Gene set enrichment analysis of PPAR-γ regulators from Murraya odorata Blanco

Predicting the bioactive compounds of Lentinula edodes and elucidating its interaction with genes associated to obesity through network pharmacology and in-vitro cell-based assay

Mushrooms are traditionally used for various medicinal purposes in traditional oriental medicine. The Japanese and Chinese are familiar with the medicinal macro fungus Lentinula edodes (Shiitake mushroom). This study aims to evaluate the role of chemical compounds from L. edodes using network pharmacology and in-vitro studies for management of Obesity. Bioactive compounds in extracts of L. edodes were identified by GC-MS analysis. Compounds were later screened for their drug-like property by Lipinski's rule. In addition, public databases (SEA, STP, Omim and DisGenet) were searched to identify genes associated with selected molecules and obesity, as well as genes that overlap obesity target genes with genes related to L. edodes. Additionally, analysis was performed using Enrichr KG to predict the disease targets of L. edodes. Finally, network was constructed between the overlapping genes and bioactive molecules using Rstudio. Further in-vitro studies were carried out using 3T3-L1 cell line. The genes related to the selected compounds and obesity were identified and overlapped. The disease targets of L. edodes was predicted by enrichment analysis and was found to be linked to obesity. Furthermore, the hub gene was found to be fatty acid amide hydrolase, and the key bioactive compound was hexadecanoic acid methyl ester. The in-vitro cell culture studies confirmed the inhibition of adipogenesis in mushroom extract-treated 3T3-L1 cells and the augmentation of adiponectin. The study suggests that the hub gene fatty acid amide hydrolase might alleviate obesity by inhibiting arachidonoyl ethanolamide signaling, which would enhance the action of fatty acid amide hydrolase and limit appetite in L. edodes extract.

Guideline directed medical therapy induced nephrotoxicity in HFrEF patients; an insight to its mechanism

Guideline Directed Medical Therapy (GDMT) has been the standard pharmacotherapy for the treatment of Heart Failure patients with reduced Ejection Fraction (HFrEF) recommended by the European Society of Cardiology (ESC). However, patients on GDMT are likely to possess nephrotoxicity as an adverse effect. We utilized multiple system biology tools like ADVER-Pred, gene enrichment analysis, molecular docking, molecular dynamic simulations, and MMPBSA analysis to predict a possible molecular mechanism of how selected combinations of GDMT may cause nephrotoxicity. As per the ACC/AHA/ESC guidelines, we categorized the drugs as category 1 including β-blockers (BB), angiotensin receptor blockers (ARB), and sodium-glucose cotransporter-2 inhibitors (SGLT2I), category 2 includes BB's, SGLT2I, and angiotensin receptor-neprilysin inhibitors (ARNI), and category 3 includes BB's, SGLT2I, and angiotensin-converting enzyme (ACE) inhibitors. Enrichment analysis predicted category 2 drugs to possess the highest number of proteins to be involved in the development of nephrotoxicity i.e. 79.41%. The targets HBA1, CBR1, ATG5, and SLC6A3 were the top hub genes with an edge count of 7 followed by GPX1 with an edge count of 6. Molecular docking studies revealed candesartan-SLC6A3 to possess the highest binding affinity of -10.2 kcal/mol. In addition, simulation studies displayed empagliflozin-CBR1 to possess the highest stability followed by candesartan-ATG5. A combination of β-blockers, ARBs, and SGLT2I are predicted to likely possess nephrotoxicity which may be due to the modulation of HBA1, CBR1, ATG5, and GPX1. In conclusion, candesartan and empagliflozin are most likely to cause nephrotoxicity via the modulation of HBA1, CBR1, ATG5, and GPX1.Communicated by Ramaswamy H. Sarma.

