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

Barosmin against postprandial hyperglycemia: outputs from computational prediction to functional responses in vitro

Previously, barosmin has been demonstrated to possess anti-diabetic action. However, its effect to inhibit α-amylase and α-glucosidase, including glucose utilization efficacy, has yet to be revealed. Hence, the current study attempted to assess the efficiency of barosmin in inhibiting the α-amylase, α -glucosidase, and dipeptidyl peptidase 4 enzymes, including glucose uptake efficacy. Molecular docking and simulation were performed using AutoDock Vina and Gromacs respectively followed by gene ontology analysis using the database for annotation, visualization, and integrated discovery. Further, in vitro enzyme inhibitory activities and glucose uptake assay were performed in L6 cell lines. Density functional theory analysis detailed mechanistic insights into the crucial interaction sites of barosmin of which the electron-dense region was prone to nucleophilic attack (O-atoms) whereas hydroxyl groups (-OH) showed affinity for electrophilic attacks. Barosmin showed good binding affinity with α-amylase (-9.2 kcal/mol), α-glucosidase (-10.7 kcal/mol), and dipeptidyl peptidase 4 (-10.0 kcal/mol). Barosmin formed stable nonbonded contacts with active site residues of aforementioned enzymes throughout 200 ns molecular dynamics simulation. Further, it regulated pathway concerned with glucose homeostasis i.e. tumor necrosis factor signaling pathway. In addition, barosmin showed α-amylase (IC50= 95.77 ± 23.33 µg/mL), α-glucosidase (IC50= 68.13 ± 2.95 µg/mL), and dipeptidyl peptidase 4 (IC50= 13.27 ± 1.99 µg/mL) inhibitory activities including glucose uptake efficacy in L6 cell lines (EC50= 12.46 ± 0.90 µg/mL) in the presence of insulin. This study presents the efficacy of the barosmin to inhibit α-amylase and α-glucosidase and glucose uptake efficacy in L6 cell lines via the use of multiple system biology tools and in vitro techniques.Communicated by Ramaswamy H. Sarma.

Effects of Dietary Terminalia chebula Extract on Growth Performance, Immune Function, Antioxidant Capacity, and Intestinal Health of Broilers

Terminalia chebula extract (TCE) has many physiological functions and is potentially helpful in maintaining poultry health, but its specific effect on the growth of broilers is not yet known. This research investigated the effects of dietary Terminalia chebula extract (TCE) supplementation on growth performance, immune function, antioxidant capacity, and intestinal health in yellow-feathered broilers. A total of 288 one-day-old yellow-feathered broilers were divided into four treatment groups (72 broilers/group), each with six replicates of 12 broilers. The broilers were given a basal diet of corn-soybean meal supplemented with 0 (control), 200, 400, and 600 mg/kg TCE for 56 d. The results demonstrated that, compared with the basal diet, the addition of TCE significantly increased (linear and quadratic, p < 0.05) the final body weight and overall weight gain and performance and decreased (linear and quadratic, p < 0.05) the feed-to-gain ratio in the overall period. Dietary TCE increased (linear, p < 0.05) the levels of IgM, IL-4, and IL-10 and decreased (linear and quadratic, p < 0.05) the level of IL-6 in the serum. Dietary TCE increased (linear and quadratic, p < 0.05) the levels of IL-2 and IL-4, decreased (linear and quadratic, p < 0.05) the level of IL-1β, and decreased (linear, p < 0.05) the level of IL-6 in the liver. Dietary TCE increased (linear and quadratic, p < 0.05) the level of IgM and IL-10, increased (linear, p < 0.05) the level of IgG, and decreased (linear and quadratic, p < 0.05) the levels of IL-1β and IL-6 in the spleen. Supplementation with TCE linearly and quadratically increased (p < 0.05) the catalase, superoxide dismutase, glutathione peroxidase, and total antioxidant capacity activities while decreasing (p < 0.05) the malonic dialdehyde concentrations in the serum, liver, and spleen. TCE-containing diets for broilers resulted in a higher (linear and quadratic, p < 0.05) villus height, a higher (linear and quadratic, p < 0.05) ratio of villus height to crypt depth, and a lower (linear and quadratic, p < 0.05) crypt depth compared with the basal diet. TCE significantly increased (linear, p < 0.05) the acetic and butyric acid concentrations and decreased (quadratic, p < 0.05) the isovaleric acid concentration. Bacteroidaceae and Bacteroides, which regulate the richness and diversity of microorganisms, were more abundant and contained when TCE was added to the diet. In conclusion, these findings demonstrate that supplementing broilers with TCE could boost their immune function, antioxidant capacity, and gut health, improving their growth performance; they could also provide a reference for future research on TCE.

Hepatitis C: The Story of a Long Journey through First, Second, and Third Generation NS3/4A Peptidomimetic Inhibitors. What Did We Learn?

