an adverse state of disease like Myocardial Infarction [15-17]. Earlier studies were evidenced that the phyto components glycosides, polyphenols, quercetin and kaempferol inhibits the mediators TNF-α, NO, IL-1β and MCP-1 responsible for inflammation [18-21].

The docking studies disclosed a perspective interaction of stated ligands towards receptor TNF-α. The interactions of phytocomponents Arenarioside, Verbascoside, Myxopyroside, 3-Formylindole and 5-Hydroxy Methyl Furfural shown hydrogen bonds to GLY A:121, ALA A: 96, ILE A:118, SER A:95, TYR A:119 illustrated in Table 3. The docking score of Arenarioside, Verbascoside, Myxopyroside, 3-Formylindole, 5-Hydroxy Methyl Furfural is around -5.0, -4.9, -5.1, -3.5, and 3.4, respectively. In current study the 5 ligands of Myxopyrum smilacifolium at the receptor TNF-α site, docking score was analysed by the use of Autodock 4.0. It has shown good docking score of about -5.1 kcal/mol between Myxpyroside and receptor TNF-α, proves that Myxopyroside inhibits the inflammatory mediator, evidenced by strong binding affinity with receptor. By using SwisADME tool, the pharmacokinetic study was studied for the components Arenarioside, Verbascoside, Myxopyroside where it revealed GI absorption is low whereas 3-Formylindole, 5-Hydroxy Methyl Furfural, 3-Formylindole GI absorption is high depicted in Table 3. Myxopyroside had shown high and mere equivalent to docking score around -5.1 kcal/mole when compared to reference natural phyto-constitutent Capsiacin and standard drug Methylprednisolone of about -4.8 kcal/mole and -5.4 kcal/mole.

Conclusion

Inflammatory mediators are responsible for various conditions of diseased state. Researches on phyto constituents were limited against inflammation. It can concluded that the phyto components in Myxopyrum smilacifolium can be explored and by modifying the SAR it may lead to finding of new moiety to treat inflammatory conditions and simultaneously the use of NSAIDs can be limited to overcome their adverse effects.

Acknowledgement

I would like express my acknowledgements to the Management of V. V. Institute of Pharmaceutical Sciences, Gudlavalleru and Prof. G. Rajitha, Professor, Institute of Pharmaceutical Technology, Sri Padmavati Mahila Visvavidyalayam, Tirupati-517502, Andhra Pradesh, India for their support.

Conflict of Interest

No conflict of interest.

References

Copyright: 2022 Raveesha Peeriga, et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.