System biology mediated assessment of molecular mechanism for sinapic acid against breast cancer: via network pharmacology and molecular dynamic simulation

Sinapic acid is a hydroxycinnamic acid widespread in the plant kingdom, known to be a potent anti-oxidant used for the treatment of cancer, infections, oxidative stress, and inflammation. However, the mode of action for its chemotherapeutic properties has yet not been unleashed. Hence, we aimed to identify potential targets to propose a possible molecular mechanism for sinapic acid against breast cancer. We utilized multiple system biology tools and databases like DisGeNET, DIGEP-Pred, Cytoscape, STRING, AutoDock 4.2, AutoDock vina, Schrodinger, and gromacs to predict a probable molecular mechanism for sinapic acid against breast cancer. Targets for the disease breast cancer, were identified via DisGeNET database which were further matched with proteins predicted to be modulated by sinapic acid. In addition, KEGG pathway analysis was used to identify pathways; a protein-pathway network was constructed via Cytoscape. Molecular docking was performed using three different algorithms followed by molecular dynamic simulations and MMPBSA analysis. Moreover, cluster analysis and gene ontology (GO) analysis were performed. A total of 6776 targets were identified for breast cancer; 95.38% of genes predicted to be modulated by sinapic acid were common with genes of breast cancer. The 'Pathways in cancer' was predicted to be modulated by most umber of proteins. Further, PRKCA, CASP8, and CTNNB1 were predicted to be the top 3 hub genes. In addition, molecular docking studies revealed CYP3A4, CYP1A1, and SIRT1 to be the lead proteins identified from AutoDock 4.2, AutoDock Vina, and Schrodinger suite Glide respectively. Molecular dynamic simulation and MMPBSA were performed for the complex of sinapic acid with above mentioned proteins which revealed a stable complex throughout simulation. The predictions revealed that the mechanism of sinapic acid in breast cancer may be due to regulation of multiple proteins like CTNNB1, PRKCA, CASP8, SIRT1, and cytochrome enzymes (CYP1A1 & CYP3A4); the majorly regulated pathway was predicted to be 'Pathways in cancer'. This indicates the rationale for sinapic acid to be used in the treatment of breast cancer. However, these are predictions and need to be validated and looked upon in-depth to confirm the exact mechanism of sinapic acid in the treatment of breast cancer; this is future scope as well as a drawback of the current study.

Feronia elephantum reverses insulin resistance in fructose-induced hyper-insulinemic rats; an in-silico, in-vitro, and in-vivo approach

ETHNOPHARMACOLOGICAL RELEVANCE

Feronia elephantum corr. (synonym: Feronia limonia, Murraya odorata, Schinus Limonia, or Limonia acidissima; common names: Bela, Kath, Billin, and Kavitha), belonging to the family Rutaceae has been known for clinical conditions such as pruritus, diarrhea, impotence, dysentery, heart diseases, and is also used as a liver tonic. However, the effect of the fruit pulp of F. elephantum on insulin resistance has yet not been reported.

AIM OF THE STUDY

The present study aimed to assess the effect of hydroalcoholic extract/fraction of F. elephantum fruit pulp on fasting blood glucose, oral glucose tolerance test, and glucose uptake in fructose-induced insulin-resistant rats and predict the gene-set enrichment of lead hits of F. elephantum with targets related to insulin resistance.

MATERIAL AND METHODS

System biology tools were used to predict the best category of fraction and propose a possible mechanism. Docking was carried out with adiponectin and its receptor (hub gene). Further, fructose supplementation was used for the induction of insulin resistance. Later, three doses of extract (400, 200, and 100 mg/kg) and a flavonoid-rich fraction (63 mg/kg) were used for treatment along with metformin as standard. The physical parameters like body weight, food intake, and water intake were measured along with oral glucose tolerance test, insulin tolerance test, glycogen content in skeletal muscles and liver, glucose uptake by rat hemidiaphragm, lipid profiles, anti-oxidant biomarkers, and histology of the liver and adipose tissue.

RESULTS

Network pharmacology reflected the potency of F. elephantum to regulate adiponectin (ADIPOQ) which may promote the reversal of insulin resistance and inhibit α-amylase and α-glucosidase. Vitexin was predicted to modulate the most genes associated with diabetes mellitus. Further, F. elephantum ameliorated the exogenous glucose clearance, promoted insulin sensitivity, reduced oxidative stress, and improved glucose and lipid metabolism. HPLC profiling revealed the presence of apigenin and quercetin in the extract for the first time.

CONCLUSION

The fruit pulp of F. elephantum reverses insulin resistance by an increase in glucose uptake and a decrease in gluconeogenesis which may be due to the regulation of multiple proteins via multiple bio-actives.