Hepatitis C viral (HCV) infection is the leading cause of liver failure and still represents a global health burden. Over the past decade, great advancements made HCV curable, and sustained viral remission significantly improved to more than 98%. Historical treatment with pegylated interferon alpha and ribavirin has been displaced by combinations of direct-acting antivirals. These regimens include drugs targeting different stages of the HCV life cycle. However, the emergence of viral resistance remains a big concern. The design of peptidomimetic inhibitors (PIs) able to fit and fill the conserved substrate envelope region within the active site helped avoid contact with the vulnerable sites of the most common resistance-associated substitutions Arg155, Ala156, and Asp168. Herein, we give an overview of HCV NS3 PIs discovered during the past decade, and we deeply discuss the rationale behind the structural optimization efforts essential to achieve pangenotypic activity.

Global Profiling of the Antioxidant Constituents in Chebulae Fructus Based on an Integrative Strategy of UHPLC/IM-QTOF-MS, MS/MS Molecular Networking, and Spectrum-Effect Correlation

An integrative strategy of UHPLC/IM-QTOF-MS analysis, MS/MS molecular networking (MN), in-house library search, and a collision cross-section (CCS) simulation and comparison was developed for the rapid characterization of the chemical constituents in Chebulae Fructus (CF). A total of 122 Constituents were identified, and most were phenolcarboxylic and tannic compounds. Subsequently, 1,3,6-tri-O-galloyl-β-d-glucose, terflavin A, 1,2,6-tri-O-galloyl-β-d-glucose, punicalagin B, chebulinic acid, chebulagic acid, 1,2,3,4,6-penta-O-galloyl-β-d-glucose, and chebulic acid, among the 23 common constituents of CF, were screened out by UPLC-PDA fingerprinting and multivariate statistical analyses (HCA, PCA, and OPLS-DA). Then, Pearson's correlation analysis and a grey relational analysis were performed for the spectrum-effect correlation between the UPLC fingerprints and the antioxidant capacity of CF, which was finally validated by an UPLC-DPPH• analysis for the main antioxidant constituents. Our study provides a global identification of CF constituents and contributes to the quality control and development of functional foods and preparations dedicated to CF.

Structural insights into modeling of hepatitis B virus reverse transcriptase and identification of its inhibitors from potential medicinal plants of Western Ghats: an in silico and in vitro study

The present study was proposed to model full-length HBV-RT and investigate the intermolecular interactions of known inhibitor and libraries of phytocompounds to probe the potential natural leads by in silico and in vitro studies. Homology modeling of RT was performed by Phyre2 and Modeller and virtual screening of ligands implemented through POAP pipeline. Molecular dynamics (MD) simulation (100 ns) and MM-GBSA calculations were performed using Schrodinger Desmond and Prime, respectively. Phytocompounds probable host protein targets gene set pathway enrichment and network analysis were executed by KEGG database and Cytoscape software. Prioritized plant extracts/enriched fraction LC-MS analysis was performed and along with pure compound, RT inhibitory activity, time-dependent HBsAg and HBeAg secretion, and intracellular HBV DNA, and pgRNA by qRT-PCR was performed in HepG2.2.15 cell line. Among the screened chemical library of 268 phytocompounds from 18 medicinal plants, 15 molecules from Terminalia chebula (6), Bidens pilosa (5), and Centella asiatica (4)) were identified as potential inhibitors of YMDD and RT1 motif of HBV-RT. MD simulation demonstrated stable interactions of 15 phytocompounds with HBV-RT, of which 1,2,3,4,6-Pentagalloyl Glucose (PGG) was identified as lead molecule. Out of 15 compounds, 11 were predicted to modulate 39 proteins and 15 molecular pathways associated with HBV infection. TCN and TCW (500 µg/mL) showed potent RT inhibition, decreased intracellular HBV DNA, and pgRNA, and time-dependent inhibition of HBsAg and HBeAg levels compared to PGG and Tenofovir Disoproxil Fumarate. We propose that the identified lead molecules from T. chebula as promising and cost-effective moieties for the management of HBV infection.Communicated by Ramaswamy H. Sarma.

