Hepatitis C Virus NS3/4A Inhibition and Host Immunomodulation by Tannins from Terminalia chebula: A Structural Perspective

Abstract

Terminalia chebula Retz. forms a key component of traditional folk medicine and is also reported to possess antihepatitis C virus (HCV) and immunomodulatory activities. However, information on the intermolecular interactions of phytochemicals from this plant with HCV and human proteins are yet to be established. Thus, by this current study, we investigated the HCV NS3/4A inhibitory and host immune-modulatory activity of phytocompounds from T. chebula through in silico strategies involving network pharmacology and structural bioinformatics techniques. To start with, the phytochemical dataset of T. chebula was curated from biological databases and the published literature. Further, the target ability of the phytocompounds was predicted using BindingDB for both HCV NS3/4A and other probable host targets involved in the immune system. Further, the identified targets were docked to the phytochemical dataset using AutoDock Vina executed through the POAP pipeline. The resultant docked complexes with significant binding energy were subjected to 50 ns molecular dynamics (MD) simulation in order to infer the stability of complex formation. During network pharmacology analysis, the gene set pathway enrichment of host targets was performed using the STRING and Reactome pathway databases. Further, the biological network among compounds, proteins, and pathways was constructed using Cytoscape 3.6.1. Furthermore, the druglikeness, side effects, and toxicity of the phytocompounds were also predicted using the MolSoft, ADVERpred, and PreADMET methods, respectively. Out of 41 selected compounds, 10 were predicted to target HCV NS3/4A and also to possess druglike and nontoxic properties. Among these 10 molecules, Chebulagic acid and 1,2,3,4,6-Pentagalloyl glucose exhibited potent HCV NS3/4A inhibitory activity, as these scored a lowest binding energy (BE) of -8.6 kcal/mol and -7.7 kcal/mol with 11 and 20 intermolecular interactions with active site residues, respectively. These findings are highly comparable with Asunaprevir (known inhibitor of HCV NS3/4A), which scored a BE of -7.4 kcal/mol with 20 key intermolecular interactions. MD studies also strongly suggest that chebulagic acid and 1,2,3,4,6-Pentagalloyl glucose as promising leads, as these molecules showed stable binding during 50 ns of production run. Further, the gene set enrichment and network analysis of 18 protein targets prioritized 10 compounds and were predicted to potentially modulate the host immune system, hemostasis, cytokine levels, interleukins signaling pathways, and platelet aggregation. On overall analysis, this present study predicts that tannins from T. chebula have a potential HCV NS3/4A inhibitory and host immune-modulatory activity. However, further experimental studies are required to confirm the efficacies.

Keywords: 1,2,3,4,6-Pentagalloyl glucose; Terminalia chebula Retz; chebulagic acid; docking; dynamics; hepatitis C virus NS3/4A; network pharmacology.

Figure 1

HCV, NS3 X-ray crystallographic structure, substrate binding pockets, and its catalytic triad residues.

Figure 2

Workflow followed in the current study.

Figure 3

Network representation of phytocompound-target-pathway.

Figure 4

Characteristics of PDB ID: 4WF8 (HCV NS3/4A crystal structure). (a) Ramachandran plot by PROCHECK. (b) Overall quality prediction by ERRAT. * On the error axis, two lines are drawn to indicate the confidence with which it is possible to reject regions that exceed that error value. ** Expressed as the percentage of the protein for which the calculated error value falls below the 95% rejection limit.

Figure 5

Stability of HCV NS3/4A (PDB ID: 4WF8). (a) Backbone RMSD and (b) per-residue backbone RMSF.

Figure 6

Intermolecular Interactions of Asunaprevir with NS3/4A. (a) Asunaprevir at catalytic triad residue site; (b) Asunaprevir at NS3/4A binding pocket; (c) Asunaprevir interaction with catalytic triad residue Ser1139.

Figure 7

Intermolecular interactions of chebulagic acid with NS3/4A. (a) Chebulagic acid at catalytic triad residue site; (b) chebulagic acid bound to NS3/4A binding pocket; (c) chebulagic acid interactions with catalytic triad residue Ser1139, His1057, and Asp1081.

Figure 8

Intermolecular Interactions of 1,2,3,4,6-Pentagalloyl glucose with NS3/4A. (a) 1,2,3,4,6-Pentagalloyl glucose at catalytic triad residue site; (b) 1,2,3,4,6-Pentagalloyl glucose bound to NS3/4A binding pocket; (c) 1,2,3,4,6-Pentagalloyl glucose interactions with catalytic triad residue Ser1139, His1057, and Asp1081.

Figure 9

MD trajectories of Asunaprevir in complex with HCV NS3/4A for a 50 ns simulation: (a) RMSD, (b) RMSF, (c) rGyr, and (d–f) residue-wise ligand–protein contacts.

Figure 10

Stability of chebulagic acid with HCV NS3/4A at 50 ns of simulation: (a) RMSD, (b) RMSF, (c) rGyr, and (d–f) residue-wise ligand–protein contacts.

Figure 11

Stability of 1,2,3,4,6-Pentagalloyl glucose with HCV NS3/4A at 50 ns of simulation: (a) RMSD, (b) RMSF, (c) rGyr, and (d–f) residue-wise ligand–protein contacts.

Figure 12

Heat map representation of phytocompounds with their probable (a) side effects and (b) toxicity.