System biology-based investigation of Silymarin to trace hepatoprotective effect

Silymarin is used as a hepatoprotective agent since ancient times which could be via its potent anti-oxidant effect. However, the mode of silymarin for the hepatoprotective effect has not been established with the targets involved in hepatic cirrhosis. The present study investigated the multiple interactions of the flavonolignans from Silybum marianum with targets involved in hepatic cirrhosis using a series of system biology approaches. Chemo-informative tools and databases i.e. DIGEP-Pred and DisGeNET were used to predict the targets of flavonolignans and proteins involved in liver cirrhosis respectively. Further, STRING was used to enrich the protein-protein interaction for the flavonolignans-modulated targets. Similarly, molecular docking was performed using AutoDock Vina. Additionally, molecular dynamics simulation and MM-PBSA calculations were carried out for the lead-hit complexes by GROMACS. Thirteen flavonolignans were identified from S. marianum, in which silymonin exhibited the highest drug-likeness score i.e. 1.09. Similarly, CTNNB1 was found to be regulated by the 12 different flavonolignans and was majorly expressed within the compound(s)-protein(s)-pathway(s) network. Further, silymonin had the highest binding affinity; binding energy -9.2 kcal/mol with the CTNNB1 and formed very stable hydrogen bond interactions with Arg332, Ser336, Lys371, and Arg475 throughout 100 ns molecular dynamic production run. The binding free energy of CTNNB1-silymonin complex was found to be -15.83 ± 2.71 kcal/mol. The hepatoprotective property of S. marianum may be due to the presence of silymonin and silychristin; this could majorly modulate CTNNB1, HMOX1, and CASP8 in combination with other flavonolignans. Our findings further suggest designing the in-vitro and in-vivo studies to validate the interaction of flavonolignans with identified targets to strengthen present findings of S. marianum as a hepatoprotective..

Ficus benghalensis promotes the glucose uptake- Evidence with in silico and in vitro

Background

Ficus benghalensis L. is traditionally used to manage diabetes; also used in various herbal formulations, and is indicated as an insulin sensitizer. Hence, present work attempted in identifying the probable lead hits to promote glucose uptake via computational approach followed by experimental evaluation of hydroalcoholic extract of Ficus benghalensis L. bark in yeast cells.

Methods

The in vitro assay for glucose uptake was performed in the baker yeast whereas in-silico study involved retrieving the phytoconstituents from open sources, and predicting for probable targets of diabetes followed by drug-likeness score, probable side effects, and ADMET profile. Homology modeling was performed to construct the target protein glucose transporter-2. In addition, the binding affinity of each ligand with glucose transporter was predicted using AutoDock 4.2.

Results

A total of 17 phytoconstituents from F. benghalensis were identified to possess the anti-diabetic effects. Among them, 4-methoxybenzoic acid scored the highest drug-likeness score and lupeol acetate had the maximum binding affinity of -8.02 kcal/mol with 9 pi-interactions via Tyr324, Phe323, Ile319, Ile200, Ile28, Phe24, and Ala451. Similarly, the extract showed the highest glucose uptake efficacy in yeast cells at 500 µg/mL.

Conclusion

Herein the present study reflected the probable activity of the phytoconstituents from F. benghalensis in promoting the glucose uptake via the in silico and in vitro approaches.

GLUT-2 mediated glucose uptake analysis of Duranta repens: In-silico and In-vitro approach

Background

Type-2 diabetes mellitus is a common metabolic disorder characterized by insulin resistance, a relative impairment in insulin secretion, and a certain degree of genetic predisposition. The rapid rise in the prevalence of diabetes mellitus around the world has assisted in the development of new pharmacologically active compounds. The current study was aimed to investigate and validate the anti-diabetic activity of wild-grown plant Duranta repens L.

Material and methods

In-silico molecular docking via AutoDock tools 4.2 and in-vitro glucose uptake assay using yeast cells was performed to investigate the anti-diabetic property of plant Duranta repens. Further, mRNA-based gene ontology enrichment analysis was performed to predict the imitated ontology by the bio-actives from Duranta repens.

Results

The in-silico study results reveal that among the 9 active phytoconstituents docked against GLUT-2 protein, α-onocerin possessed the highest binding affinity of -10.23 kcal/mol with no predicted adverse effects and also complies with Lipinski's rule of five. Also, in-vitro studies reflected in a 5 mM glucose solution, hydro-alcoholic extract of Duranta repens at different concentrations enhanced glucose uptake in yeast cells.