Piperazine-derived small molecules as potential Flaviviridae NS3 protease inhibitors. In vitro antiviral activity evaluation against Zika and Dengue viruses

Since 2011 Direct Acting antivirals (DAAs) drugs targeting different non-structural (NS) viral proteins (NS3, NS5A or NS5B inhibitors) have been approved for clinical use in HCV therapies. However, currently there are not licensed therapeutics to treat Flavivirus infections and the only licensed DENV vaccine, Dengvaxia, is restricted to patients with preexisting DENV immunity. Similarly to NS5 polymerase, the NS3 catalytic region is evolutionarily conserved among the Flaviviridae family sharing strong structural similarity with other proteases belonging to this family and therefore is an attractive target for the development of pan-flavivirus therapeutics. In this work we present a library of 34 piperazine-derived small molecules as potential Flaviviridae NS3 protease inhibitors. The library was developed through a privileged structures-based design and then biologically screened using a live virus phenotypic assay to determine the half-maximal inhibitor concentration (IC₅₀) of each compound against ZIKV and DENV. Two lead compounds, 42 and 44, with promising broad-spectrum activity against ZIKV (IC₅₀ 6.6 µM and 1.9 µM respectively) and DENV (IC₅₀ 6.7 µM and 1.4 µM respectively) and a good security profile were identified. Besides, molecular docking calculations were performed to provide insights about key interactions with residues in NS3 proteases' active sites.

Target-specificity of different amyrin subunits in impeding HCV influx mechanism inside the human cells considering the quantum tunnel profiles and molecular strings of the CD81 receptor: a combined in silico and in vivo study

HCV is a hepatotropic RNA virus recognized for its frequent virulence and fatality worldwide. Despite many vaccine development programs underway, researchers are on a quest for natural bioactive compounds due to their multivalent efficiencies against viral infections, considering which the current research aimed to figure out the target-specificity and therapeutic potentiality of α, β, and δ subunits of amyrin, as novel bioactive components against the HCV influx mechanism. Initially, the novelty of amyrin subunits was conducted from 203 pharmacophores, comparing their in-silico pharmacokinetic and pharmacodynamic profiles. Besides, the best active site of CD81 was determined following the quantum tunneling algorithm. The molecular dynamic simulation was conducted (100 ns) following the molecular docking steps to reveal the parameters- RMSD (Å); Cα; RMSF (Å); MolSA (Ų); Rg (nm); PSA (Å); SASA (Ų), and the MM-GBSA dG binding scores. Besides, molecular strings of CD81, along with the co-expressed genes, were classified, as responsible for encoding CD81-mediated protein clusters during HCV infection, resulting in the potentiality of amyrins as targeted prophylactics in HCV infection. Finally, in vivo profiling of the oxidative stress marker, liver-specific enzymes, and antioxidant markers was conducted in the DMN-induced mice model, where β-amyrin scored the most significant values in all aspects.

Exploring the Potential of Phytocompounds for Targeting Epigenetic Mechanisms in Rheumatoid Arthritis: An In Silico Study Using Similarity Indexing

Finding structurally similar compounds in compound databases is highly efficient and is widely used in present-day drug discovery methodology. The most-trusted and -followed similarity indexing method is Tanimoto similarity indexing. Epigenetic proteins like histone deacetylases (HDACs) inhibitors are traditionally used to target cancer, but have only been investigated very recently for their possible effectiveness against rheumatoid arthritis (RA). The synthetic drugs that have been identified and used for the inhibition of HDACs include SAHA, which is being used to inhibit the activity of HDACs of different classes. SAHA was chosen as a compound of high importance as it is reported to inhibit the activity of many HDAC types. Similarity searching using the UNPD database as a reference identified aglaithioduline from the Aglaia leptantha compound as having a ~70% similarity of molecular fingerprints with SAHA, based on the Tanimoto indexing method using ChemmineR. Aglaithioduline is abundantly present in the shell and fruits of A. leptantha. In silico studies with aglaithioduline were carried out against the HDAC8 protein target and showed a binding affinity of -8.5 kcal mol. The complex was further subjected to molecular dynamics simulation using Gromacs. The RMSD, RMSF, compactness and SASA plots of the target with aglaithioduline, in comparison with the co-crystallized ligand (SAHA) system, showed a very stable configuration. The results of the study are supportive of the usage of A. leptantha and A. edulis in Indian traditional medicine for the treatment of pain-related ailments similar to RA. Our study therefore calls for further investigation of A. leptantha and A. edulis for their potential use against RA by targeting epigenetic changes, using in vivo and in vitro studies.

Chemoprofiling and insilico prioritization of bioactive compounds from Laetiporus versisporus (Lloyd) Imazeki reveals potential Bcl-2 inhibitor

Laetiporus versisporus (Lloyd) Imazeki is an edible mushroom that grows abundantly in kodaikanal hills (India) during rainy season. Till now, there is a dearth of reports on chemoprofile and anticancer potential of this mushroom. In our recent study, L.versisporus ethanolic extract was reported to confer hepato-protective activity against DEN-induced HCC rats and also found to downregulate Bcl-2 activity. Moreover, the phytocompounds of a related species namely, L. sulphurous is also reported to potentially modulate Bcl-2 in glioblastoma. Hence, by this study, the bioactive compounds from L. versisporus ethanolic extract were profiled using LC-MS analysis and were virtually screened against ligand binding site of Bcl-2 in order to predict potential moieties with anticancer efficacies. Further, the top 3 potential hits were shortlisted based on MMGBSA score, ADME properties and stable complex formation during MD simulation. Amongst these hits, (6S)-1alpha, 25-dihydroxy vitaminD36,19-sulfurdioxide adduct was found to be highly promising in terms of binding affinity and ADME features comparable to the known inhibitor (DRO), thus shall be further probed for therapeutic efficacy using experimental validations for effective and natural mode of combating Bcl-2 mediated cancers.Communicated by Ramaswamy H. Sarma.

The long and stumble way to find potential active compounds from plants for defeating hepatitis B and C: review

Hepatitis is a liver illness caused by virus such as hepatitis A virus, hepatitis B virus and hepatitis C virus. Hepatitis B and C are considerably more usual and induce more cirrhosis and dead worldwide than hepatitis A. Although drugs that are currently often used in the medication of hepatitis B and C, the finding of recent drug from various resources including herbal has been intensively developed. Therefore, the purpose of this review is to consider the possibility of plant’s compounds as anti-HBV and anti-HCV. From the results of a review of several articles, several plant’s compound have shown effectiveness againts HBV and HCV by in silico, in vitro and in vivo studies. In conclusion, several plant’s active compounds are possibility to be developed as anti-hepatitis B and C.

Investigation of the inhibition effect of 1,2,3,4,6-pentagalloyl-β-D-glucose on gastric cancer cells based on a network pharmacology approach and experimental validation

Background

Gastric cancer (GC) is ranked as the third leading cause of cancer-related mortality worldwide. 1,2,3,4,6-Pentagalloyl-β-D-glucose (β-PGG) has various pharmacological activities and has been shown to suppress cancer development. However, the mechanism by which β-PGG inhibits gastric cancer has not been elucidated.

Objective

This study explored the potential targets and mechanism of β-PGG in GC using the network pharmacology approach combined with in-vitro experiments.

Methods

The PharmMapper software was used to predict the potential targets of β-PGG, and GC-related genes were identified on the GeneCards database. PPI analysis of common genes was performed using the STRING database. The potential regulatory mechanism of β-PGG in GC was explored through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. The binding ability of key genes and target proteins was verified by molecular docking. The effects of β-PGG on genes and proteins were evaluated using the CCK-8 assay, cell cycle analysis, apoptosis assay, real-time fluorescence quantification polymerase chain reaction (qRT-PCR), and Western blotting.

Results

Eight hub genes involved in cell cycle progression and apoptosis were identified. Cancer-related signaling pathways were identified using the Cytoscape tool. Some of those genes were significantly enriched in the p53 signaling pathway. The CCK-8 assay showed that β-PGG inhibited the proliferation of GC cells. Cell cycle and apoptosis experiments revealed that β-PGG induced cell cycle arrest and apoptosis of gastric cancer cells. qRT-PCR and Western blot analysis showed that β-PGG inhibited β-PGG cells by modulating the p53 signaling pathway.

Conclusion

In the present study, the targets and mechanism of β-PGG in gastric cancer were explored. The results indicate that β-PGG can be used to develop treatments for GC.

Targeting non-structural proteins of Hepatitis C virus for predicting repurposed drugs using QSAR and machine learning approaches

Hepatitis C virus (HCV) infection causes viral hepatitis leading to hepatocellular carcinoma. Despite the clinical use of direct-acting antivirals (DAAs) still there is treatment failure in 5–10% cases. Therefore, it is crucial to develop new antivirals against HCV. In this endeavor, we developed the “Anti-HCV” platform using machine learning and quantitative structure–activity relationship (QSAR) approaches to predict repurposed drugs targeting HCV non-structural (NS) proteins. We retrieved experimentally validated small molecules from the ChEMBL database with bioactivity (IC₅₀/EC₅₀) against HCV NS3 (454), NS3/4A (495), NS5A (494) and NS5B (1671) proteins. These unique compounds were divided into training/testing and independent validation datasets. Relevant molecular descriptors and fingerprints were selected using a recursive feature elimination algorithm. Different machine learning techniques viz. support vector machine, k-nearest neighbour, artificial neural network, and random forest were used to develop the predictive models. We achieved Pearson’s correlation coefficients from 0.80 to 0.92 during 10-fold cross validation and similar performance on independent datasets using the best developed models. The robustness and reliability of developed predictive models were also supported by applicability domain, chemical diversity and decoy datasets analyses. The “Anti-HCV” predictive models were used to identify potential repurposing drugs. Representative candidates were further validated by molecular docking which displayed high binding affinities. Hence, this study identified promising repurposed drugs viz. naftifine, butalbital (NS3), vinorelbine, epicriptine (NS3/4A), pipecuronium, trimethaphan (NS5A), olodaterol and vemurafenib (NS5B) etc. targeting HCV NS proteins. These potential repurposed drugs may prove useful in antiviral drug development against HCV.