Conclusion

Duranta repens extract enhanced the glucose uptake in yeast cells which may be due to the presence of α-onocerin; possessed the better interaction. Also, no adverse effects were predicted for α-onocerin. Thus, it can be speculated  that Duranta repens may possess anti-diabetic activity which may be due to α-onocerin and other related bioactives; needs to be further confirmed vi a  experimental studies.

Anti-diabetic potential of Corn silk (Stigma maydis): An in-silico approach

Corn silk is known to possess anti-diabetic activity, the current study is aimed to predict the binding affinity of bio-actives from corn silk against targets involved in diabetes mellitus i.e. Protein Tyrosine Phosphatase 1-B (PTP1B), Glucose Transporter-1 (GLUT1), Dipeptidyl Peptidase-4 (DPP4), α-glucosidase, and α-amylase. The 3D molecular structure of bio-actives was retrieved from the PubChem database and the structure of targets was retrieved from protein data bank. Later, hetero atoms were removed using Discovery studio visualizer 2019. Molecular docking was performed using Autodock4.0. Ten different poses were obtained from which the pose possessing the highest binding affinity was visualized for protein-ligand interaction in Discovery studio visualizer 2019. Twenty-six bio-actives were docked against five different targets i.e. PTPN1B, GLUT1, DPP4, α-glucosidase, and α-amylase from which flavones were found to possess the highest binding affinity towards PTPN1B with a binding energy of -8.5 kcal/mol. Similarly, β-carotene, gallotannins, 3-O-caffeoylquinic acid, and stigmasterol were predicted to possess the highest binding affinity towards GLUT1, DPP4, α-glucosidase, and α-amylase with binding energy -11.1 kcal/mol, -10.7 kcal/mol, -8.9 kcal/mol, and -9.8 kcal/mol respectively. Our study screened the anti-diabetic potential of 26 bio-actives towards five different diabetic proteins indicating a possibility of bio-actives from corn silk to possess anti-diabetic potential which needs to be further validated via experimental protocols; this serves as a future scope as well as lacuna for the present study. Thus, bio-actives from corn silk have anti-diabetic potential and can be used in the future to investigate and develop novel anti-diabetic molecule.

Exploring the therapeutic mechanisms of Cassia glauca in diabetes mellitus through network pharmacology, molecular docking and molecular dynamics

Cassia glauca is reported as anti-diabetic medicinal plant and is also used as an ethnomedicine. However, its mode of action as an anti-diabetic agent has not been clearly elucidated. Hence, the present study investigated the probable mechanism of action of C. glauca to manage diabetes mellitus via network pharmacology and molecular docking and simulations studies. The reported bioactives from C. glauca were retrieved from an open-source database, i.e. ChEBI, and their targets were predicted using SwissTargetPrediction. The proteins involved in the pathogenesis of diabetes were identified from the therapeutic target database. The targets involved in diabetes were enriched in STRING, and the pathways involved in diabetes were identified concerning the KEGG. Cytoscape was used to construct the network among bioactives, proteins, and probably regulated pathways, which were analyzed based on edge count. Similarly, molecular docking was performed using the Glide module of the Schrodinger suite against majorly targeted proteins with their respective ligands. Additionally, the drug-likeness score and ADMET profile of the individual bioactives were predicted using MolSoft and admetSAR2.0 respectively. The stability of these complexes were further studied via molecular dynamics simulations and binding energy calculations. Twenty-three bio-actives were retrieved from the ChEBI database in which cassiarin B was predicted to modulate the highest number of proteins involved in diabetes mellitus. Similarly, GO analysis identified the PI3K-Akt signaling pathway to be primarily regulated by modulating the highest number of gene. Likewise, aldose reductase (AKR1B1) was majorly targeted via the bioactives of C. glauca. Similarly, docking study revealed methyl-3,5-di-O-caffeoylquinate (docking score −9.209) to possess the highest binding affinity with AKR1B1. Additionally, drug-likeness prediction identified cassiaoccidentalin B to possess the highest drug-likeness score, i.e. 0.84. The molecular dynamics simulations and the MMGBSA indicate high stability and greater binding energy for the methyl-3,5-di-O-caffeoylquinate (ΔG_bind = −40.33 ± 6.69 kcal mol⁻¹) with AKR1B1, thus complementing results from other experiments. The study identified cassiarin B, cassiaoccidentalin B, and cinnamtannin A2 as lead hits for the anti-diabetic activity of C. glauca. Further, the PI3K-Akt and AKR1B1 were traced as majorly modulated pathway and target, respectively.

Cassia glauca is reported for anti-diabetic action and is also used as an ethnomedicine.

Identification of α-amylase inhibitors from flavonoid fraction of Feronia elephantum and its integration with in-silico studies

Postprandial hyperglycemia is associated with an increase in blood glucose levels after a meal, which is further associated with various risk factors like cardiovascular diseases. α-amylase is a digestive enzyme and secreted by the salivary glands and pancreas, which helps to catalyze the hydrolysis of the internal α-1,4-glycosidic linkages in starch breaking them into smaller units. Hence, the present study is aimed to identify flavonoids from the fruit pulp of Feronia elephantum as α-amylase inhibitors via in-silico and in-vitro protocols. In-silico tools like ADVERPred, PubChem, MolSoft, Discovery studio 2019, and Autodock 4.0 were used to predict the information related to phytoconstituents, drug-likeness character, and probable side effects. In-vitro α-amylase inhibitory activity was performed with five different concentrations of flavonoid fraction of hydroalcoholic extract of the fruit pulp of Feronia elephantum using 1% starch solution and DNS reagent. Four flavonoids were identified from 25 bio-actives present in the fruit pulp of Feronia elephantum. Three bio-actives were predicted to possess a positive drug-likeness score, from which 5,4-dihydroxy3-3(3-methyl-but2-enyl)3,5,6-trimethoxy-flavone-7-O-β-d-Glucopyranoside was predicted to possess the highest drug-likeness score of 0.70. Vitexin and 5,4-dihydroxy3-3(3-methyl-but2-enyl)3,5,6-trimethoxy-flavone-7-O-β-d-Glucopyranoside were predicted to possess nephrotoxicity as an adverse effect. The percent inhibition of α-amylase by a flavonoid-rich fraction at 100 μg/ml was found to be 45.95% as compared to standard acarbose with 74.79% inhibition at 100 μg/ml. Further, docking studies predicted that vitexin possessed the highest binding affinity (binding energy - 7.98 kcal/mol) as compared to standard acarbose with binding energy - 5.24 kcal/mol. There were no significant side effects predicted, in-vitro α-amylase inhibitory activity of the flavonoid-rich fraction may be due to the presence of vitexin, predicted via in-silico molecular docking; further, which needs to be further validated via in-vivo protocols.

Identification of PTP1B regulators from Cymbopogon citratus and its enrichment analysis for diabetes mellitus

PTP1B is identified as the insulin signaling pathway downregulator; involved in pancreatic β-cell apoptosis. Further, it associates in regulating multiple pathways in diabetes mellitus; kindled us to identify the binding affinity of bioactives from Cymbopogon citratus by targeting PTP1B and identify the probably associated with it; further identifying the probable pathways involved in diabetes mellitus. In this regard, ChEBI database was used to retrieve bio-actives from C. citrates and 3D structures for the same were obtained from the PubChem database. The energy of bioactives was minimized and converted into ligand and the docking was carried using autodock 4.0 against PTP1B. Further, multiple characters of bio-actives like drug-likeness score, ADMET profile, probable adverse effects, and boiled egg model for bioavailability were also studied. Swertiajaponin was predicted for the highest drug-likeness score i.e. 0.26. However, swertiajaponin was predicted with the highest probable side effect of nephrotoxicity with pharmacological activity of 0.478. Similarly, swertiajaponin was predicted for the highest binding affinity with PTP1B with the binding energy of - 8.3 kcal/mol. Likewise, KEGG identified 80 pathways associated with PTP1B modulation in which 7 pathways were involved in diabetes mellitus in which FoxO signaling pathway was predicted to have the least false discovery rate by modulating 7 genes. Swertiajaponin could act as the potent inhibitor of PTP1B; scored highest druglikeness score but possessed minimum GIT absorptivity; further, PTP1B was identified to be linked with multiple pathways that are concerned with diabetes mellitus.